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Series GSE84705 Query DataSets for GSE84705
Status Public on Aug 08, 2018
Title Regulated Capture of Vk Gene Topologically Associating Domains by Transcription Factories
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Antigen receptor gene recombination requires stochastic, monoallelic choice of a single variable gene in each lymphocyte progenitor. However, how this occurs remains unknown. Herein, we report that prior to Vκ to Jκ gene recombination, Igκ alleles reside within spatially different nuclear niches defined by elongating RNA Polymerase II (e-Pol II) and cyclin D3 complexes assembled on the nuclear matrix. Upon cell cycle exit, and cyclin D3 downregulation, only the Vκ allele in the more constrained e-Pol II niche was transcribed. Chromatin modeling and single cell RNA-seq revealed that the nuclear niche favored Vκ flanking CTCF sites, thus shaping the transcribed repertoire. Furthermore, multiple contiguous Vκs oriented away from CTCF sites were preferentially transcribed. Cyclin D3 also repressed monoallelic protocadherin and olfactory genes. These studies of Igκ reveal a general mechanism by which regulated, stochastic chromatin loop capture by fixed e-Pol II complexes generates diversity and couples cell cycle exit to monogenic choice.
 
Overall design Bulk and Single Cell RNA-seq of B6 x CAST F1 hybrid small pre-B cells and bulk RNA-seq of Ccnd3-/- pro-B cells
 
Contributor(s) Karki S, Kennedy D, Mclean K, Grzybowski A, Maienschein-Cline M, Banerjee S, Xu H, Davis E, Mandal M, Labno C, Powers SE, Le Beau MM, Dinner A, Singh H, Ruthenburg A, Clark M
Citation(s) 30157436
Submission date Jul 21, 2016
Last update date May 15, 2019
Contact name Mark Maienschein-Cline
E-mail(s) mmaiensc@uic.edu
Organization name University of Illinois at Chicago
Department Research Resources Center
Lab Center for Research Informatics
Street address 1819 W Polk Ave, Rm 336 M/C 789
City Chicago
State/province IL
ZIP/Postal code 60612
Country USA
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (75)
GSM2247856 run1289_lane12_read2_indexN701-S502=Nov18_Cell_42
GSM2247860 run1289_lane12_read2_indexN701-S517=Nov18_Cell_1
GSM2247864 run1289_lane12_read2_indexN702-S508=Nov18_Cell_64
Relations
BioProject PRJNA330864
SRA SRP079248

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

Supplementary file Size Download File type/resource
GSE84705_RAW.tar 340.0 Kb (http)(custom) TAR (of TXT)
GSE84705_bulk_VJk_and_l_subset.txt.gz 2.8 Kb (ftp)(http) TXT
GSE84705_bulk_VJk_and_l_summary.txt.gz 3.1 Kb (ftp)(http) TXT
GSE84705_bulk_expression_count.txt.gz 145.8 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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