the-chrop-approach-combines-chip-mass-spectrometry-to-dissect-locus

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin

Chromatin is a highly dynamic nucleoprotein complex made of DNA and proteins that controls various DNA-dependent processes. Chromatin structure and ...

European Institute of Oncology

Two-dimensional liquid chromatography separation (2-DL), based on chromatofocusing for first dimension and hydrophobicity for second, can be used as a complementary method to two-dimensional gel electrophoresis (2-DE). A platform now available, ProteomeLab PF 2D provided by Beckman Coulter, (Fullerton, CA, USA), assembles these methods in automation. This system was applied to resolve large numbers of urine proteins. Reproducibility and sensitivity in protein resolution were evaluated in this study using urines collected from male blood donors. About 1000 peaks were detected at a pH range of 4.0-8.5 by applying 1 mg of proteins. Furthermore, the same fractions showing peaks with high absorbance intensities in second dimension were collected and subjected to matrix-assisted laser desorption/ionization-time of flight/mass spectrometry analysis for identification. The results showed that the 2-DL provides high reproducibility of two-dimensional protein map, and lends fractions to subsequent mass spectrometry analysis without the further need for extraction or solubilization of samples as required for spots excised from 2-DE gels. In addition, this system also allows to separate particularly proteins with 40-9 kDa molecular weight.

Proteome profile of human urine with two-dimensional liquid phase fractionation.

Aquaporins (AQPs) are an ubiquitous family of proteins characterized by sequence similarity and the presence of two NPA (Asp-Pro-Ala) motifs. At present, 13 human AQPs are known and they are divided into two subgroups according to their ability to transport only water molecules (AQP0, AQP1, AQP2, AQP4, AQP5, AQP6, and AQP8), or also glycerol and other small solutes (AQP3, AQP7, AQP9, AQP10, AQP12). The genomic, structural, and functional aspects of this family are briefly described. In particular, proteomic approaches to identify and characterize the most studied AQPs, mainly through SDS-PAGE followed by MS analysis, are discussed. Moreover, the clinical importance of the best studied aquaporin (AQP1) in human diseases is also provided.

Proteomic knowledge of human aquaporins.

The human Arg (Abl2) nonreceptor tyrosine kinase has a role in cytoskeletal rearrangements by its C-terminal F-actin- and microtubule-binding sequences. We have previously identified Arg transcripts with different 5'- and 3'-ends, named respectively long and short 1A and 1B (1AL, 1AS, 1BL, 1BS) and long and short C-termini (CTL and CTS), that have different expression patterns in various cell types. The combination of the different ends permits to predict eight putative full-length Arg transcripts and corresponding proteins. By Reverse Transcription-Long PCR we show here that all eight full-length transcripts are endogenously expressed in Caki-1 cells and the two bands, approximately 10 kDa different, shown by 1-D Western blots of Hek293T and Caki-1 lysates correspond to the full-length Arg protein isoforms with different C-termini. 2-D Western blot analysis evidenced different high molecular weight and slight acidic specific spots in Hek293T and Caki-1 lysates. The cellular localization of two Arg isoforms (1BLCTL and 1BLCTS) transfected in Caki-1 and Hek293T cells was cytoplasmic, and some differences in cytoskeleton interactions have been evidenced. Moreover, in Hek293T cells only the transfected 1BLCTS isoform gives rise to a large intracytoplasmic cylindrical structure containing phalloidin-positive amorphous actin aggregates. The presence of eight full-length Arg isoforms with different cellular expression may imply a diverse functional role in normal and neoplastic cells.

Eight full-length abelson related gene (Arg) isoforms are constitutively expressed in caki-1 cell line and cell distribution of two isoforms has been analyzed after transfection.

Chromatin is a highly dynamic, well-structured nucleoprotein complex of DNA and proteins that controls virtually all DNA transactions. Chromatin dynamicity is regulated at specific loci by the presence of various associated proteins, histones, post-translational modifications, histone variants, and DNA methylation. Until now the characterization of the proteomic component of chromatin domains has been held back by the challenge of enriching distinguishable, homogeneous regions for subsequent mass spectrometry analysis. Here we describe a modified protocol for chromatin immunoprecipitation combined with quantitative proteomics based on stable isotope labeling by amino acids in cell culture to identify known and novel histone modifications, variants, and complexes that specifically associate with silent and active chromatin domains. Our chromatin proteomics strategy revealed unique functional interactions among various chromatin modifiers, suggesting new regulatory pathways, such as a heterochromatin-specific modulation of DNA damage response involving H2A.X and WICH, both enriched in silent domains. Chromatin proteomics expands the arsenal of tools for deciphering how all the distinct protein components act together to enforce a given region-specific chromatin status.

The proteomic investigation of chromatin functional domains reveals novel synergisms among distinct heterochromatin components.

Chromatin is a highly structured nucleoprotein complex made of histone proteins and DNA that controls nearly all DNA-dependent processes. Chromatin plasticity is regulated by different associated proteins, post-translational modifications on histones (hPTMs) and DNA methylation, which act in a concerted manner to enforce a specific "chromatin landscape", with a regulatory effect on gene expression. Mass Spectrometry (MS) has emerged as a powerful analytical strategy to detect histone PTMs, revealing interplays between neighbouring PTMs and enabling screens for their readers in a comprehensive and quantitative fashion. Here we provide an overview of the recent achievements of state-of-the-art mass spectrometry-based proteomics for the detailed qualitative and quantitative characterization of histone post-translational modifications, histone variants, and global interactomes at specific chromatin regions. This synopsis emphasizes how the advances in high resolution MS, from "Bottom Up" to "Top Down" analysis, together with the uptake of quantitative proteomics methods by chromatin biologists, have made MS a well-established method in the epigenetics field, enabling the acquisition of original information, highly complementary to that offered by more conventional, antibody-based, assays.

Mass spectrometry-based proteomics for the analysis of chromatin structure and dynamics.

Chromatin is the macromolecular nucleoprotein complex that governs the organization of genetic material in the nucleus of eukaryotic cells. In chromatin, DNA is packed with histone proteins into nucleosomes. Core histones are prototypes of hyper-modified proteins, being decorated by a large number of site-specific reversible and irreversible post-translational modifications (PTMs), which contribute to the maintenance and modulation of chromatin plasticity, gene activation, and a variety of other biological processes and disease states. The observations of the variety, frequency and co-occurrence of histone modifications in distinct patterns at specific genomic loci have led to the idea that hPTMs can create a molecular barcode, read by effector proteins that translate it into a specific transcriptional state, or process, on the underlying DNA. However, despite the fact that this histone-code hypothesis was proposed more than 10years ago, the molecular details of its working mechanisms are only partially characterized. In particular, two questions deserve specific investigation: how the different modifications associate and synergize into patterns and how these PTM configurations are read and translated by multi-protein complexes into a specific functional outcome on the genome. Mass spectrometry (MS) has emerged as a versatile tool to investigate chromatin biology, useful for both identifying and validating hPTMs, and to dissect the molecular determinants of histone modification readout systems. We review here the MS techniques and the proteomics methods that have been developed to address these fundamental questions in epigenetics research, emphasizing approaches based on the proteomic dissection of distinct native chromatin regions, with a critical evaluation of their present challenges and future potential. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.

Article	Year
Proteome profile of human urine with two-dimensional liquid phase fractionation. Proteomics\| PubMed ID: 15912557	2005
Proteomic knowledge of human aquaporins. Proteomics\| PubMed ID: 17044001	2006
Eight full-length abelson related gene (Arg) isoforms are constitutively expressed in caki-1 cell line and cell distribution of two isoforms has been analyzed after transfection. Journal of cellular biochemistry\| PubMed ID: 18810762	2008
The proteomic investigation of chromatin functional domains reveals novel synergisms among distinct heterochromatin components. Molecular & cellular proteomics : MCP\| PubMed ID: 23319141	2013
Mass spectrometry-based proteomics for the analysis of chromatin structure and dynamics. International journal of molecular sciences\| PubMed ID: 23466885	2013
Biochemical systems approaches for the analysis of histone modification readout. Biochimica et biophysica acta\| PubMed ID: 24681439	2014

Monica Soldi

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