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IP-MS analysis of the human INO80 complex composition and interactome

ABSTRACT: The project aimed to investigate the composition/interactome of the human INO80 complex. To this end, INO80B - a core INO80 complex subunit - was endogenously tagged with V5 epitope tag at its C terminus in MCF-7 cells, and co-immunoprecipitation followed by LC-MS/MS analysis was performed using anti-V5 Abs.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Andrey Tvardovskiy

LAB HEAD: Till Bartke

PROVIDER: PXD020712 | Pride | 2023-12-10

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	INO80B_V5_IP_1.raw	Raw
	INO80B_V5_IP_2.raw	Raw
	INO80B_V5_IP_3.raw	Raw
	INO80B_V5_IP_MS.mgf	Mgf
	WT_control_1.raw	Raw

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Publications

Decoding chromatin states by proteomic profiling of nucleosome readers.

Lukauskas Saulius S Tvardovskiy Andrey A Nguyen Nhuong V NV Stadler Mara M Faull Peter P Ravnsborg Tina T Özdemir Aygenli Bihter B Dornauer Scarlett S Flynn Helen H Lindeboom Rik G H RGH Barth Teresa K TK Brockers Kevin K Hauck Stefanie M SM Vermeulen Michiel M Snijders Ambrosius P AP Müller Christian L CL DiMaggio Peter A PA Jensen Ole N ON Schneider Robert R Bartke Till T

Nature 20240306 8004

DNA and histone modifications combine into characteristic patterns that demarcate functional regions of the genome<sup>1,2</sup>. While many 'readers' of individual modifications have been described<sup>3-5</sup>, how chromatin states comprising composite modification signatures, histone variants and internucleosomal linker DNA are interpreted is a major open question. Here we use a multidimensional proteomics strategy to systematically examine the interaction of around 2,000 nuclear proteins wi ...[more]

PMID: 38448585

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GRK2 influences the phosphorylation of PER proteins by LC-MS/MS

Project description:To test whether GRK2 influences the phosphorylation of PER proteins, we used mass spectrometry to identify residues in V5-tagged murine PER2 that may be differentially phosphorylated upon GRK2 overexpression in Neuro2A cells.

2015-07-22 | PXD002290 | Pride

Control of developmentally primed erythroid genes by combinatorial corepressor actions

Project description:How transcription factors (TFs) cooperate within large protein complexes to allow rapid modulation of gene expression during development is still largely unknown. Here we show that the key haematopoietic LIM-domain-binding protein-1 (LDB1) TF complex contains several activator and repressor components that together maintain an erythroid-specific gene expression programme primed for rapid activation until differentiation is induced. A combination of proteomics, functional genomics and in vivo studies presented here identifies known and novel co-repressors, most notably the ETO2 and IRF2BP2 proteins, involved in maintaining this primed state. The ETO2â??IRF2BP2 axis, interacting with the NCOR1/SMRT co-repressor complex, suppresses the expression of the vast majority of archetypical erythroid genes and pathways until its decommissioning at the onset of terminal erythroid differentiation. Our experiments demonstrate that multimeric regulatory complexes feature a dynamic interplay between activating and repressing components that determines lineage-specific gene expression and cellular differentiation. ChIP-Sequencing profiles of the IRF2BP2, GFI1B and LSD1 proteins were generated using mouse erythroleukemia (MEL) cells. RNA-seq experiments of Irf2bp2-WT, Irf2bp2-KD, Eto2-WT, Eto2-KD, Gfi1b-WT, Gfi1b-KD, Lsd1-WT, Lsd1-KD, MEL-non-induced, and MEL-induced stages were performed using standard RNA-seq protocol. Illumina HiSeq 2000 (standard TruSeq RNA sequencing protocol) was used for the sequencing.

2015-11-19 | E-GEOD-59859 | biostudies-arrayexpress

Identification of the BRD1 interactome and its impact on schizophrenia risk

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A functional genomics approach identifies the GATA factor SERPENT as a tissue-specific partner of CLOCK/CYCLE in the Drosophila circadian clock

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ChIP-Seq analysis of V5-tagged budding yeast Rif1

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2023-11-19 | E-MTAB-13452 | biostudies-arrayexpress

Genome-wide identification of MBD2 and MBD3 binding sites by ChIP-seq

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Quantitative ChIP-MS analysis of histone modifications present on H3K4me1- and H3K4me3-enriched mono-nucleosomes purified from crosslinked IMR-90 cells

Project description:The INO80 complex is a chromatin remodeler that regulates DNA replication, repair, and transcription. Although the INO80 complex plays a crucial role in various chromatin-associated processes, the mechanism of its recruitment to specific genomic loci is not well understood. Here we used a native ChIP-MS approach to quantitatively profile modifications present on nucleosomes co-purified with INO80 from MNAse-digested HeLa chromatin.

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Chip-chip from wt and ino80 mutant cells with Htz1

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