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Series GSE80799 Query DataSets for GSE80799
Status Public on Feb 15, 2018
Title Implications of CpG islands on chromosomal architectures and modes of global gene regulation
Sample organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by array
Third-party reanalysis
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary In this study, we present the critical implication of CpG islands (CGI) on the general rules for chromatin structural architectures and gene regulation mechanisms. Through integrative biological big data analyses, we found that the linear gene arrangements in chromosomes harbor the critical evidences for spatial gene segregation and different modes of gene localization between CGI-containing (CGI+) and CGI-less (CGI-) genes within the nucleus. CGI- genes, which are generally located within the nuclear periphery (chromosomal territories) as heterochromatin, are converted to euchromatin and internalized into the nuclear center only when activated. However, CGI-centered regulations keep CGI+ genes from heterochromatin formation and located within nuclear center regardless of their activities. We also show these different localization behaviors make CGI+ and CGI- genes to be regulated by distinct transcriptional regulation mechanisms: CGI- genes are regulated by local bindings of transcription factors, while CGI+ genes are strongly engaged in the 3-dimensional long-range chromosomal interactions.

This SuperSeries is composed of the SubSeries listed below.
Overall design Re-analyses diverse published datasets of ChIP-seq, RNA-seq, gene expression microarray, DNaseI-seq, DamID-seq, MeDIP-seq, ChIA-pet, and Hi-C.

Refer to individual Series
Citation(s) 29529258
Submission date Apr 28, 2016
Last update date May 17, 2018
Contact name Jonghwan Kim
Phone 512-232-8046
Organization name University of Texas at Austin
Department Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology
Lab Kim Lab
Street address 2506 Speedway NMS 4.246
City Austin
State/province TX
ZIP/Postal code 78712
Country USA
This SuperSeries is composed of the following SubSeries:
GSE80791 CpG island mediated linear and spatial gene partitioning (ChIP-seq)
GSE80792 CpG island mediated linear and spatial gene partitioning (MOE430V2)
GSE80793 CpG island mediated linear and spatial gene partitioning (RNA-seq)
BioProject PRJNA319994

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Supplementary data files not provided

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