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| Status |
Public on May 01, 2023 |
| Title |
Enhancers of the PAIR4 regulatory module promote distal VH gene recombination at the Igh locus |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
While extended loop extrusion across the entire Igh locus controls VH-DJH recombination, local regulatory sequences, such as the PAIR elements, may also activate VH gene recombination in pro-B-cells. Here we show that PAIR-associated VH8 genes contain a conserved putative regulatory element (V8E) in their downstream sequences. To investigate the function of PAIR4 and its V8.7E, we deleted all 14 PAIRs in the Igh 5’-region, which reduced distal VH gene recombination over a 100-kb distance on either side of the 890-kb deletion. Reconstitution by insertion of PAIR4-V8.7E strongly activated distal VH gene recombination. PAIR4 alone resulted in lower induction of recombination, indicating that PAIR4 and V8.7E function as one regulatory unit. The pro-B-cell-specific activity of PAIR4 depends on CTCF, as mutation of its CTCF-binding site led to sustained PAIR4 activity in pre-B and immature B-cells and in PAIR4 activation in T-cells. Notably, insertion of V8.8E was sufficient to activate VH gene recombination. Hence, enhancers of the PAIR4-V8.7E module and V8.8E element activate distal VH gene recombination and thus contribute to the diversification of the BCR repertoire in addition to loop extrusion.
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| Overall design |
VDJ-Seq: Nine experimental conditions, with three biological replicates each, associated with control samples (Igh(+/+)). RNA-Seq: two control (Igh(_delta_890/+) and two experimental (Igh(P4V/P4V)) samples. total RNA-Seq: two control samples. ChIP-Seq: Four control samples, single replcates.
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| Contributor(s) |
Hill L, Jaritz M, Schindler K, Tagoh H, Kostanova-Poliakova D, Sun Q, Schwickert TA, Leeb M, Skarnes WC, Busslinger M |
| Citation(s) |
37337907 |
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| Submission date |
Oct 05, 2022 |
| Last update date |
Jul 31, 2023 |
| Contact name |
Meinrad Busslinger |
| E-mail(s) |
[email protected]
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| Organization name |
IMP
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| Lab |
Busslinger
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| Street address |
Campus-Vienna-Biocenter 1
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| City |
Vienna |
| ZIP/Postal code |
A-1030 |
| Country |
Austria |
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| Platforms (5)
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| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL16417 |
Illumina MiSeq (Mus musculus) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
| GPL30172 |
NextSeq 2000 (Mus musculus) |
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| Samples (59)
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| Relations |
| BioProject |
PRJNA887428 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE214869_RAW.tar |
1.6 Gb |
(http)(custom) |
TAR (of BW, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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