Kromatin Isolering av RNA Purification (kvitre)

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Summary

Chirp er en roman og rask teknikk for å kartlegge genomisk bindingssteder lange noncoding RNA (lncRNAs). Metoden utnytter den spesifisitet av anti-sense fliser oligonukleotider for å tillate opptellingen av lncRNA-bundet genomisk nettsteder.

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Chu, C., Quinn, J., Chang, H. Y. Chromatin Isolation by RNA Purification (ChIRP). J. Vis. Exp. (61), e3912, doi:10.3791/3912 (2012).

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Abstract

Lange noncoding RNAS er sentrale regulatorer av kromatin stater for viktige biologiske prosesser som dosering kompensasjon, imprinting, og utviklingsmessige genuttrykk 1,2,3,4,5,6,7. Den nylige oppdagelsen av tusenvis av lncRNAs i forbindelse med konkrete kromatin modifisering komplekser, som Polycomb Undertrykkende Complex 2 (PRC2) som medierer histone H3 lysin 27 trimethylation (H3K27me3), foreslår brede roller for mange lncRNAs i å håndtere kromatin stater i et gen-spesifikk mote 8,9. Mens noen lncRNAs er tenkt å fungere i CIS på nærliggende gener, andre lncRNAs jobbe i trans å regulere fjernt beliggende gener. For eksempel Drosophila lncRNAs roX1 og roX2 binder mange regioner på X-kromosomet av mannlige celler, og er kritisk for dosering kompensasjon 10,11. Imidlertid er de eksakte plasseringen av deres bindingssteder ikke kjent på høy oppløsning. Tilsvarende kan mennesker lncRNA HOTAIR påvirke PRC2 belegg på hundreds av gener genom-wide 3,12,13, men hvor spesifisitet oppnås er uklart. LncRNAs kan også tjene som modulære stillasene å rekruttere montering av flere protein komplekser. Den klassiske trans-acting RNA stillaset er TERC RNA som fungerer som mal og stillaset for telomerase komplekse 14; HOTAIR kan også tjene som et stillas for PRC2 og en H3K4 demethylase kompleks 13.

Tidligere studier kartlegging RNA utleiegrad på kromatin har avdekket betydelige innsikt 15,16, men bare på ett enkelt gen locus av gangen. Utleiegraden stedene i de fleste lncRNAs er ikke kjent, og rollene til lncRNAs i kromatin regulering har vært mest utledes fra de indirekte virkningene av lncRNA forstyrrelse. Akkurat som kromatin immunoprecipitation etterfulgt av microarray eller dyp-sekvensering (Chip-chip eller chip-seq, henholdsvis) har kraftig forbedret vår forståelse av protein-DNA vekselvirkninger på en genomisk skala, her vi illustrere en recently publisert strategi for å kartlegge lang RNA utleiegrad genom-wide med høy oppløsning 17. Denne metoden, Chromatin Isolering av RNA Purification (kvitring) (figur 1), er basert på slektskap fangst av målet lncRNA: kromatin kompleks av flislegging antisens-oligos, som deretter genererer et kart over genomisk bindingssteder i en oppløsning på flere hundre baser med høy følsomhet og lavt bakgrunn. Chirp er aktuelt for mange lncRNAs fordi utformingen av affinity-prober er grei gitt RNA sekvensen og krever ingen kunnskap om RNA struktur eller funksjonelle domener.

Protocol

1. Probe Design

Design anti-følelse DNA flislegging prober for selektiv uthenting av RNA mål av Chirp.

  1. Design anti-sense oligo probes i bruk den elektroniske sonden designer hos singlemoleculefish.com 18.
  2. Bruk disse parametrene: antall prober = 1 probe / 100 bp av RNA lengde, 2) Target GC% = 45, 3) Oligonucleotide lengde = 20, 4) Mellomrom lengde = 60-80. Bryt RNA inn i segmenter hvis for lang for designeren. Utelat områder av gjentakelser eller omfattende homologi.
  3. Bestill anti-sense DNA prober med BiotinTEG ved 3-prime end.
  4. Etiketten sonder etter sine posisjoner langs RNA. Skille dem i to bassenger, slik at "selv" pool inneholder alle sonder 2 nummerering, 4, 6 osv. og "odd" pool inneholder prober nummerering 1, 3, 5 osv. Fortynn pool av sonder til 100 mikrometer konsentrasjon og Oppbevar ved -20 ° C.
  5. Alle eksperimenter skal utføres ved hjelpbegge bassengene, som fungerer som interne kontroller for hverandre. Ekte RNA-avhengige signal ville være til stede fra begge bassengene, mens probe-spesifikke lyder ville være unik for hver pool. Dette gjelder for både kvitre-qPCR og chirp-seq.

2. Harvests Celler

Samle celler som skal brukes til chirp eksperiment.

  1. Grow celler i vev kultur plater eller kolber til confluency. Skyll med fosfat saltløsning (PBS) én gang og trypsinize. Slukk trypsin med> 2x volum av media, pipette opp og ned for å løsne cellene og resuspender i single cellesuspensjon. Overfør alle medier og resuspendert celler inn i 50 ml Falcon rør. 20 millioner celler er vanligvis tilstrekkelig for en chirp prøve.
  2. Spinn cellene ved 800RCF for 4 min. Sug media og Resuspender 40 millioner celler i 40 ml PBS, kombinere rør om nødvendig. Spinn cellene ved 800RCF for 4 min. Dekanter PBS, forsiktig aspirer på en vinkel gjenværende væske.
  3. 3. Cross-link Cells og samle cellepelleten

    Kryssbindingsfordelingen samlet celler med glutaraldehyd å bevare RNA-Chromatin interaksjoner og forberede cellepelleten.

    1. Utfør alle trinnene ved romtemperatur.
    2. Forbered 1% glutaraldehyd i romtemperatur PBS. Forbered 10 ml per 10 millioner celler (0,4 ml 25% glutaraldehyd lager + 9,6 mL PBS). Glutaraldehyde må brukes fersk.
    3. Trykk bunnen av Falcon rør for å løsne pellets. Resuspender cellepelleten i 1% glutaraldehyd, starter med et lite volum for å unngå biter, deretter fylle opp til full volum. Inverter å blande. Kryssbindingsfordelingen for 10min ved romtemperatur på en ende-til-ende shaker eller rotator.
    4. Slukke kryssbinding reaksjon med 1/10th volum på 1,25 M glysin i romtemperatur i 5 min.
    5. Snurr på 2000RCF i 5 min. Aspirer supernatanten og vask pellet med 20 mL kjølt PBS gang, spinning på 2000RCF i 5 min.
    6. Aspirer og resuspender wforaskes, tverrbundet pellet med 1 ml kjølt PBS per 20 millioner celler. Overfør hver ml til en Eppendorf rør og spinn på 2000RCF for 3 min ved 4 C. Ta så mye PBS som mulig med pipettespissen nøye.
    7. Flash-fryse cellen pellets i flytende nitrogen og oppbevar ved -80 ° C på ubestemt tid.

    4. Cellelyse

    Lyse krysskoblet celler til å forberede celle lysate.

    1. Tin frosne celle pellets ved romtemperatur. Trykk vanskelig å løsne og blande cellepelleten. Spinn ned pellet ved 2000RCF for 3 min ved 4 ° C. Bruk en skarp 10 mL pipette for å fjerne eventuelle gjenværende PBS.
    2. På en elektronisk balanse (nøyaktig til 1 mg) tara massen av en tom Eppendorf rør (våre rør veier 1.060 gram veldig konsekvent). Veie hver pellet og registrere sin vekt. En full 15 cm rett av tverrbundet Jakten celler veier vanligvis 100 mg.
    3. Supplement Lysis buffer (10X massen av pellets, en f.eks ml for 100 mg) med FRESh proteasehemmer, PMSF og Superase-i (se vedlagte buffer liste). Bland godt.
    4. Legg 10X volumet supplert Lysis Buffer til hvert rør og resuspender pelleten. For små pellets <25 mg, resuspender i 250 mL supplert lysis buffer. Suspensjon skal være glatt. Hvis ikke, dele suspensjonen i 500 mL alikvoter og bruke en motorisert pellet mikser til å bryte opp klumper. Fortsett straks til sonikator.

    5. Sonikator

    Shear DNA ved sonicating krysskoblet celle lysates.

    1. Sonicate celle lysate i Bioruptor i 15 ml Falcon rør. Bruk <1,5 ml lysate i hvert rør, og for raskere sonikator, sonicate ikke mer enn to rørene på en gang.
    2. Sonicate i en 4 ° C vannbad ved høyeste innstilling med 30 sekunder på, 45 sekunder av puls intervaller. Sjekk lysate hvert 30 min. Fortsett sonicating inntil cellen lysate ikke lenger grumset. Dette kan ta så lite som 30 min og så mange som fire timer. Talletav rør, vil prøvevolum, badet temperatur, og perioden med sonikator tid påvirke hvor lang tid prosessen tar. Rør vil trolig sonicate ved ulike priser, så pool dem sammen hver 30 min og redistribuere inn originale rør for å sikre homogenitet. Merk: glutaraldehyd-krysskoblet celler tar vesentlig lengre tid å sonicate enn formaldehyd ekvivalenter.
    3. Når lysate snur klar, overføre 5 mL lysate til en frisk Eppendorf rør. Legg 90 mL DNA Protease K (PK) Buffer (se buffer liste) og 5 mL PK. Vortex å spinne og mixe ned kort. Inkuber i 45 min ved 50 ° C.
    4. Pakk DNA med Qiagen PCR rensing kit. Eluer DNA i 30 mL Qiagen eluering Buffer (EB) og sjekke DNA størrelse på 1% agarose gel. Dersom mesteparten av DNA smøre er 100-500 bp, er sonikator fullført. Hvis ikke, fortsetter å sonicate.
    5. Sentrifuger sonicated prøver på 16100RCF i 10 min ved 4 ° C. Kombiner supernatants, alikvoter i 1 ml prøver og flash-fryse i flytende nitrogen. Oppbevares ved -80 ° C.

    6. Kvitre

    Hybridize biotinylated DNA prober til RNA og isolere bundet kromatin.

    1. Thaw rør av kromatin ved romtemperatur.
    2. Forbered Hybridisering Buffer (se buffer liste, forberede 2 ml per ml av kromatin). Vortex å blande.
    3. For en typisk kvitre prøve ved hjelp av 1 ml lysate, fjerne 10 mL for RNA-inngang og 10 mL for DNA-inngang og plass i Eppendorf-rør. Hold på is inntil videre bruk.
    4. Overfør 1 mL kromatin til 15 ml Falcon rør. Tilsett 2 mL Hybridisering Buffer til hvert rør. For total volum <1,5 ml, bruke Eppendorf-rør.
    5. Tin prober ved romtemperatur. Nanodrop prober for å sjekke beløpet hvis du ikke har brukt det i lang tid (100 mikrometer sondene skulle spec ~ 500-600 ng / mL hjelp enkelt strand DNA innstilling). Legg passende mengde prober til bestemte rør (100 pmol sonde per 1 ml kromatin, 1 mL av 100 pmol / mL probe per 1 ml kromatin).Bland godt. Inkuber ved 37 ° C i 4 timer med risting.
    6. Med 20 min igjen for hybridisering, forberede C-1 magnetiske kuler (som er lagret ved 4 º C). Bruk 100 mL per 100 pmol av sonder. Vask med 1 ml unsupplemented Lysis Buffer tre ganger, ved hjelp av DynaMag-2 magnet stripe til separate perler fra buffer.
    7. Resuspender perler i original volum av Lysis buffer; supplere med frisk PMSF, PI og Superase-in. Etter 4 timers hybridisering reaksjonen er ferdig, tilsett 100 mL perler i hvert rør. Bland godt. Inkuber ved 37 ° C i 30 min med risting.
    8. Forbered vaskebuffer (5 ml per prøve). Vortex å blande. Forvarm til 37 ° C. Legg PMSF før bruk.
    9. Vask perler med 1 ml vaskebuffer fem ganger. På den første vask, bruk DynaMag-15 magnetstripen til egne perler, decant og Resuspender i 1 ml vaskebuffer. Overføring volum til 1,5 ml Eppendorf rør. Inkuber ved 37 ° C med risting i 5 min.
    10. Ved senere vask, spinner ned hvert rør på en minicentrifugeSetter prøve på DynaMag-2 magnetstripen i 1 min. Dekanter prøven, tørke noen drypp med en Kimwipe, resuspender i 1 ml vaskebuffer. Inkuber ved 37 ° C med risting i 5 min. Gjenta i fem totalt vask.
    11. Endelig vask, resuspender perlene godt. Fjern 100 mL og satt til side for RNA isolering. Reserve 900 mL for DNA brøkdel. Plasser alle rør på DynaMag-2 magnetstripen og fjerne vaskebuffer. Spinn alle rør ned kort; plassere dem på magnet stripen. Fjern den siste bit av vaskebuffer helt med en skarp 10 mL pipette tips.

    7. RNA Isolation

    Utdrag RNA brøkdel fra kvitre prøver å quantitate av Qrt-PCR.

    1. Ta 100 mL perle prøver og 10 mL RNA INPUT prøven. Legg 85 mL RNA PK Buffer pH 7,0 til RNA INPUT. Resuspender perler i 95 mL RNA PK Buffer pH 7,0. Tilsett 5 mL Proteinease K og Inkuber ved 50 ° C i 45 min med ende-til-ende risting.
    2. Kort spinne ned alle rør ogkoke prøver for 10 min på varme blokk ved 95 ° C.
    3. Chill prøver på is, tilsett 500 mL TRIzol, vortex kraftig i 10 sek. Inkuber ved romtemperatur i 10 min. Oppbevares ved -80 ° C eller gå videre til trinn 4.
    4. Tilsett 100 mL kloroform til TRIzol behandlet prøvene. Vortex kraftig i 10 sek. Snurr på 16100RCF på en stasjonær sentrifuge i 15 min ved 4 ° C.
    5. Fjern ~ 400 mL vandig supernatant, unngå organisk og grensesnitt.
    6. Legg 600 mL (1,5 volum) 100% etanol og bland godt. Spinn prøven gjennom MIRNeasy mini kolonner. Vask 1x med RWT (MIRNeasy mini kit), 2x med RPE per produsentens protokoll. Eluer med 30 mL nukleasefritt H 2 O (NFH 2 O).
    7. Unn RNA eluatet med DNA-free per produsentens protokoll. Etter at reaksjonen er ferdig, varme prøven i 15 minutter ved 65 ° C til helt inaktivere eventuelle gjenværende DNase.
    8. Bruk 1 mL RNA isolere per brønn for QRT-PCR-analyse for å bekrefte lncRNAhenting. GAPDH blir ofte brukt som en negativ kontroll.

    8. DNA

    Utdrag DNA fraksjon fra kvitre prøver å identifisere ved sekvensering eller quantitate av qPCR.

    1. Forbered DNA eluering Buffer (se buffer liste), 150 mL per prøve, inkludert DNA INPUT.
    2. Tilsett 1 0μL RNase A (10 mg / ml) og 10 mL RNase H (10 U / mL) per ml av DNA eluering buffer, og virvle å blande.
    3. Resuspender hver prøve av perler i 150 mL av DNA eluering buffer med RNases. (Resuspender DNA INPUT i 140 mL) Inkuber ved 37 ° C i 30 min med risting.
    4. Separate perler og supernatanten på DynaMag-2 magnetstripen. Fjern supernatanten og legge til merket rør.
    5. Utarbeide en andre delmengde av DNA eluering buffer med 10 mL RNase A (10 mg / ml) og RNaseH (10 U / mL) nøyaktig som gjøres i 8.2). Tilsett 150 mL til hver prøve (inkludert DNA-inngang), inkuber, og fjern supernatanten. Samle all supernatanten (should være ~ 300 mL).
    6. Tilsett 15 mL PK til hver prøve. Inkuber ved 50 ° C i 45 min med risting.
    7. Pre-spinner ned gule fase-lock gel rør (5PRIME). Overføring DNA-prøver til fase-lock gel rør, og legg 300 mL PhOH: kloroform: Isoamyl per prøve. Rist kraftig i 10 min, og spinne ned på en Borstemmaskin sentrifuger ved 16100RCF i 5 min ved 4 ° C. Ta vandig fra toppen (~ 300 mL). Legg 3 mL GlycoBlue, 30 mL NaOAc, og 900 mL 100% EtOH. Bland godt og oppbevar ved -20 ° C over natten.
    8. Spinn prøver på 16100RCF i 30 min ved 4 ° C.
    9. Dekanter supernatanten forsiktig. Tilsett 1 ml 70% EtOH og virvle å blande. Snurr på 16100RCF i 5 min. Fjern supernatanten ved pipette. Lufttørke for 1min. Resuspender i 30 mL EB.
    10. DNA-prøver er klare for analyse av qPCR eller forberedelse av high-throughput sekvensering biblioteker per Illumina protokollen.

    10. Representative Resultater

    Figur 1 Figur 2 viser anrikning av menneskelig telomerase RNA (TERC) fra Jakten celler enn GAPDH, et rikt cellulære RNA som fungerer som en negativ kontroll. Flertallet av TERC RNA (~ 88%) til stede i cellen ble dratt ned ved å utføre kvitre, mens bare 0,46% av GAPDH RNA ble hentet frem, viser en berikelse faktor på ~ 200 fold. Uspesifikke prober som prober rettet LacZ RNA, som ikke er uttrykt i pattedyrceller (figur 2), kan brukes som ekstra negative kontroller.

    DNA regioner forventes å binde målet lncRNA er typisk beriket enn negative regioner målt ved qPCR. Figur 3 viser qPCR validering av fire HOTAIR-bundet steder i primære humane foreskin fibroblaster at vi bestemt ved å utføre kvitre-seq i samme celle linje, mens TERC og GAPDH DNA-områder SErve som negativ kontroll regioner. Både "selv" og "odd" probe setter ga sammenlignbare anrikning av forventede HOTAIR-bundet områder enn negative regioner, et kjennetegn på ekte lncRNA-bindingssteder.

    High-throughput sekvensering av kvitre beriket DNA gir en global kart over lncRNA-bindingssteder. Den Drosophila lncRNA roX2 er kjent for å samhandle med X-kromosomet på en måte som er nødvendig for doseringen kompensasjon. Figur 4 viser roX2 binding profil over en del av X-kromosomet. Både "selv" og "rare" prøver har blitt sekvensert og deres unike lyder har blitt eliminert å produsere et spor av overlappende signaler. Hver "peak" indikerer her en sterk stedet roX2 bindende. Den komplette spor og liste over roX2 målgener har blitt beskrevet i Chu et al. 2011 17.

    Figur 1.
    Figur 1. Flow diagram av chirp proseDure. Kromatin er tverrbundet til lncRNA: protein-addukter i vivo Biotinylated fliser sonder er hybridisert å målrette lncRNA, og kromatin komplekser blir renset ved hjelp av magnetiske streptavidin perler, fulgt av strenge vasker.. Vi Eluer lncRNA bundet DNA eller proteiner med en cocktail av Rnase A og H. A antatte lncRNA bindende sekvensen er skjematisert i oransje. Tidligere publisert i Chu et al. 2011. 17

    Figur 2.
    Figur 2. Kvitre beriker for menneskelig TERC RNA. TERC-asDNA prober hente ~ 88% av mobilnettet TERC RNA og undetectable GAPDH. LacZ-asDNA prober brukes som negative kontroller og hente verken RNAS. Mean + sd vises. Tidligere publisert i Chu et al. 2011. 17

    Figur 3.
    Figur 3. HOTAIR kvitre-qPCR i primær menneskelig foreskin fibroblaster. NFKBIA, HOXD3-4, SERINC5 og ABCA2 er regioner som samhandler med HOTAIR. TERC og GAPDH fungerte som negative kontroller. Mean + sd vises. Tidligere publisert i Chu et al. 2011. 17

    Figur 4.
    Figur 4. Kvitre-seq data av roX2 RNA i SL2 Drosophila celler. "Even" og "odd" ble sekvensert separat; sine data fusjonere å reflektere bare vanlige topper i begge. Det fusjonerte sporet vises. Tidligere publisert i Chu et al. 2011. 17

Discussion

Her har vi beskrevet kvitre-seq, en metode for kartlegging in vivo lncRNA bindingssteder genom-wide. De viktigste parametrene for suksess er de delte bassenger av flislegging oligonukleotid prober og glutaraldehyd crosslinking. Utformingen av affinity-prober er grei gitt RNA sekvensen og krever ingen forkunnskaper i RNA struktur eller funksjonelle domener. Vår suksess med roX2, TERC, og HOTAIR - tre ganske forskjellige RNA i to arter - antyder at kvitre-seq er sannsynlig generalizable til mange lncRNAs. Som med alle eksperimenter, er omsorg og riktig kontroller er nødvendig for å tolke resultatene. Ulike lncRNA kan kreve titrering av forholdene, og klok endring av forhold som valg av forskjellige affinitet sonder eller crosslinkers, kan fremheve ulike aspekter av RNA-kromatin interaksjoner. Som Chip-seq, ikke alle bindende hendelser er nødvendigvis funksjonelle, og flere studier er nødvendig for å fastslå de biologiske konsekvensene av RNA occupancy på kromatin. Likevel, forutser vi mange interessante anvendelser av denne teknologien for forskere fra andre kromatin-tilknyttede lncRNAs, som nå nummer i tusenvis 8,9. Akkurat som Chip-seq har åpnet døren for genom-wide undersøkelser av DNA-protein interaksjoner, kan kvitre-seq studier av den "RNA interactome" åpenbare mange nye muligheter for biologi.

Disclosures

C. Chu og HY Chang er navngitt som oppfinnere på en patentsøknad basert på denne metoden.

Acknowledgments

Vi takker T. Hung, MC. Tsai, O. Manor, E. Segal, M. Kuroda, T. Swigut, og I. Shestopalov for diskusjoner. Støttet av Byrået for vitenskap, teknologi og forskning Singapore (CC), NIH R01-CA118750 og R01-HG004361 (HYC), og California Institute for regenerativ medisin (HYC). HYC er en Early Career Scientist av Howard Hughes Medical Institute.

Materials

Name Company Catalog Number Comments
Buffer List:
Dissolve a pellet of complete protease inhibitor in 1 ml water as 50x stock. Make 100 mM PMSF in isopropanol (100x stock). Superase-in is used as 200x stock. Store all at -20 °C.
Lysis Buffer:
50 mM Tris-Cl pH 7.0
10 mM EDTA
1% SDS
Always add PMSF, P.I. and Superase-in fresh before use except when washing beads
Proteinase K Buffer (for DNA)
100 mM NaCl
10 mM TrisCl pH 8.0 (For RNA use pH 7.0)
1 mM EDTA
0.5% SDS
Add 5% by volume Proteainse K (Ambion AM2546 20 mg/ml) fresh before use
Hybridization Buffer
750 mM NaCl
1% SDS
50 mM Tris-Cl pH 7.0
1 mM EDTA
15% formamide (store in the dark at 4 °C)
Always add PMSF, P.I. and Superase-in fresh before use
Wash Buffer
2x NaCl and Sodium citrate (SSC) (diluted from 20x SSC Invitrogen stock)
0.5% SDS
Always add PMSF fresh before use
DNA elution Buffer
50 mM NaHCO3
1% SDS
Table of specific reagents and equipment:
Glutaraldehyde (EM grade) Sigma-Aldrich G5882-10x10ml
Motorized pellet mixer VWR international V8185-904
Protease inhibitor Roche Group 11873580001
PMSF Sigma-Aldrich 78830
Superase-in Ambion AM2696
Bioruptor Diagenode UCD-200
Falcon tubes (for sonication) Corning 430790
Proteinase K Ambion AM2546
PCR purification kit Qiagen 28106
C-1 magnetic beads Invitrogen 65002
PMSF Sigma-Aldrich P7626-25G
DynaMag-15 magnet Invitrogen 123-01D
DynaMag-2 magnet Invitrogen 123-21D
MIRNeasy mini kit Qiagen 217004
Rnase H Epicentre Biotechnologies R0601K
Rnase A Sigma-Aldrich R4875-100MG
Phase Lock Gel Heavy 5 PRIME 2302810
Trizol Invitrogen 15596-018
Phenol:chloroform:Isoamyl Invitrogen 15593-031
Chloroform Ricca RSOC0020-1C
GlycoBlue Ambion AM9515
Glycine JT Baker 4057-06
PBS, pH 7.4 Invitrogen 10010-049
Elution Buffer (EB) Qiagen 19086
20x SSC Invitrogen 15557-036
10% SDS Invitrogen 15553-027
DNA-free Ambion AM1906
Buffer kit Ambion AM9010
Formamide Invitrogen 15515-026

DOWNLOAD MATERIALS LIST

References

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Comments

84 Comments

  1. hi,i has a great interest on CHIRP and your works are highly appreciated,but i want to know that where can i find the buffer list?thank you

    Reply
    Posted by: tang n.
    May 5, 2012 - 4:16 AM
  2. Hi there, thanks for the interest in our paper. As you pointed out the original article lacked the buffer list, which we have uploaded a while ago. Hope it helps!

    Reply
    Posted by: Ci C.
    December 18, 2012 - 5:20 PM
  3. Hello, I'm trying to perform ChIRP experiments and your protocol is very helpful to me.

    However, I have a question about the final concentration of biotinylated probes and the volume of the beads.
    My probes are 100µM so 1µL corresponds to 100pmol. I have 50 probes and my question is : should I use 100µL of magnetic C1 beads per 100pmol of probe, so in my case, 50 probes x 100µL = 5mL of beads ?

    Thanks a lot for the answer ?

    Reply
    Posted by: Sylvain F.
    October 31, 2012 - 4:47 AM
  4. I also have this question!

    Reply
    Posted by: Guihai f.
    November 28, 2012 - 7:51 AM
  5. Hi guys, thanks for the interest in our paper. That's indeed a common question I get, so apologize for not explaining that more clearly in the paper. The 100uM concentration refers to all probes, so if you have ² probes in the pool the individual concentration is 50uM per probe, and if you have 50 probes it's ²uM per probe. It follows that as you scale up number of probes in the pool you do not have to scale up the amount of beads to add. As a caution though, we have noticed that when I use too many probes the concentration of each probe drops too much and it actually adversely affects yield. Try not to use more than 50 probes if possible.

    Reply
    Posted by: Ci C.
    December 18, 2012 - 5:23 PM
  6. what is the fucntion of the Buffer kit ? I can not find it in the protocol.

    Thanks for your time!

    Reply
    Posted by: Guihai f.
    November 1, 2012 - 12:50 AM
  7. The buffer kit is simply a convenient collection of buffers provided by Ambion that includes 5M NaCl, 1M Tris, 0.5M EDTA, etc..

    Reply
    Posted by: Ci C.
    December 18, 2012 - 5:25 PM
  8. Hi, I refer to your paper in HOTAIR ChIRP. You used 48 oligo probes for this ncRNA. I am trying to do a HOTAIR ChIRP. I am wondering if the number of probes can be smaller to reduce cost without a huge compromise on specificity. Furthermore, I am not doing sequencing but a specific check on a genomic region of interest, so I supposed the background noise may be lower? Thank you!

    Reply
    Posted by: Yi Fang L.
    November 8, 2012 - 5:11 AM
  9. We share your desire to reduce number of probes used. In preliminary testing I've found that you can use as few as 1 probe per ²00 nucleotide of RNA target RNA. But that number has to be doubled considering if you need both "even" and "odd" set, so effectively tiling density is 1 probe / 100nt.

    Reply
    Posted by: Ci C.
    December 18, 2012 - 5:28 PM
  10. Hello,
    I enjoyed your paper very much.

    At the end of the video, and in the figure, you mention that in this process you can isolate RNA binding proteins that were associated with the RNA. My questions are: have you had success in doing this? What is the protocol for isolating the proteins? Do you just isolate the protein fraction from the Trizol, or is there a more specialized method? Is there a paper that may lay out use of this method?

    Thank you for your help.

    Reply
    Posted by: Gavin J.
    January 18, 2013 - 12:09 PM
  11. Hi,
    Great protocol. Just one question. You mention that all ChIRP steps have to be performed at 37C. I can imagine this is important for the hybridisation steps, but I was wondering why this was needed for the washing steps as well?

    Many thanks

    Reply
    Posted by: Sebastian V.
    March 15, 2013 - 10:21 AM
  12. The washing should be performed at 37C just like you would wash a northern blot at elevated temperatures. If this is logistically difficult for you, just warming up the buffer to 37C and washing on a room temp. shaker works well too.

    Reply
    Posted by: Ci C.
    March 15, 2013 - 1:47 PM
  13. Hello,
    Thanks for the detailed and very helpful protocol. Can you tell me what kind of DNA yields to expect from the pull down per input cell amount? I know it will depend on the lncRNA targeted, but I need an idea of what kind of amounts to expect. Could you tell me what you got for your HOTAIR hybridizations? My own hybs only result in a few nanograms of DNA, and I don't know how to determine whether that is nonspecific DNA binding to my beads or whether it is actual lncRNA-bound DNA? How do you control for this? Thank you for your help in advance.

    Reply
    Posted by: blake e.
    March 20, 2013 - 5:44 AM
  14. Hi,

    Congrats for setting up such a protocol. It might have been discussed already but I would like to have an idea about the typical amounts of DNA and RNA that one might expect from 20 x 10 ^6 cells. This of course is transcript specific, but should we expect nanograms, picograms for either DNA and RNA?

    Also have you tried FA instead of glutaraldehyde for x-linking? Many thanks for your time

    Reply
    Posted by: Antonis A.
    November 26, 2013 - 12:15 PM
  15. Hi,

    Thanks for the detailed protocol. I am about to embark on it over the next week or so and had a question regarding the sonication. You advise a Bioruptor for this step however we only have a Covaris available. Would that provide acceptable sonication and do you have any advice regarding appropriate settings?

    Thank you

    Joshua

    Reply
    Posted by: joshua b.
    March 2, 2014 - 12:24 AM
  16. Yes Covaris works, we've found that it generally reduces sonication time by 30-50% compared with Diagenode. Actual time and intensity needs to be optimized for each machine and cell line.

    Reply
    Posted by: Ci C.
    March 3, 2014 - 5:51 PM
  17. Hi,

    Thanks for the detailed protocol. I am about to embark on it over the next week or so and had a question regarding the sonication. You advise a Bioruptor for this step however we only have a Covaris available. Would that provide acceptable sonication and do you have any advice regarding appropriate settings?

    Thank you

    Joshua

    Reply
    Posted by: joshua b.
    March 2, 2014 - 6:32 AM
  18. To all interested ChIRPers, hybridization can be performed overnight instead of 4hours. Doing so greatly reduces hands-on time. Happy ChIRPing!

    Reply
    Posted by: Ci C.
    March 3, 2014 - 8:14 PM
  19. Hi Ci,

    I have one more issue to resolve regarding ChIRPseq that I would appreciate your input on please (or other ChIRPers that have had similar problems).

    We have been unable to produce lysates using glutaraldehyde despite following the protocol to the letter and getting the Sigma brand that is recommended. Even before sonication, the DNA is degraded to a thick band below 200bp. When we try exactly the same process but substitute 1% formaldehyde (which we normally use for ChIP and 3C) or even plain PBS, the DNA is fine. We have even tried doing everything on ice and reducing the centrifuge steps to only 500g but to no avail.

    My questions therefore are:

    1/ Has your team had similar issues with glutaraldehyde in the past or found it to behave quite differently to formaldehyde (apart from needed longer sonication and harder centrifuging)?
    2/ Though you have shown glutaraldehyde to give a better signal to noise ratio, could we still expect to get usable data using 1% formaldehyde or is it not worth the time and effort?

    Thank you for your time

    Joshua Betts

    Reply
    Posted by: joshua b.
    April 16, 2014 - 8:07 AM
  20. Dear Joshua,

    Thanks for your interest in our protocol. It's unfortunate to hear that you're experiencing DNA degradation. We've never experienced this issue, nor have we heard similar problems from our collaborators who successfully did ChIRP. Usually we're more concerned with RNA integrity, naturally, and if you're careful that's not a problem either.

    Could you tell me how you're extracting DNA, especially prior to sonication?

    Regarding alternative crosslinking methods, for certain lncRNAs we've found that strong formaldehyde crosslinking also works (3% for 30min is a good starting point). 1% formaldehyde usually does not work.

    Best,
    Chu

    Reply
    Posted by: Ci C.
    April 16, 2014 - 1:55 PM
  21. Dear Chu,

    Thank you for your advice - I will try the protocol again but substitute 3% formaldehyde for the glutaraldehyde. Does that require any other adjustments apart from slower centrifuge spins and shorter sonication times?

    In regards to my DNA isolation, I lysed the cells as per the protocol and then treated with proteinase K for 45mins (at 50deg or 65deg - either seemed ok). I then RNAse treated the sample and either phenol chloroform extracted the DNA or instead used the Qiagen PCR columns before running the product on a 1% agarose gel. The columns gave more of a smear on the gel, whilst the phenol chloroform extraction just had a broad band below 100bp.

    When I performed exactly the same procedures on formaldehyde treated cells, I obtained a bright band of gDNA at the top of the gel as well as a more faint diffuse band below 100bp. This is what we normally see when working with formaldehyde. Am I right to expect a strong band of genomic DNA on the gel when using glutaraldehyde before sonication, or does the glutaraldehyde break the gDNA down during the fixation process? Does your glutaraldehyde fixed sample normally start as a broad smear even prior to sonication?

    Our group has a lot of experience with ChIPseq, 3C and 4Cseq library preparation but we have never dealt with glutaraldehyde before so are unsure what to expect.

    Any further suggestions would be greatly appreciated.

    Thanks

    Joshua

    Reply
    Posted by: joshua b.
    April 24, 2014 - 9:26 AM
  22. Before preparing your ChIRP library for sequencing, do you check your DNA size distribution (for example using Agilent Bioanalyzer). If so, do you see a similar distribution to that seen for a typical ChIP sample (200-800 bp range)?

    Reply
    Posted by: Eric S.
    August 29, 2014 - 2:43 PM
  23. Dear Chu
    I have two questions:
    1.In designing your chirp oligos have you tried to reduce the spacer between biotin-oligonucleotides. Is there any steric reason for choosing 1 probe / 100nt?
    2. Did you tried to crosslink adherent cells directly on plate? we have problem in properly resuspend our differentiated murine myoblasts in PBS+glutaraldehyde.

    thanks in advance
    regards

    Mariangela

    Reply
    Posted by: Mariangela M.
    October 16, 2014 - 9:56 AM
  24. Dear Mariangela,

    1. It's both a cost consideration (fewer probes are cheaper) and also a biochemical noise consideration (more probes introduce higher chances for probe:DNA direct hybridization).

    2. Yes we've found no difference fixing on plate vs. in suspension. Feel free to pick and choose what works best for you.

    Best,
    Chu

    Reply
    Posted by: Ci C.
    October 17, 2014 - 10:43 PM
  25. Dear ChIRP community,

    We are having problems getting ChiRP peaks with our transcripts. We have tried ChiRPing against 4 different transcripts and for all of them we were able to get very good fold enrichments in the genomic locus of each transcript (on average 50 to 200 x over background) capturing native transcription but we cannot find other binding sites in the genome for any of them. We have good reasons to believe that some or all of our transcripts are chromatin localized and we also know that the signal in the genomic loci is RNA dependent because it is dramatically reduced when we ChiRP after knocking down our transcripts of interest.

    Our transcripts are low in expression, on average 3 to 10 copies per cell. Any ideas as to how can we improve/solve the issue? Is it abundance that is limiting the system? Has anyone experienced/solved something similar?
    We tried the normal protocol, and now we are trying with 3 % FA in parallel to glut. Any suggestions would be very welcomed!

    Antonis

    Reply
    Posted by: Antonis A.
    November 13, 2014 - 5:18 AM
  26. Hi Antonis, I'm afraid the copy number is simply too low. In all of the ChIRP paper published so far I don't think anyone went that low.

    Your enrichment of the genomic loci could be complicated by ChIRP probes pulling down the DNA directly. Do an RNase-control to see if the signal is still there.

    Reply
    Posted by: Ci C.
    November 13, 2014 - 8:52 AM
  27. Dear Chu,

    Thank you for the prompt reply-yes I know that with such expression levels, ChIRP is challenging. I can try the RNase control but as mentioned I am confident about the RNA-dependence of the signal, because it falls back to LacZ levels when I knock down the transcripts. I guess we will have to try increasing the sensitivity of the experiment. Could an increase in x-linking time help here, have you guys tried 20 min of glut x-linking?

    Reply
    Posted by: Antonis A.
    November 18, 2014 - 3:28 AM
  28. Hello,
    I enjoyed your paper very much.

    At the end of the video, and in the figure, you mention that in this process you can isolate RNA binding proteins that were associated with the RNA. My questions are: have you had success in doing this? What is the protocol for isolating the proteins? Do you just isolate the protein fraction from the Trizol, or is there a more specialized method? Is there a paper that may lay out use of this method?

    Thank you for your help.

    Reply
    Posted by: jason h.
    November 26, 2014 - 10:15 PM
  29. Dear ChIRPers, we're happy to announce that you can now officially design and order ChIRP from Biosearch Technologies (Single molecule fish). Scientists developing ChIRP probes using the Stellaris probe designer and following the guidelines from our publication can now email Sheila Semaan at Biosearch Technologies, Inc. for help with ordering the probes in the proper format. Sheila’s contact info is as follows:

    Sheila J. Semaan, Ph.D., Associate Product Manager
    Biosearch Technologies, Inc.
    Email: ssemaan@biosearchtech.com

    Reply
    Posted by: Ci C.
    December 17, 2014 - 9:33 AM
  30. Dear ChIRP community,

    You can soon study RNA-protein interactions in vivo using ChIRP-mass spec. The story is coming out in Cell on April 2nd. Stay tuned!

    Reply
    Posted by: Ci C.
    March 25, 2015 - 5:42 AM
  31. Hello, thank you for the protocol! I also want to perform a RNA pulldown using your protocol and i am very excited for your RNA-protein interaction protocol! I have one question regarding the biotin oligos. Do they need to be 3' biotinylated or can they also be 5' biotinylated. Have you tested this? And you say nothing about (salt, HPLC) purification of the oligos. Thanks for answering my questions.

    Reply
    Posted by: Christine C.
    March 30, 2015 - 10:01 AM
  32. and is it necessary to order Biotin-TEG oligos or is "standard" biotin sufficient?

    Reply
    Posted by: Christine C.
    March 30, 2015 - 11:33 AM
  33. Hi Christine, thanks for your interest in our technique. Regarding your questions:

    1) 3' biotinylation is preferred, because oligos are synthesized 3' to 5'. This way, we ensure all oligos start with a biotin tag. 5' biotin tags are usually added to a synthesized oligo, and that increases the chance of untagged probes, which is less than ideal. However if you can ensure high tagging efficiency on 5' end, and the cost is advantageous, I don't see why it won't work!

    2) We use a disposable reverse phase column called "Glen-Pak DNA purification cartridge," which is a very efficient and cost-effective system. These are really short DNA probes and HPLC or PAGE would be necessary (also probably can't tell tag from untag probes).

    3) TEG ensures no steric hindrance, I don't have hard evidence on this but I think it's necessary.

    Reply
    Posted by: Ci C.
    March 30, 2015 - 10:03 PM
  34. Thank you for your answers! As I am performing your protocol with the aim of an RNA-protein pulldown, i have some other questions regarding the protocol, if you don't mind.

    - in the protocol before washed your magnetic beads in unsupplemented lysis buffer and you blocked the magnetic beads using BSA and yeast RNA- in the latest protocol you don't block. Why is that?

    - ChIRP-MS requires 100 Mio cells, ChIRP-seq 20 Mio cells. If i want to perform ChIRP-MS (or western blot) do i need 100 pmol of probe for each 20 Mio cells --> 500 pmol of probe for ChIRP-MS? --> 500 µl beads(??)

    Reply
    Posted by: Christine C.
    April 8, 2015 - 8:12 AM
  35. Hi Christine,

    - We no longer block as there's no difference in results, and we prefer a more streamlined protocol. BSA would also potentially contaminate ms results.

    - yes scale up beads accordingly. We do 1ml beads per experiment routinely. It gets expensive, but hopefully you'd only have to do it once or twice, and validate with western in a smaller scale later. For western of more abundant chirp hits, I do from 1/5 of cell pellets, but for less abundant ones I still use full amount.

    Reply
    Posted by: Ci C.
    April 8, 2015 - 11:36 PM
  36. Dear ChIRPers,

    ChIRP mass spec has just come online today at Cell. We're very pleased to introduce a very robust and straight-forward method that's optimized to study lncRNA:protein interactions. Check out the story at:

    http://www.cell.com/cell/abstract/S0092-8674(15)00312-8

    Happy ChIRPing!

    Best,
    Chu

    Reply
    Posted by: Ci C.
    April 2, 2015 - 9:00 PM
  37. Dear ChIRPers,

    Now you can easily design and order ChIRP probes with the latest optimization from Biosearch Technologies, the company that invented Single Molecule FISH.

    https://www.biosearchtech.com/chirpdesigner/

    Best,
    Chu

    Reply
    Posted by: Ci C.
    April 2, 2015 - 10:24 PM
  38. Hi, i'm trying to perform ChIRP-western and i have some questions concerning the methods.

    1) for a control, i also want to see if my RNA is present: how can i get a small aliquot of post-ChIRP beads to perform RNA elution with this aliquot
    2) for the protein biotin elution buffer: resuspend beads in what volume?
    3) for ChIRP-MS lysates are incubated with 30µl beads - can i reuse them?

    thank you in advance!

    Reply
    Posted by: Carolin C.
    April 14, 2015 - 7:18 AM
  39. Hi Carolin,

    thank you for your interested in our method.

    1) yes that's what we we as well. Simply take a 1% or 10% aliquot of your post-wash beads, and extract RNA.

    2) that's dependent on your starting beads volume. But there's a practical constraint, you don't want to have so much volume that after addition of TCA will exceed the capacity of an eppendorf tube.

    3) I'm not sure if I understand your question. Reuse lysate or beads?

    Reply
    Posted by: Ci C.
    April 15, 2015 - 12:20 AM
  40. thank you for the answers!
    to 2) again: if my beads are 100µl starting volume - so i resuspend 2x in biotin elution buffer and pool. Is 2x100µl then enough? and then add 25% of 100%TCA (50µl)?
    to 3) my question is, if i reuse the beads in the hybridization step. and just add another 70 µl beads (=100µl beads)

    Reply
    Posted by: Carolin C.
    April 24, 2015 - 11:23 AM
  41. so what do you recommend for my previous questions 2) and 3)

    another question: how do you calculate the amount of RNA retrieved? I retrieve only 10% of my RNA of interest calculated as % of Input. Furthermore,when i took a sample of what hasn't bound (after hybridization and capture of the beads) i get only 15% (fraction of washing doesn't include much RNA). so where has my RNA gone? i repeated several times… degradation?

    Reply
    Posted by: Carolin C.
    May 20, 2015 - 5:13 AM
  42. Hi, Carolin
    I am also, using ChiRP. Can you tell me the equation you used to calculate the % of your retrieval

    thanks

    Reply
    Posted by: u.
    June 28, 2016 - 1:22 AM
  43. Hi Carolin, May I ask in the end with your 10-20% retrieval rate of RNA, can you identify new proteins by MS via UV crosslink? Thanks.

    Reply
    Posted by: Zhenqiu H.
    May 17, 2018 - 6:20 PM
  44. Dear ChIRPers, we're glad to introduce the Magna ChIRP kit from Millipore. It's a simple pre-made reagent set for scientists who prefer the reliability and user-friendliness of a reputable brand.

    https://www.emdmillipore.com/US/en/product/EZ--Magna-ChIRP-RNA-Interactome-Kit---Isolation-and-characterization-of-non-coding-RNA%3Achromatin-complexes,MM_NF-17-10495

    Happy ChIRPing!

    Best,
    Chu

    Reply
    Posted by: Ci C.
    April 15, 2015 - 12:35 AM
  45. Hi Chu

    Thanks for sharing this information.
    Did anyone try this kit already and how good is it? Kits are easy to use and save time for reagents.

    Reply
    Posted by: Liu Z.
    April 16, 2015 - 5:17 PM
  46. Dear Chu,

    Many thanks for your excellent protocol. I'm designing a probe set and have been looking at the probes you designed for HOTAIR and XIST for inspiration. I noticed that some of the probes designed for XIST target the sequence at multiple loci (e.g. Probe 10), albeit ocassionally with a single base mismatch. Either way, I assume this may reduce the number of probes needed. Could I ask whether this was a deliberate design strategy and, if so, does the Biosearchtech ChIRP designer incorporate this strategy?

    Thanks

    Reply
    Posted by: Sebastian V.
    April 16, 2015 - 11:31 AM
  47. Dear Chu

    I feel exciting when I am reading your chirp paper in molecular cell. I have 2 questions that need your input.

    1) Have you or others you know tried in vivo tissue samples and if so how it works? I realized that your molecular cell and the latest cell paper used cell lines primarily.

    2) If I have a non-coding RNA which is 400 bp alone, and cannot generate more than 8 probes based on the parameters provided by https://www.biosearchtech.com/chirpdesigner/ ? What should I do ? Could I just reduce the spacer length between odd and even probes ? do you think it will increase background due to the increased probe density?

    Thanks

    Zhiyong

    Reply
    Posted by: Liu Z.
    April 16, 2015 - 4:49 PM
  48. Hi Zhiyong,

    Thank you for your kind words about our paper. Regarding your questions:

    1) Yes we have ChIRPed in drosophila tissues with great success. The key is probably to have small enough chunks of tissue that can be crosslinked effectively and thoroughly.

    2) Email the Biosearchtech team and they can help you manually reduce the number of probes.

    Good luck!

    Best,
    Chu

    Reply
    Posted by: Ci C.
    May 22, 2015 - 11:15 PM
  49. hey there, i was able to retrieve RNA with your method, but i'm not retrieving RNA bound protein (even though i did see a milky pellet after TCA and acetone treatment). i cross link with UV but the other steps i perform are just the same you are doing.
    i'm not so sure about this competetive elution method by using free d-biotin - and do you no longer add protease inhibitors in your buffer? the beads are simply eluted by using biotin buffer, rotate sample for 20 min,RT and 10 min mixing at 65°C (x2). This is it? then everything should be in my buffer and i continue with TCA precipitation ON.
    sorry if i this sounds stupid to you. i'm just looking for mistakes i could have made...

    Reply
    Posted by: Carolin C.
    June 10, 2015 - 10:32 AM
  50. Hi Carolin, I'm glad you're able to get RNA yield, that's a very good sign. The reason that you're not getting proteins could be: 1) mass spec instrument not sensitive enough. The quality of your results varies A LOT with who runs your mass spec. We've had amazing experience with Bill Lane at Harvard. 2) UV cross linking is known to be super low yield. Unless your lncRNA is very abundant or you're prepared to start with a huge amount of material, I would suggest formaldehyde as your first step. 3) TCA and cold acetone with give you a tiny pellet no matter what (the detergent acts as a carrier that will precipitate by itself even in the absence of proteins). So unless you see a sizable pellet, the presence of a pellet itself doesn't mean anything. d-biotin elution is complete, assuming you're using the C1 beads and biotin from invitrogen. Protease inhibitors are absent at the elution step, because your solution should be quite pure and free of contaminating proteases at that point assuming good lab practice. Hope this helps!

    Reply
    Posted by: Ci C.
    June 10, 2015 - 5:45 PM
  51. hey ci! thank you for your answers!
    1) i'm doing western blot as a start, later on i will do mass spec - so thank you for your tip&hint! as i already know a 100% candidate to get retrieved with my (cytoplasmic) mRNA, i stained for this candidate and got no result.
    2) you also mentioned uv-crosslinking in your first protocol, do you have a comment or any experience on the time of cross linking or amount of joules? so far i cross linked 150mj/cm^2 but I'm thinking to increase that. also i need to scale up my cells/beads/probe as you're saying. i do not know if formaldehyde cross linking works in my case, as i have cytosolic mrna.
    3) yes I'm using c1 dynabeads and d-biotin from invitrogen! thanks for the explanation, that helps!

    thank you very much for your quick answers, tips and hints!

    Reply
    Posted by: Carolin C.
    June 11, 2015 - 8:43 AM
  52. hey there, repeated the experiment - this time i used 200 Mio MEF cells - 10 ml lysate and 1 ml beads, 10µl probe. i also increased cross linking to 300 mj/cm^2 - still no proteins (known RNA binding protein) detectable via western blot. i confirmed RNA pulldown via qPCR after cross linking from a small fraction of beads.
    is sonication necessary?
    any troubleshooting ideas?

    Reply
    Posted by: Carolin C.
    June 17, 2015 - 11:38 AM
  53. I would start with formaldehyde first. UV is known to cross link very inefficiently, and certain residues of contact may not be amenable to photocrosslinking at all. Yes sonication is necessary to soluble the cell lysate.

    Reply
    Posted by: Ci C.
    June 19, 2015 - 2:37 PM
  54. i'm using your 25%TCA / Aceton precipitation method to precipitate my proteins. Have you also experienced a pH change (when adding laemmli it turns green/yellow) due to rest TCA? And i think i don't get my pellet resuspended - even after mixing and resuspending. Isn't boiling for 30 min, 95°C destroying the proteins?

    Posted by: Carolin C.
    July 10, 2015 - 7:30 AM
  55. Yes I have had similar experiences before: pH change usually can be prevented by more careful and thorough acetone washes (although need to care not to disturb pellet), and over drying will cause difficulty in resuspension. I never air dry for over a minute. Boiling is completely fine. Try using the LDS samples buffer / Bis-tris gel system from invitrogen, these work great on chirp samples. If you are still having issues with pH, you can manually adjust a little with a moderate alkaline buffer.

    Posted by: Ci C.
    July 10, 2015 - 10:59 PM
  56. Hi Carolin,

    I've the same problem as you had. I could only retrieve 10-15% of RNA when compare to input RNA. Could you please share how you sort this problem?

    Thank you in advance!

    Reply
    Posted by: Ganeshkumar A.
    July 23, 2015 - 4:25 AM
  57. Hi Ganeshkumar, unfortunately i didn't solve the problem… but i found more RNA of interest in my beads when i directly resuspended them in trizol (leaving out proteinase K treatment) - since i'm interested in my proteins bound to the RNA the proteinase K treatment step is of no importance to me. But so far i still couldn't retrieve my RNA bound proteins.

    Reply
    Posted by: Carolin C.
    July 23, 2015 - 5:19 AM
  58. Hi Carolin,

    Thanks for your immediate reply. I'll also avoid Proteinase K step and try again.
    I've one more question. We always do two step RT-qPCR. So, the amount of RNA that I retrieve isn't enough to perform a RT reaction. How do you do your RT-qPCR? This question maybe a bit stupid, but i really wanna sort out all the issues as early as possible.

    Thanks in advance.

    Reply
    Posted by: Ganeshkumar A.
    July 23, 2015 - 5:27 AM
  59. Hello,
    my RNA amount is also quite low, measured by Nanodrop (Once i measured with qubit and could't get anything). I'm using max. volume possible for RT reaction and adapt for input, not bound… Then i perform qPCR with my cDNA

    But i suppose you cannot skip proteinase K step when your lysate is formaldehyde treated, or you need to boil it first to reverse the crosslink. i diluted my beads in trizol when i had non-crosslinked samples to check for retrieval percentage

    Posted by: Carolin C.
    July 23, 2015 - 7:12 AM
  60. We always do a one-step qRT-PCR (i.e. each qPCR well runs it's own RT). This in my hands is much more sensitive and convenient as well (you don't have to measure RNA or cDNA, just load equal portions of each sample). We use Strategene Brilliant II SYBR reagents and Roche 480 machine. Let me know if this helps with yield detected.

    Posted by: Ci C.
    August 4, 2015 - 8:32 AM
  61. Hi Ci,

    I did gene specific cDNA synthesis with 10ng of RNA from all conditions and treated with RNase H and A (in excess) and then proceeded to qPCR. This worked good for me and I'm getting around 14-25 fold enrichment in my odd and even probe samples when compared to input.

    Thank you and Carolin for your suggestions.

    Posted by: Ganeshkumar A.
    August 4, 2015 - 10:43 AM
  62. Hello,
    i have not yet retrieved any RNA bound protein, so i'm thinking about what issues to sort out. i have to say i can retrieve my RNA of interest (but only max. 20% of input)

    i'm wondering about the protein amount in your formaldehyde cross linked, sonicated and hypotone lysed cell lysats. I experienced the protein amount (measured with Bradford) to be 5-8 fold lower compared to uncross linked or Uv cross linked cells treated with a NP40 lysis buffer.
    Why is that, and will it affect my experiments? Any ideas why the protein amount is so low?
    Thank you in advance!

    Reply
    Posted by: Christine C.
    July 23, 2015 - 5:47 AM
  63. Hi Christine, off the top of my head the two main reason for less protein detected upon cross linking is 1) insufficient sonication, and 2) insufficient reverse cross linking (i.e. boiling). Regarding 1), you have to titrate sonication time of your lysate, and pick the minimum sonication required to release all proteins and RNA of interest. To test this, precipitate the lysate post sonication for 10 min at max speed, and run qRTPCR against your RNA of interest and western against the protein on both the supernatant and pellet, the latter resuspended in appropriate buffer. This way you'll know if there's anything left to be solubilized. 3% cross linked lysates can take significantly longer to solublized than your typical ChIP cross linking.

    Regarding 2), do no less than 30min boiling in sample buffer. I've titrate that also, and 10min or 20min recovers much less protein.

    Let me know if these help and let's start from here. Good luck!

    Reply
    Posted by: Ci C.
    August 4, 2015 - 8:29 AM
  64. Hello,
    Many thanks again for this superb protocol. I'm currently trying to optimise this for mRNA pull-down from fixed cells. I've tried various fixing conditions in parallel and dot-blotted for my RBP of interest vs a non-binding protein (GAPDH) after performing ChIRP. I found that 1% glutaraldehyde (10 min) samples blotted strongly for my RBP, but produced an equally strong signal for GAPDH. The latter was also the case for 3% formaldehyde (10 min), but blots of both GAPDH and my RBP weren't as strong. The only sample that showed a slightly stronger signal of the RBP vs GAPDH was 1% formaldehyde (10 min), but both signals were quite weak. All samples were sonicated for several 30 sec ON and 45 OFF cycles at maximum intensity before foaming to produce sheared RNA of <500 bp in optically clear samples.

    I tested the expression of mRNA of interest in samples pulled down with my tiling oligo set compared with a run using non-targeting scrabled oligos. A capture on unfixed cells produced a very high target yield in the tiling oligo sample and no mRNA in the scrambled control sample. However, performing the same pull down in the 1% formaldehyde-fixed+sonicated samples dramatically increased background (GAPDH mRNA) compared to the scrambled control. I'm curious if you found anything similar during the development of ChIRP and ChIRP-MS and if you might have any solutions? Would extra sonication perhaps help?

    Many thanks

    Sebastian Vencken PhD
    Post-Doctoral Researcher

    Reply
    Posted by: Sebastian V.
    September 13, 2015 - 8:06 PM
  65. Hi Sebastian,

    Have you had any luck adapting this technique to mRNA capture?

    Best,
    Mike

    Reply
    Posted by: Michael K.
    December 7, 2016 - 4:48 PM
  66. Mixed results to be honest. We went forward with 1% formaldehyde and tried different forms of sonication (incl. covaris which didn't give us effective fragmentation). Biased background was still an issue and the copurification of our RBP (Ago+miRNA) was much lower than expected. This has apparently successfully been performed before (https://www.ncbi.nlm.nih.gov/pubmed/23325846) but we didn't manage to reproduce these results for our target.

    Reply
    Posted by: Sebastian V.
    December 8, 2016 - 4:15 AM
  67. Thanks for the feedback. Does your miR-CATCH work well/better? Similar idea, no sonication, and probes attached to beads first. Have you ever tried to use this to look for bound proteins?

    I also ran across this mRNA pulldown from yeast (https://www.ncbi.nlm.nih.gov/pubmed/27641505). They also attached the oligos to the beads first, but the buffers look more like ChIRP.

    Reply
    Posted by: Michael K.
    December 8, 2016 - 11:44 AM
  68. We've had some pretty good results (and publications) from miR-CATCH, but have also discovered that the performance can be very dependent on both the target and oligo design.
    With thorough optimisation we managed to reduce background in miR-CATCH, but each target was a new challenge in this respect.

    We hoped that ChIRP would significantly reduce the issue of background, but we have found balancing fragmentation and signal to be difficult. Dot blots for Ago2 gave us very high background signal in scrambled controls when using gluteraldehyde, while 1% formaldehyde gave some better signal differentiation, but at reduced strength. If I'd take ChIRP further for mRNA:RBP(:miRNA) capture, I'd look at the sonication and fixing steps again as there may be further room for improvement. Unfortunately, I've moved to other things for now.

    Reply
    Posted by: Sebastian V.
    December 9, 2016 - 10:42 AM
  69. Hello!

    Many thanks for the detailed protocol, however i am having trouble at crosslinking and sonication steps! I am sorry if it sounds silly but I just want to identifiy what I am missing/doing wrong.

    In the near future, I want to scale up for ChIRP MS, however first want to get these steps right as CHIRP MS would consume 10 times the beads.

    Crosslinking - When I add Glycine to quench formaldehyde, it doesnt change color?

    Sonication - As used by your team, I am using Bioruptor to sonicate the Hela S3 lysate (20 Mi. cells/1ml supplemeted lysis buffer) in 15 ml falcon (Corning) with a probe attached to the cap. I cant seem to get a clear lysate as shown in your video. I have tried sonicating starting from 30 cycles to 300 cycles and it just froths towards the end. After centrifugation to remove cell debris, the lysate is still considerably cloudy.

    I see that a lot of people are working on optimising this method and would appreciate any tips / tricks that might help me get going.

    Looking forward to some suggestions.

    Best regards,
    Minakshi
    PhD Student

    Reply
    Posted by: Minakshi G.
    September 30, 2015 - 5:06 AM
  70. Hi Minakshi, thanks for your interest in our protocol. Re your questions:

    - glycine doesn't change the color of formaldehyde, just glutaraldehyde.
    - check our bioruptor to make sure power is normal and probes are centered correctly. It shouldn't take more than a couple hours even for hardy cell lines. Frosting is strange and indicates to me that you may not be centering the probe correctly and thus losing efficiency.

    Reply
    Posted by: Ci C.
    November 2, 2015 - 2:46 PM
  71. Hi,
    I would have a question regarding the usage of formamide. My concern is that once the bottle is opened and the
    formamide is exposed to oxygen, it will begin to oxidize to formic acid. Do you take any precautions to prevent oxidation? How do you store formamide for further use? Sigma suggests to purge formamide with nitrogen and store it frozen to prevent oxidation.

    Thanks a lot for your help.

    Best wishes,
    matjaz

    Reply
    Posted by: Matjaz B.
    November 2, 2015 - 4:53 AM
  72. Hi Matjaz, thank you for your interest in our technique. formamide is indeed subject to oxidation and ionization. Re-deionization is laborious, so we tried our best to protect the reagents by parafilming around the bottle cap after each use and store it at 4C. I usually run through a 1 liter bottle in a year with repeated opening and closing, and have not observed any effect on results over time. Hope this helps.

    Reply
    Posted by: Ci C.
    November 2, 2015 - 2:44 PM
  73. Hello,

    I have another technical question. Even though our probes are very specific (we detect target RNA using different probes with high specificity), we have problem with high DNA background signal. Have you also had a similar problem? One way to resolve the issue would be to pre-clear lysates with beads before the hybridisation step. Have you ever implemented this step? If yes, have you done the pre-clearing in lysis buffer with or without hybridisation buffer?

    Many thanks,

    - matjaz

    Reply
    Posted by: Matjaz B.
    November 3, 2015 - 7:36 AM
  74. Hi Ci,

    Thanks for providing such an excellent protocol. I have a question about probe design. The 3' half of lncRNA I interested in (5kb in length) was fully cover by repeat elements. Because ChIRP probe Designer ignored the repeat sequence when designing probe, I found almost no probe target to the 3' half of this lncRNA. I'm afraid that I will miss all proteins bind to the 3' end of lncRNA if I only use the probe target to the 5' end of lncRNA. I wonder how do you handle lncRNA contains large number of repeat sequence?

    Thanks for any help.

    Sincerely,
    Jian-You

    Reply
    Posted by: Jian-You L.
    December 3, 2015 - 9:48 PM
  75. Hi all!

    Thank you for sharing this protocol!
    I have just analysed the RT-qPCR results coming from the RNA samples in order to analyse the lncRNA retrieval and I have retrieved a very small percentage of the lncRNA. From the input and the ChIRP samples I have used the same volume of sample (for the qPCR, around 36ng for the input and 21g for the ChIRP) and I have obtained a Ct of 30 for the input and 37 for the ChIRP measuring my lncRNA of interest. How do you normalise the results? Do you use the same volume or ng of the different RNA samples? Do you use a normalisation method similar to the ChIP one? https://www.thermofisher.com/uk/en/home/life-science/epigenetics-noncoding-rna-research/chromatin-remodeling/chromatin-immunoprecipitation-chip/chip-analysis.html

    Thank you in advance

    Isabel

    Reply
    Posted by: Isabel R.
    December 17, 2015 - 9:30 AM
  76. Hi, Isabel
    we experience along time to optimize the protocol in our lab around 9 month for lncRNA and we found the result unstable for different lncRNAs but for your normalization we usually use a normalized methods like Chip experiment for both GAPDH and our target,
    Hope that helps
    for more contact amr@mail.ustc.edu.cn

    Reply
    Posted by: u.
    December 8, 2016 - 7:17 PM
  77. Dear Chu:
    Recently I'm trying to perform ChIRP experiments and your detailed protocol is very helpful. However, I have some questions about cell lysis and sonication.
    1. I find that the supplemented lysis buffer cannot lyse the crosslinked cells. The crosslinked cells are only resuspended, after a few minutes they will sink to the bottom of the tube, is it normal?
    2. You emphasize that lysis buffer should be added fresh Protease Inhibitor, PMSF and Superase-in then proceed immediately to sonication after resuspended smooth, however, a sample will be added appropriate supplemented lysis buffer in proportion then devided into several parts to sonicate by limiting ultrasound equipment, and will it be affected?
    3. I only have a Covaris available for sonication in lab, I tried many times but could not find an appropriate setting. My DNA size distribution is normally a bright band of gDNA at the top, a bright band above 2000bp and a diffuse band from 2000bp to 100bp, if I continued to sonicate, the diffuse band would below 100bp, and there were considerably cloudy after centrifuged the sonicated samples. I want to know what and how much influence if DNA smear is less than 100bp or more than 500 bp? Do you have any advice regarding it?
    Looking forward to some suggestions, thank you in advance!
    Best regards
    mixue
    Ph.D. Student

    Reply
    Posted by: he j.
    July 17, 2016 - 3:37 AM
  78. Dear Dr CHU.
    First of all, sorry for my english, but I'm french.
    I work on lncRNA and I really appreciate your two articles on ChIRP and Chirp-MS, and since some months I try to set it up, but unfortunately without result until now.
    => I designed the probes as you know but my lncRNA is about 2.3kb so i was able to design only 26 probes. I also ordered your Positive and Negative Control.
    => I amplified the cells until 200 to 300 million and I cross linked them with 3% formaldehyde 30min and stop it with Glycine 0.125M 5 to 10 min, as you mention.
    => My sonication was tested in order to have a smear of DNA between 100 and 600bp and it took between 120 and 140min. I use a Bioruptore in cold room and I have to change water and ice every 15min in order to maintain the low temperature. Samples are centrifuged and debris are removed.
    => I use 2 to 3 aliquots of 1mL of lysed cells for each test, and the indicated quantity of probes. Of course before incubation, samples are pre-incubated with prewashed beads.
    => First incubation is done at 37 ° C in a shaking system, overnight. Second incubation (after addition of the prewashed beads) is done at 37 ° C for 1 hour.
    => Wash is done 5 times with wash buffer, then samples are eluted (using elution buffer freshly prepared with Sigma-Aldrich Biotine) and precipitated with TCA and Aceton. Pellet are directly dissolved in Laemmli, incubated 30min at 95°C and loaded with 12% acrylamide gel. After 1h at 200V the gel is stained with Coomassie Blue and destained 3 times 45min.
    I found NO BANDS even with Positive and negative controls, but after elution, when I checked the presence of my lncRNA in the sample selected with my probes, the result is positive.

    Could you tell me what are the possible mistakes that I could do ....?
    Thanks a lot.

    Reply
    Posted by: Sebastien C.
    January 3, 2017 - 5:02 AM
  79. Dear Dr. Chu,

    Good day! I am Anchilie, a PhD student, and I am really interested in applying your discovered technique in plants. I am currently doing the ChiRP-MS in Arabidopsis but I don't seem to get any RNA-bound proteins in my sample.

    I would just like to briefly tell you how I do the ChiRP-MS in plants. First, I harvest 3g of 14-day old seedlings and crosslinked it with 1% formaldehyde. From these, I then do nuclear extraction and do sonication. From the 1mL sonicated chromatin, I dilute it with 2mL of hybridization buffer, add 1ul probe and 100ul of beads and incubated then in 37C for O/N or 4 hours at 37C. From then I wash the beads 5x and precipitated the proteins using the biotin elution buffer and TCA method. The samples in 1x Laemmli buffer were submitted to LC/MS. I also check the enrichment in the qPCR and are enriched by 500-fold. However, upon analyzing my samples, the mass spec results only detected mitochondrial and chloroplastic proteins in the control and non-coding RNA

    I also tried many things like using 3% formaldehyde and UV crosslinking. I also did direct boiling of beads in Laemmli buffer. I also tried increasing the amount of material 10x accompanied with increasing the probe and the beads.
    But it doesn't really help.

    I would really appreciate to receive some feedback from you and your group with this matter.

    Best regards,
    Anchilie

    Reply
    Posted by: Anchilie M.
    February 27, 2017 - 4:49 AM
  80. Dear Anchilie,

    I am doing CHIRP in arabidopsis, you are the only only doing CHIRP as far as I know. I met some problems. I couldn't enrich my non coding RNA. So I want to know how did you do your CHIRP? Could you please share your protocol with me? Thanks!

    Reply
    Posted by: Zhi-Hong L.
    June 19, 2017 - 7:56 AM
  81. Hi guys, can anyone help me how the percentage calculation for lncRNA retrieval is done.

    Thank you

    Reply
    Posted by: Sunil B.
    June 22, 2017 - 3:58 PM
  82. Hi,

    Thank you for sharing this protocol, I have a question. If I want to study the potential interaction between a protein and a long non coding RNA in rDNA locus (or eventually with the rDNA directly), do you think that your kit will work ?
    Thank you for your answer

    Reply
    Posted by: Burette M.
    April 12, 2018 - 3:27 AM
  83. Dear professor,
    Thank you for sharing this protocol! It helps me a lot. I have a question to ask. Since ultrasound may break the hydrogen bond, I want to ask whether it is necessary to perform sonication when I study weak RNA-RNA interaction, for example: lncRNA-miRNA interaction?

    Reply
    Posted by: Zihao L.
    May 26, 2018 - 10:52 PM
  84. Dear professor,

    Any idea if using a probe-based sonication (like the Branson sonifier) would work? Anyone has tried it ?
    in the previous lab, we were using the bioruptor however we don't have it where I am now unfortunately and needed help to optimize it on the Branson or probe-based sonifiers?

    Thanks

    Reply
    Posted by: Anonymous
    March 1, 2020 - 4:26 AM

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