|
| 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
Other
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.
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| |
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| 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
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| |
|
| Citation(s) |
29529258 |
| |
| Submission date |
Apr 28, 2016 |
| Last update date |
May 17, 2018 |
| Contact name |
Jonghwan Kim |
| E-mail(s) |
jybella@utexas.edu
|
| 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) |
| GSE80795 |
CpG island mediated linear and spatial gene partitioning (other data sets) |
| GSE80797 |
CpG island mediated linear and spatial gene partitioning (pA+ RNA-seq profile) |
|
| Relations |
| BioProject |
PRJNA319994 |
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