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Series GSE57149 Query DataSets for GSE57149
Status Public on Mar 24, 2015
Title Differential features of lamina-associated domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The nuclear lamina interacts with the genome through megabase-size lamina-associated domains (LADs). LADs have been identified in proximity labeling assays and recently by chromatin immunoprecipitation-sequencing (ChIP-seq) of A- and B-type lamins. LADs localize mainly to the nuclear periphery, they are gene-poor and largely heterochromatic. Here, we show that the mode of chromatin fragmentation for ChIP, namely either bath sonication (used to date for ChIP of nuclear lamins) or digestion with micrococcal nuclease (MNase) leads to the discovery of distinct sets of lamin-interacting domains (which we refer to as LiDs) with distinct gene content, histone composition enrichment and relationship to lamin B1-interacting domains. We find that total genome coverage by lamin A/C ('LMNA') LiDs identified in sonicated or MNase-digested chromatin is similar (~730 megabases). Over half of these domains, however, are uniquely detected in sonicated or MNase-digested chromatin. Whereas sonication-specific LMNA LiDs are gene-poor and devoid of a broad panel of histone modifications, MNase-specific LMNA LiDs are of higher gene density and are enriched in H3K9me3, H3K27me3 and in histone variant H2A.Z. Analysis of published LMNB1 LADs and of LMNB1 LiDs identified by ChIP-seq further shows that LMNA can associate with 'open' chromatin domains displaying euchromatin features which are not associated with LMNB1. The differential genetic and epigenetic properties of lamin-interacting chromatin domains indicate the existence of distinct LiD populations identifiable in different chromatin contexts, including nuclease-accessible 'open' regions presumably localized in the nuclear interior.
Overall design There are two experiments of two samples each for LMNA ChIPs (ChIP and Input), and one LMNB1 ChIP sample, so 5 samples in total. The difference between the experiments are the chromatin fragmentation method (see extract protocols 1 and 2). One uses sonication while the other uses micrococcal nuclease (MNase).
Contributor(s) Collas P, Lund E, Duband-Goulet I, Buendia B
Citation(s) 25602132
Submission date Apr 29, 2014
Last update date May 15, 2019
Contact name Philippe Collas
Organization name University of Oslo
Department Institute of Basic Medical Sciences
Street address PO Box 1112 Blindern
City Oslo
ZIP/Postal code 0317
Country Norway
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (5)
GSM1376179 Hela_sonic_LMNA
GSM1376180 Hela_sonic_Input
GSM1376181 Hela_digest_LMNA
BioProject PRJNA245783
SRA SRP041532

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Supplementary file Size Download File type/resource
GSE57149_RAW.tar 40.0 Kb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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