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Series GSE156413 Query DataSets for GSE156413
Status Public on Aug 20, 2020
Title Loss of CBX2 induces genome instability and senescence-associated chromosomal rearrangements
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Polycomb group proteins play important roles in developmental and cell proliferation processes. We demonstrate that the PRC1 protein CBX2 is critical for heterochromatin homeostasis, chromosome stability and the prevention of premature cellular senescence. Purpose: Use of Next-generation sequencing (NGS) to assess transcriptional (RNAseq) profiles and changes in chromatin accessibility in WT and Cbx2-/- fibroblasts prior to the onset of premature senescence.
 
Overall design Methods: RNA-seq and ATAC-seq profiles of Passage 2 mouse embryonic fibroblasts (MEFs) from wild-type (WT) and Cbx2 knockout (Cbx2-/-) mice were maintained in high glucose DMEM (Gibco/Thermo Fisher, Waltham, MA, USA) supplemented with 10% FBS (Hyclone, GE Healthcare, Chicago, IL, USA), 1/100 (v/v) sodium pyruvate, 1/100 (v/v) L-Glutamine and 1/100 (v/v) Penicillin/Streptomycin (all Gibco/Thermo Fisher) before cell collection for ATAC-seq and RNAseq.
Results: Integrative transcriptome analysis and ATAC-seq revealed a significant dysregulation of transcripts involved in DNA repair, chromocenter formation and tumorigenesis in addition to changes in chromatin accessibility of genes involved in amyotrophic lateral sclerosis, basal transcription factors and folate metabolism.
Conclusions: The presence of transcriptional dysregulation and altered chromatin accessibility at key loci in Cbx2-/- cells combined with extensive centromere and telomere defects suggest a prominent role for CBX2 in heterochromatin homeostasis and the regulation of nuclear architecture.
 
Contributor(s) Baumann C, Zhang X, De La Fuente R
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Submission date Aug 18, 2020
Last update date Aug 20, 2020
Contact name Claudia Baumann
Organization name University of Georgia
Department Physiology and Pharmacology
Lab College of Veterinary Medicine
Street address 501 DW Brooks Drive
City Athens
State/province GA
ZIP/Postal code 30605
Country USA
 
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL28457 DNBSEQ-G400 (Mus musculus)
Samples (8)
GSM4730400 RNAseq-WT-1
GSM4730401 RNAseq-WT-2
GSM4730402 RNAseq-Cbx2-1
Relations
BioProject PRJNA657852
SRA SRP277935

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Supplementary file Size Download File type/resource
GSE156413_Control-VS-Knockout.DEseq2_Method.GeneDiffExp.txt.gz 3.0 Mb (ftp)(http) TXT
GSE156413_Integrative_ATAC_Seq_Cbx2_Annotated_Peaks.xls.gz 23.8 Kb (ftp)(http) XLS
GSE156413_Standard_ATAC_Seq_Cbx2_Annotated_Peaks.xls.gz 10.3 Kb (ftp)(http) XLS
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Processed data are available on Series record

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