1. Locus-specific chromatin profiling of evolutionarily young transposable elements
- Author
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Darren Taylor, Robert Lowe, Claude Philippe, Kevin C. L. Cheng, Olivia A. Grant, Nicolae Radu Zabet, Gael Cristofari, Miguel R. Branco, Barts & The London School of Medicine and Dentistry [London, UK] (Blizard Institute), Queen Mary University of London (QMUL), Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), ANR-11-LABX-0028,SIGNALIFE,Réseau d'Innovation sur les Voies de Signalisation en Sciences de la Vie(2011), ANR-16-CE12-0020,RETROMET,Rendre unique l'ADN répété ou comment révéler la régulation épigénétique des rétrotransposons L1 dans les cellules somatiques humaines à une résolution inégalée.(2016), ANR-19-CE12-0032,ImpacTE,Réseau de régulation et élément LINE-1 : impact global des éléments transposables récents sur l'activité génique chez les Mammifères(2019), Université Nice Sophia Antipolis (1965 - 2019) (UNS), Cristofari, Gael, Centres d'excellences - Réseau d'Innovation sur les Voies de Signalisation en Sciences de la Vie - - SIGNALIFE2011 - ANR-11-LABX-0028 - LABX - VALID, Rendre unique l'ADN répété ou comment révéler la régulation épigénétique des rétrotransposons L1 dans les cellules somatiques humaines à une résolution inégalée. - - RETROMET2016 - ANR-16-CE12-0020 - AAPG2016 - VALID, and Réseau de régulation et élément LINE-1 : impact global des éléments transposables récents sur l'activité génique chez les Mammifères - - ImpacTE2019 - ANR-19-CE12-0032 - AAPG2019 - VALID
- 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 - 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.
- Published
- 2021
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