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Interactions between basic helix-loop-helix transcription factors and nucleosomes

ABSTRACT: In solution crosslinking mass spectrometry of transcription factors in complex with nucleosomes

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Jan Seebacher

LAB HEAD: Nicolas Thoma

PROVIDER: PXD033181 | Pride | 2023-05-23

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	3165_annot_noM.fasta	Fasta
	3259_JS.fasta	Fasta
	E4_221129_JS_3259_CB_Por1_4mM_DSSO_S01_FAIMS_5ul.csv	Csv
	E4_221129_JS_3259_CB_Por1_4mM_DSSO_S01_FAIMS_5ul.fasta	Fasta
	E4_221129_JS_3259_CB_Por1_4mM_DSSO_S01_FAIMS_5ul.raw	Raw

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1 - 5 of 17

Publications

Cooperation between bHLH transcription factors and histones for DNA access.

Michael Alicia K AK Stoos Lisa L Crosby Priya P Eggers Nikolas N Nie Xinyu Y XY Makasheva Kristina K Minnich Martina M Healy Kelly L KL Weiss Joscha J Kempf Georg G Cavadini Simone S Kater Lukas L Seebacher Jan J Vecchia Luca L Chakraborty Deyasini D Isbel Luke L Grand Ralph S RS Andersch Florian F Fribourgh Jennifer L JL Schübeler Dirk D Zuber Johannes J Liu Andrew C AC Becker Peter B PB Fierz Beat B Partch Carrie L CL Menet Jerome S JS Thomä Nicolas H NH

Nature 20230705 7969

The basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members<sup>1</sup>. Here we investigate how chromatinized E-boxes are engaged by two structurally diverse bHLH proteins: the proto-oncogene MYC-MAX and the circadian transcription factor CLOCK-BMAL1 (refs. <sup>2,3</sup>). Both transcription factors bind to E-boxes preferentially near the nucleosomal entry-exit sites. Structural studies with engineered or native nuc ...[more]

PMID: 37407816

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Nucleosomes gate cofactor access to the transcription factor p53 P53_USP7TRAF_FL_NCP

Project description:In solution crosslinking mass spectrometry of transcription factor p53 with the members of the ubiquitin proteasome system (UPS) on chromatin.

2025-07-31 | PXD054141 | Pride

Nucleosomes gate cofactor access to the transcription factor p53 P53-pos8-NCP

Project description:In solution crosslinking mass spectrometry of transcription factor p53 with the members of the ubiquitin proteasome system (UPS) on chromatin.

2025-07-31 | PXD054140 | Pride

A basic helix-loop-helix transcription factors network mediates the brassinosteroid signal

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-03-05 | E-GEOD-51121 | biostudies-arrayexpress

An overview of the basic helix-loop-helix proteins.

Project description:The basic helix-loop-helix proteins are dimeric transcription factors that are found in almost all eukaryotes. In animals, they are important regulators of embryonic development, particularly in neurogenesis, myogenesis, heart development and hematopoiesis.

| S-EPMC463060 | biostudies-literature

Prg1 is regulated by the basic helix-loop-helix transcription factor Math2

Project description:Math2 (NEX-1/NeuroD6) is a member of the bHLH transcription factor family and is involved in neuronal differentiation and maturation. In the present study, we identified the genes targeted by Math2 using DNA microarrays and cultured rat cortical cells transfected with Math2. Of the genes regulated by Math2, we focused on plasticity-related gene 1 (Prg1). Prg1 expression induced by Math2 was confirmed in cultured rat cortical cells and PC12 cells analyzed by real-time quantitative PCR. Examining the promoter region of rat Prg1, we found four E-boxes designated -E1 to -E4 (CANNTG) which were recognized by the bHLH transcription factor. Using chromatin immunoprecipitation (ChIP) assays, we found that Math2 directly bound to the E-box(es) in the Prg1 promoter. The reporter assay of Prg1 showed that -E1 was critical for the regulation of the Prg1 expression by Math2. Then, the functional role of Math2 and Prg1 was investigated in PC12 cells. Seventy-two hours after transfection of Math2 or Prg1, neurite length and number was significantly induced in PC12 cells. Co-transfection with Prg1-siRNA completely inhibited Math2-mediated morphological changes. Our results suggest that Math2 directly regulates Prg1 expression and Math2-Prg1 cascade plays an important role in neurite outgrowth in PC12 cells.

2008-07-27 | GSE11829 | GEO

A basic helix-loop-helix transcription factors network mediates the brassinosteroid signal

Project description:This SuperSeries is composed of the SubSeries listed below.

2014-03-05 | GSE51121 | GEO

Histone interaction landscapes visualized by crosslinking mass spectrometry in intact cell nuclei

Project description:Cells organize their actions partly through tightly controlled protein-protein interactions – collectively termed the interactome. Here we use crosslinking mass spectrometry (XL-MS) to chart the interactome of intact human nuclei. We overall identified ~8700 crosslinks, of which 2/3 represent links connecting distinct proteins. From this data we constructed an overview of the nuclear interactome. We observed that the histone proteins on the nucleosomes expose well-defined crosslinking hot-spots. For several nucleosome-interacting proteins, such as USF3 and Ran GTPase, the data allowed us to build models of their binding mode to the nucleosome. For HMGN2 the data guided the construction of a refined model of the interaction with the nucleosome, based on complementary NMR, XL-MS and modeling. Excitingly, several isoform-specific interactors seem to exist for distinct histone H1 variants and the analysis of crosslinks carrying post-translational modifications allowed us to extract how specific modifications influence the nucleosome interactome. Overall, our data depository will support future structural and functional analysis of cell nuclei, including the nucleoprotein assemblies they harbor.

2018-07-23 | PXD007513 | Pride

Phylogenetic analysis of the human basic helix-loop-helix proteins.

Project description:BackgroundThe basic helix-loop-helix (bHLH) proteins are a large and complex multigene family of transcription factors with important roles in animal development, including that of fruitflies, nematodes and vertebrates. The identification of orthologous relationships among the bHLH genes from these widely divergent taxa allows reconstruction of the putative complement of bHLH genes present in the genome of their last common ancestor.ResultsWe identified 39 different bHLH genes in the worm Caenorhabditis elegans, 58 in the fly Drosophila melanogaster and 125 in human (Homo sapiens). We defined 44 orthologous families that include most of these bHLH genes. Of these, 43 include both human and fly and/or worm genes, indicating that genes from these families were already present in the last common ancestor of worm, fly and human. Only two families contain both yeast and animal genes, and no family contains both plant and animal bHLH genes. We suggest that the diversification of bHLH genes is directly linked to the acquisition of multicellularity, and that important diversification of the bHLH repertoire occurred independently in animals and plants.ConclusionsAs the last common ancestor of worm, fly and human is also that of all bilaterian animals, our analysis indicates that this ancient ancestor must have possessed at least 43 different types of bHLH, highlighting its genomic complexity.

| S-EPMC116727 | biostudies-literature

Helix-loop-helix/basic helix-loop-helix transcription factor network represses cell elongation in Arabidopsis through an apparent incoherent feed-forward loop.

Project description:Cell elongation is promoted by different environmental and hormonal signals, involving light, temperature, brassinosteroid (BR), and gibberellin, that inhibit the atypical basic helix-loop-helix (bHLH) transcription factor INCREASED LEAF INCLINATION1 BINDING bHLH1 (IBH1). Ectopic accumulation of IBH1 causes a severe dwarf phenotype, but the cell elongation suppression mechanism is still not well understood. Here, we identified a close homolog of IBH1, IBH1-LIKE1 (IBL1), that also antagonized BR responses and cell elongation. Genome-wide expression analyses showed that IBH1 and IBL1 act interdependently downstream of the BRASSINAZOLE-RESISTANT1 (BZR1)-PHYTOCHROME-INTERACTING FACTOR 4 (PIF4)-DELLA module. Although characterized as non-DNA binding, IBH1 repressed direct IBL1 transcription, and they both acted in tandem to suppress the expression of a common downstream helix-loop-helix (HLH)/bHLH network, thus forming an incoherent feed-forward loop. IBH1 and IBL1 together repressed the expression of PIF4, known to stimulate skotomorphogenesis synergistically with BZR1. Strikingly, PIF4 bound all direct and down-regulated HLH/bHLH targets of IBH1 and IBL1. Additional genome-wide comparisons suggested a model in which IBH1 antagonized PIF4 but not the PIF4-BZR1 dimer.

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In vitro crosslinking of PAX8 and PRDM3

Project description:MS crosslinking of PAX8 and PRDM3 using standard DSSO-based crosslinking

2021-03-09 | PXD021708 | Pride