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Series GSE221288 Query DataSets for GSE221288
Status Public on Jan 01, 2023
Title Gene regulatory loops at lamina-associated domains
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The nuclear lamina provides a repressive chromatin environment at the nuclear periphery. However, whereas most genes in lamina-associated domains (LADs) are repressed, approximately ten percent reside in local euchromatic contexts and are expressed. How these genes are regulated and whether they are able to contact regulatory elements in LADs or outside LADs remains unclear. Here, we integrate transcriptomic, chromatin states, microscopy and publicly available enhancer-capture Hi-C data to show that expressed genes in LADs are able to connect to enhancers in LADs and inter-LADs. Our data favor a model where the spatial topology of chromatin at the nuclear lamina is compatible with transcriptional regulation in this dynamic nuclear compartment.
Overall design Using public enhancer capture Hi-C (ECHI-C) data for differentating adipocytes, we have analyzed enhancer connections in chromatin at the nuclear lamina in human primary adipose stem cells (ASCs). We have mapped lamin A/C (LMNA/C) enrichment throughout the genome by ChIP-seq of lamin AC on Day 0, 1 and 3 of in vitro adipogenic differentiation. Six histone modifications (H3K4me3, H3K4me1, H3K27ac, H3K27me3, H3K36me3, and H3K9me3) were also mapped from proliferating ASC (Pro; day minus 2 before induction of differentiation) in culture to learn chromatin states. These datasets provide a genomic context to characterize sites of chromatin (enhancer) interactions in lamina-associated domains in the adipose lineage.
Contributor(s) Pickering SH, Abdelhalim M, Madsen-Østerbye J, Collas P
Citation(s) 36833261
Submission date Dec 19, 2022
Last update date Mar 08, 2023
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 (3)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (13)
GSM6857883 D0_LMNA_Rep1
GSM6857884 D0_LMNA_Rep2
GSM6857885 D1_LMNA_Rep1
BioProject PRJNA913836

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Supplementary file Size Download File type/resource
GSE221288_RAW.tar 7.0 Gb (http)(custom) TAR (of BED, BEDGRAPH, BROADPEAK, BW, NARROWPEAK)
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Raw data are available in SRA
Processed data provided as supplementary file

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