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Enhancer bound proteome of intronic Ig Emu enhancer with E1 box mutation 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 enhancer, which governs the rearrangement and expression of the Ig mu heavy chain allele. 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 E1 box of the core enhancer region was mutated (E1mt).The E1mt abrogates binding of proteins recognizing the E1 box (e.g. YY1). Max LFQ quantitative proteomics was employed in an approach incubating wild-type and control DNA with (unlabeled) nuclear extracts.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): B Cell

DISEASE(S): Lymphoma

SUBMITTER: Gerhard Mittler

LAB HEAD: Gerhard Mittler

PROVIDER: PXD045704 | Pride | 2024-10-25

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	LFQ_EnhancerMAR_E1mut_ForHeatmap.txt	Txt
	LFQ_MAR_E1mut_Impute_2SampleTest_pValues.txt	Txt
	MusMusculus_30112021.fasta	Fasta
	Rep01_00001616___A_EnhancerMAR_WT_gb01_01.raw	Raw
	Rep01_00001616___A_EnhancerMAR_WT_gb01_02.raw	Raw

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Project 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 enhancer, which governs the rearrangement and expression of the Ig mu heavy chain allele. 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 5’ and 3’ MAR (matrix attachment region) sequences were deleted (and substituted with the murine Ig mu locus DNA flanking the MARs).The Delta MAR mutant abrogates binding of proteins recognizing MAR elements. SILAC quantitative proteomics was employed in a label swap approach incubating wild-type and control DNA with labeled and non-labled protein extracts, respectively.

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