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Locus-specific chromatin profiling of evolutionarily young transposable elements
- Source :
- Nucleic Acids Research, Nucleic Acids Research, Oxford University Press, 2021, ⟨10.1093/nar/gkab1232⟩, Nucleic Acids Research, 2021, ⟨10.1093/nar/gkab1232⟩
- Publication Year :
- 2021
- Publisher :
- HAL CCSD, 2021.
-
Abstract
- 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 HiChIP and a newly developed mapping tool (PAtChER) yields accurate protein enrichment profiles at individual repetitive loci. Using this approach, we reveal previously unappreciated variation in the epigenetic profiles of young TE loci in mouse and human cells. Insights gained using our method will be invaluable for dissecting the molecular determinants of TE regulation and their impact on the genome.
- Subjects :
- Transposable element
[SDV]Life Sciences [q-bio]
Interspersed repeat
Locus (genetics)
[SDV.GEN] Life Sciences [q-bio]/Genetics
Computational biology
Biology
Genome
03 medical and health sciences
Mice
0302 clinical medicine
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]
Genetics
Animals
Humans
Epigenetics
Epigenomics
030304 developmental biology
Regulation of gene expression
0303 health sciences
[SDV.GEN]Life Sciences [q-bio]/Genetics
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Genomics
Repetitive dna
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Chromatin
[SDV] Life Sciences [q-bio]
Gene Expression Regulation
Epigenetics and chromatin
DNA Transposable Elements
[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]
Transposable elements
030217 neurology & neurosurgery
Subjects
Details
- Language :
- English
- ISSN :
- 03051048 and 13624962
- Database :
- OpenAIRE
- Journal :
- Nucleic Acids Research, Nucleic Acids Research, Oxford University Press, 2021, ⟨10.1093/nar/gkab1232⟩, Nucleic Acids Research, 2021, ⟨10.1093/nar/gkab1232⟩
- Accession number :
- edsair.doi.dedup.....20f316ea247b21d01ad753bb39352483