PXD029313 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | rs143348853 in vitro DNA pulldown |
Description | Non-coding variants coordinate transcription factor (TF) binding and chromatin mark enrichment changes over regions spanning >100 kb. We named these molecularly coordinated regions “variable chromatin modules” (VCMs), providing a conceptual framework of how regulatory variation might shape complex traits. To better understand the molecular mechanisms underlying VCM formation, here, we mechanistically dissect an uncharacterized VCM-modulating non-coding variant that is associated with reduced chronic lymphocytic leukemia (CLL) predisposition and disease progression. This common, germline variant constitutes a 5-bp indel that controls the activity of an AXIN2 gene-linked VCM by creating a MEF2 binding site, which, upon binding, activates a super-enhancer-like regulatory element. This triggers a big change in TF binding activity and chromatin state at an enhancer cluster spanning >150 kb, coinciding with long-range chromatin compaction and AXIN2 up-regulation. Our results support a model in which the indel acts as an AXIN2 VCM-activating TF nucleation event, which modulates CLL pathology. |
HostingRepository | PRIDE |
AnnounceDate | 2022-04-21 |
AnnouncementXML | Submission_2022-04-21_01:30:52.872.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Gerard Llimos Aubach |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | Orbitrap Fusion Lumos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-10-25 00:03:22 | ID requested | |
⏵ 1 | 2022-04-21 01:30:53 | announced | |
Publication List
Llimos G, Gardeux V, Koch U, Kribelbauer JF, Hafner A, Alpern D, Pezoldt J, Litovchenko M, Russeil J, Dainese R, Moia R, Mahmoud AM, Rossi D, Gaidano G, Plass C, Lutsik P, Gerhauser C, Waszak SM, Boettiger A, Radtke F, Deplancke B, A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation. Nat Commun, 13(1):2042(2022) [pubmed] |
Keyword List
submitter keyword: rs143348853, DNA pulldown, genetic variant, indel |
Contact List
Bart Deplancke |
contact affiliation | Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland |
contact email | bart.deplancke@epfl.ch |
lab head | |
Gerard Llimos Aubach |
contact affiliation | EPFL |
contact email | gerardllimosaubach@gmail.com |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD029313
- Label: PRIDE project
- Name: rs143348853 in vitro DNA pulldown