Proteomics

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Enhancer bound proteome of intronic Ig Emu CORE enhancer with reverse DNA sequence polarity control bait


ABSTRACT: 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.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): B Cell

DISEASE(S): Lymphoma

SUBMITTER: Gerhard Mittler  

LAB HEAD: Gerhard Mittler

PROVIDER: PXD045637 | Pride | 2024-10-25

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
Rep01_EnhancerMARrev_FWD_01.raw Raw
Rep01_EnhancerMARrev_FWD_02.raw Raw
Rep01_EnhancerMARrev_FWD_03.raw Raw
Rep01_EnhancerMARrev_FWD_04.raw Raw
Rep01_EnhancerMARrev_FWD_05.raw Raw
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