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| Status |
Public on Aug 19, 2021 |
| Title |
Locus-specific chromatin profiling of evolutionarily young transposable elements [HiChIP] |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Other
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| Summary |
Despite a vast expansion in the availability of epigenomic data, our knowledge of the chromatin landscape at interspersed repeats remains highly limited by difficulties in mapping short-read sequencing data to these regions. In particular, little is known about the locus-specific regulation of evolutionarily young transposable elements (TEs), which have been implicated in genome stability, gene regulation and innate immunity in a variety of developmental and disease contexts. Here we propose an approach for generating locus-specific protein-DNA binding profiles at interspersed repeats, which leverages information on the spatial proximity between repetitive and non-repetitive genomic regions. We demonstrate that the combination of Hi-ChIP and a newly developed mapping tool (PAtChER) yields accurate protein enrichment profiles at individual repetitive loci. Using this approach, we show that young TEs display locus- and tissue-specific chromatin profiles in both mice and humans. Insights gained using our method will be invaluable for dissecting the molecular determinants of TE regulation and their impact on the genome.
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| Overall design |
Methylated DNA was immunoprecipitated from Hi-C libraries, and ends were mapped using a pipeline (PAtChER) that uses 3D information to map repetitive reads, producing ChIP-like profiles.
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| Contributor(s) |
Taylor D, Lowe R, Philippe C, Cheng KC, Cristofari G, Branco MR |
| Citation(s) |
34908129 |
| |
| Submission date |
Aug 17, 2021 |
| Last update date |
Dec 16, 2021 |
| Contact name |
Miguel R Branco |
| E-mail(s) |
m.branco@qmul.ac.uk
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| Organization name |
Blizard Institute
|
| Street address |
4 Newark Street
|
| City |
London |
| ZIP/Postal code |
E1 2AT |
| Country |
United Kingdom |
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| Platforms (2) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE182306 |
Locus-specific chromatin profiling of evolutionarily young transposable elements |
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| Relations |
| BioProject |
PRJNA755722 |
| SRA |
SRP332929 |
