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CFAP43 interactome - A SF-TAP tagged CFAP43 fusion protein was expressed in HEK293T cells. Protein complexes were purified by tandem affinity purification to identify the CFAP43-associated protein complex.

ABSTRACT: A SF-TAP tagged CFAP43 fusion protein was expressed in HEK293T cells. Protein complexes were purified by tandem affinity purification to identify the CFAP43-associated protein complex.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Cell Culture, Fibroblast

DISEASE(S): Disease Free

SUBMITTER: Karsten Boldt

LAB HEAD: Karsten Boldt

PROVIDER: PXD009786 | Pride | 2019-04-11

REPOSITORIES: Pride

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FAM183b interactome - The evolutionary conserved FOXJ1 target gene Fam183b is essential for motile cilia in Xenopus but dispensable for ciliary function in mice

Project description:A SF-TAP tagged FAM183b fusion protein was expressed in HEK293T cells. Protein complexes were purified by tandem affinity purification to identify the FAM183b-associated protein complex.

2018-10-08 | PXD009409 | Pride

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2021-06-14 | PXD010108 | Pride

CRISPR/Cas9-mediated knockout and endogenous complex analysis of Cluap1/ IFT38

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2018-04-04 | PXD008343 | Pride

Coeevolution of a transcriptional network by compensatory trans and cis mutations

Project description:Transcriptional networks have been shown to evolve very rapidly, prompting questions as to how such changes arise and are tolerated. Recent comparisons of transcriptional networks across species have implicated variations in the cis-acting DNA sequences near genes as the main cause of divergence. What is less clear is how these changes interact with trans-acting changes occurring elsewhere in the genetic circuit. Here, we report the discovery of a system of compensatory trans and cis mutations in the yeast AP-1 transcriptional network that allows for conserved transcriptional regulation despite continued genetic change. We pinpoint a single species, the fungal pathogen Candida glabrata, in which a trans mutation has occurred very recently in a single AP-1 family member distinguishing it from its Saccharomyces ortholog. Comparison of chromatin immunoprecipitation profiles between Candida and Saccharomyces shows that, despite their different DNA binding domains, the AP-1 orthologs regulate a conserved block of genes. This conservation is enabled by concomitant changes in the cis-regulatory motifs upstream of each gene. Thus, both trans and cis mutations have perturbed the yeast AP-1 regulatory system in such a way as to compensate for one another. This demonstrates an example of “co-evolution” between a DNA-binding transcription factor and its cis-regulatory site, reminiscent of the co-evolution of protein binding partners. 3 Experiments were performed. Three replicates CgAp1-TAP was ChIPped under MMS treatment (GSM397447..GSM397449), two replicates each of ScYap1R79K and ScYap4K252R (GSM594724..GSM594727), were ChIPped under MMS treatment.

2010-09-17 | E-GEOD-15818 | biostudies-arrayexpress

ChIP-Seq of Myf5, MyoD, Snai1, HDAC1, HDAC2, E47 and empty vector controls in mouse skeletal myoblasts or myotubes

Project description:In skeletal myogenesis, the transcription factor MyoD activates distinct transcriptional programs in progenitors compared to terminally differentiated cells. Using ChIP-seq and gene expression analyses, we show that in primary myoblasts, Snail-HDAC1/2 repressive complex bind and exclude MyoD from its targets. Notably, Snail binds E-box motifs that are G/C-rich in their central dinucleotides, and such sites are almost exclusively associated with genes expressed during differentiation. By contrast, Snail does not bind the A/T-rich E-boxes associated with MyoD targets in myoblasts. Thus, Snai1-HDAC1/2 prevents MyoD occupancy on differentiation-specific regulatory elements and the change from Snail- to MyoD-binding often results in enhancer switching during differentiation. Furthermore, we show that a regulatory network involving Myogenic Regulatory Factors (MRFs), Snail/2, miR-30a and miR-206 acts as a molecular switch that controls entry into myogenic differentiation. Together, these results reveal a regulatory paradigm that directs distinct gene expression programs in progenitors versus terminally differentiated cells. Genome wide binding sites of various transcription factors and chromatin modifiers in muscle cells

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2012-07-04 | E-GEOD-24904 | biostudies-arrayexpress

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