PXD045637-1

PXD045637 is an original dataset announced via ProteomeXchange.

Title	Enhancer bound proteome of intronic Ig Emu CORE enhancer with reverse DNA sequence polarity control bait
Description	The specificity of humoral immune responses depends on the functional rearrangement and expression of only one allele of immunoglobulin (Ig) genes. Here, we analyzed the comprehensive proteome of the murine Ig Emu CORE enhancer, which governs the rearrangement and expression of the Ig mu heavy chain allele. The Ig Emu consists of a CORE enhancer (harboring a multitude of transcription factor binding sites) and two 5’ and 3’ flanking MAR (matrix attachment region) elements. By mass spectrometry of proteins bound at wild type versus mutant Emu enhancers, we identified Emu-binding proteins and associated multi-protein complexes. We found that the MSL/MOF complex, a regulator of gene dosage compensation in flies, binds Emu via transcription factor YY1 and facilitates Emu-driven chromatin looping and promoter interaction. Msl2 gene knockout in primary pre-B cells or Mof heterozygosity in mice reduced mu gene expression. In this data set we compare proteins binding to the wild-type Emu versus a DNA bait control for which the Emu CORE sequence was switched to its reverse polarity sequence (the flanking MARs sequence are wild-type). The latter conserves the DNA GC content but virtually destroys all sequence-specific transcription factor binding sites. Of note, DNA repetitive sequences that can also be bound by DNA interacting proteins are kept functional by this control bait. SILAC quantitative proteomics was employed in a label swap approach incubating wild-type and control DNA with labeled and non-labled protein extracts, respectively.
HostingRepository	PRIDE
AnnounceDate	2024-10-25
AnnouncementXML	Submission_2024-10-25_02:10:53.528.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Gerhard Mittler
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-09-25 03:30:32	ID requested
⏵ 1	2024-10-25 02:10:53	announced

10.1016/J.CELREP.2024.114456;

submitter keyword: AP-MS, reverse ChIP, LC-MS, SILAC, DNA protein interaction,Immunoglobulin Ig Emu enhancer

Gerhard Mittler
contact affiliation	Max Planck Institute of Immunobiology and Epigenetics Proteomics Unit Stuebeweg 51 79108 Freiburg Germany
contact email	mittler@ie-freiburg.mpg.de
lab head
Gerhard Mittler
contact affiliation	Proteomics Unit, Max Planck Institute of Immunobiology and Epigenetics
contact email	mittler@ie-freiburg.mpg.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD045637
     1. Label: PRIDE project
     2. Name: Enhancer bound proteome of intronic Ig Emu CORE enhancer with reverse DNA sequence polarity control bait