Endogenous Genomic Sites
Endogenous Genomic Sites - Related Videos
09:31
Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
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Cited by 56 •
2016
We describe a protocol for amplifying retroviral integration sites from the genomic DNA of infected cells, sequencing the amplified virus-host junctions, and then mapping these sequences to a reference genome. We also describe techniques to quantify the distribution of integration sites relative to various genomic annotations using BEDTools.
07:05
Chromatin Immunoprecipitation to Identify Target Protein Binding Sites on Genomic DNA
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2025
In this video, we demonstrate the chromatin immunoprecipitation technique to identify protein binding sites on specific regions of the genomic DNA of oligodendrocyte precursor cells via the selective immunoprecipitation of protein-bound chromatin fragments. This method helps to study the interaction of several regulatory proteins, including transcription factors involved in gene regulation.
01:49
Conserved Binding Sites
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2020
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function. Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
08:31
Genome Editing
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2023
A well-established technique for modifying specific sequences in the genome is gene targeting by homologous recombination, but this method can be laborious and only works in certain organisms. Recent advances have led to the development of “genome editing”, which works by inducing double-strand breaks in DNA using engineered nuclease enzymes guided to target genomic sites by either proteins or RNAs that recognize specific sequences. When a cell attempts to repair this damage, mutations can be...
11:50
Genome-Wide Mapping of Histone Modifications and Transcription Factor Binding Sites in Neuroendocrine Small Cell Lung Cancer Cell Lines Using CUT&RUN
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2026
An optimized Cleavage Under Targets and Release Using Nuclease followed by next generation sequencing (CUT&RUN-seq) protocol is described for neuroendocrine small cell lung cancer cell lines. It enables genome-wide mapping of various histone modifications and transcription factor (e.g. E2F7) binding sites to investigate epigenetic and transcriptional deregulation in SCLC pathobiology.
FAQs
The surrounding regulatory sequences and chromatin environment can influence how a locus functions. Examining or modifying a sequence in its native chromosomal position therefore supports more representative observations of gene activity, expression patterns, and genome organization than analyses conducted outside that context. This distinction is especially important when researchers want results that reflect normal cellular regulation.
After a site-specific nuclease or recombinase acts at the selected locus, cellular repair pathways determine how the DNA is changed. Homology-directed repair can support insertion or alteration using matching sequence information, whereas end joining can produce different repair outcomes. The pathway engaged therefore influences whether material is inserted, removed, or otherwise modified.
These enzymes provide the targeting step that directs genetic manipulation to a selected chromosomal locus. Their action creates the opportunity for subsequent cellular repair or recombination processes to change the site. Because the locus remains within its chromosome, researchers can examine the resulting change while retaining the surrounding regulatory and chromatin context.
A typical workflow begins by selecting the chromosomal locus relevant to the biological question. Researchers then direct a site-specific nuclease or recombinase to that sequence and allow cellular DNA repair or recombination processes to act. The resulting insertion, removal, or alteration is interpreted in relation to the locus’s native regulation and chromatin environment.
They are useful when researchers need to investigate gene function or expression under conditions that preserve the chromosome’s native organization. Applications described for this approach include functional genomics, disease modeling, genetic engineering, and development of precise genome-editing strategies. The native setting can make these studies more representative of how genetic changes operate within cells.
Studying altered endogenous sites can reveal how a genetic sequence contributes to gene function, expression, and genome organization. Because the locus remains associated with its native regulatory and chromatin environment, observed effects can be interpreted in that biological context. This supports analyses of how targeted insertions, removals, or other changes influence genomic behavior.