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Series GSE124409 Query DataSets for GSE124409
Status Public on Nov 08, 2020
Title Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Background: The eukaryotic genome is folded into higher-order conformation accompanied with constrained dynamics for coordinated genome functions. However, the molecular machinery underlying these hierarchically organized three-dimensional (3D) chromatin architecture and dynamics remains poorly understood.
Results: Here by combining imaging and sequencing, we studied the role of lamin B1 in chromatin architecture and dynamics. We found that lamin B1 depletion leads to chromatin redistribution and decompaction. Consequently, lamina-associated domains (LADs) are detached from the nuclear periphery. The inter-chromosomal interactions and overlap between chromosome territories are increased. Moreover, Hi-C data revealed that lamin B1 is required for the integrity and segregation of chromatin compartments but not for the topologically associating domains (TADs). Using live cell single molecule tracking, we further proved that depletion of lamin B1 leads to increased chromatin dynamics, owing to chromatin decompaction and redistribution toward nucleoplasm.
Conclusions: Taken together, our data suggest that lamin B1 and chromatin interactions at the nuclear periphery promote LAD maintenance, genomic compartmentalization into chromosome territories and A/B compartments and confine chromatin dynamics, supporting its crucial role in chromatin higher-order structure and chromatin dynamics.
Overall design Analysis of chromatin 3D structure, lamina associated domains and gene expression data in wild-type and LMNB1-knockout MDA-MB-231 breast cancer cell lines. There are 2 replicates for each Hi-C sample, 3 replicates for each lamin A ChIP-seq sample and 3 replicates for each RNA-seq sample.
Web link
Contributor(s) Li M, Chang L
Citation(s) 33155082
Submission date Dec 27, 2018
Last update date Nov 10, 2020
Contact name Mengfan Li
Organization name Peking University
Street address No.5 Yiheyuan Road
City Beijing
ZIP/Postal code 100871
Country China
Platforms (2)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (20)
GSM3532128 Hi-C WT rep1
GSM3532129 Hi-C WT rep2
GSM3532130 Hi-C LMNB1-KO rep1
BioProject PRJNA511977
SRA SRP174547

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE124409_KO_merged_peaks.bed.gz 9.4 Kb (ftp)(http) BED
GSE124409_RAW.tar 846.0 Mb (http)(custom) TAR (of BW, MATRIX, TAR)
GSE124409_WT_merged_peaks.bed.gz 5.7 Kb (ftp)(http) BED
GSE124409_fpkm_DESeq2_output.txt.gz 1.8 Mb (ftp)(http) TXT
GSE124409_raw_counts.txt.gz 249.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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