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Series GSE40984 Query DataSets for GSE40984
Status Public on Oct 18, 2012
Title Non-coding transcription within the Igh distal VH region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells
Organism Mus musculus
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Non-coding sense and antisense germline transcription within the immunoglobulin heavy chain locus precedes V(D)J recombination and has been proposed to be associated with Igh locus accessibility, although its precise role remains elusive. However, no global analysis of germline transcription throughout the Igh locus has been done. Therefore, we performed directional RNAseq, demonstrating the locations and extent of both sense and antisense transcription throughout the Igh locus. Surprisingly, the majority of antisense transcripts are localized around two PAIR elements in the distal IghV region. Importantly, long-distance loops measured by 3C are observed between these two active PAIR promoters and Eμ, the start site of Iμ germline transcription, in a lineage- and stage-specific manner, even though this antisense transcription is Eμ-independent. YY1-/- pro-B cells are greatly impaired in distal VH gene rearrangement and Igh locus compaction, and we demonstrate that YY1 deficiency greatly reduces antisense transcription and PAIR-Eμ interactions. ChIP-seq shows high level YY1 binding only at Eμ, but low levels near some antisense promoters. PAIR-Eμ interactions are not disrupted by DRB, which blocks transcription elongation without disrupting transcription factories once they are established, but the looping is reduced after heat shock treatment, which disrupts transcription factories. We propose that transcription-mediated interactions, most likely at transcription factories, initially compact the Igh locus, bringing distal VH genes close to the DJH rearrangement, which is adjacent to Eμ. Therefore, we hypothesize that one key role of non-coding germline transcription is to facilitate locus compaction, allowing distal VH genes to undergo efficient rearrangement.
Overall design In order to determine the amount and location of sense and antisense non-coding RNA in the Igh locus, we prepared total RNA from CD19+ RAG1-/- pro-B cells. Samples were either pre-enriched in custom Agilent arrays, or directly sequenced. Data from one sample for each condition is included as reflected in the publication.
Contributor(s) Verma-Gaur J, Schaffer L, Head SR, Feeney AJ, Schork NJ, Torkamani A
Citation(s) 23027941
Submission date Sep 19, 2012
Last update date May 15, 2019
Contact name Lana Schaffer
Organization name TSRI
Department DNA Array Core
Lab Head
Street address 10550 North torrey Pines Road
City San Diego
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (2)
GSM1006370 Rag1-/- proB
GSM1006371 Rag1-/- proB_IGH_Enriched
Affiliated with GSE40822
BioProject PRJNA175487
SRA SRP015812

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Supplementary file Size Download File type/resource
GSE40984_RAW.tar 1.6 Mb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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