Dataset Information

Chromatin isolation for mass spectrometry

ABSTRACT: The histone acetyl-reader BRD4 is an important regulator of chromatin structure and transcription, yet factors modulating its activity have remained elusive. Here we describe two complementary screens for genetic and physical interactors of BRD4, which converge on the folate pathway enzyme MTHFD1. We show that a fraction of MTHFD1 resides in the nucleus, where it is recruited to distinct genomic loci by direct interaction with BRD4. Inhibition of either BRD4 or MTHFD1 results in similar changes in nuclear metabolite composition and gene expression, and pharmacologic inhibitors of the two pathways synergize to impair cancer cell viability in vitro and in vivo. Our finding that MTHFD1 and other metabolic enzymes are chromatin-associated suggests a direct role for nuclear metabolism in the control of gene expression. BRD4 is an important chromatin regulator with roles in gene regulation, DNA damage, cell proliferation and cancer progression1-4. The protein is recruited to distinct genomic loci by the interaction of its tandem bromodomains with acetylated lysines on histones and other nuclear proteins5. There, BRD4 acts as a transcriptional activator by P-TEFb-mediated stimulation of transcriptional elongation6. The activating function of BRD4 on key driver oncogenes like MYC have made this epigenetic enzyme an important therapeutic target in both BRD4 translocated and BRD4 wild-type cancers3,7-12, and at least seven bromodomain inhibitors have reached the clinical stage13. Genome-wide studies have identified the role of BRD4-induced epigenetic heterogeneity in cancer cell resistance14, and factors defining BRD4 inhibitor response15,16. However, despite its clinical importance and the broad role of BRD4 in chromatin organization, surprisingly little is known about factors that are directly required for BRD4 function. To systematically expand the list of known BRD4 interactors5 and to characterize proteins directly required for BRD4 function, we developed a strategy of two complementary screens for genetic and physical partners of BRD4. The two approaches converge on a single factor, methylenetetrahydrofolate dehydrogenase 1 (MTHFD1). Our description of a transcriptional role for this C-1-tetrahydrofolate synthase highlights a direct connection between nuclear folate metabolism and cancer regulation.

INSTRUMENT(S): Orbitrap Fusion Lumos, LTQ Orbitrap Velos, Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Chronic Myeloid Leukemia Cell

SUBMITTER: Peter Májek

LAB HEAD: Stefan Kubicek

PROVIDER: PXD013090 | Pride | 2019-04-04

REPOSITORIES: Pride

ACCESS DATA

Publications

MTHFD1 interaction with BRD4 links folate metabolism to transcriptional regulation.

Sdelci Sara S Rendeiro André F AF Rathert Philipp P You Wanhui W Lin Jung-Ming G JG Ringler Anna A Hofstätter Gerald G Moll Herwig P HP Gürtl Bettina B Farlik Matthias M Schick Sandra S Klepsch Freya F Oldach Matthew M Buphamalai Pisanu P Schischlik Fiorella F Májek Peter P Parapatics Katja K Schmidl Christian C Schuster Michael M Penz Thomas T Buckley Dennis L DL Hudecz Otto O Imre Richard R Wang Shuang-Yan SY Maric Hans Michael HM Kralovics Robert R Bennett Keiryn L KL Müller Andre C AC Mechtler Karl K Menche Jörg J Bradner James E JE Winter Georg E GE Klavins Kristaps K Casanova Emilio E Bock Christoph C Zuber Johannes J Kubicek Stefan S

Nature genetics 20190527 6

The histone acetyl reader bromodomain-containing protein 4 (BRD4) is an important regulator of chromatin structure and transcription, yet factors modulating its activity have remained elusive. Here we describe two complementary screens for genetic and physical interactors of BRD4, which converge on the folate pathway enzyme MTHFD1 (methylenetetrahydrofolate dehydrogenase, cyclohydrolase and formyltetrahydrofolate synthetase 1). We show that a fraction of MTHFD1 resides in the nucleus, where it i ...[more]

PMID: 31133746

Similar Datasets

Project description:This study was conducted to determine the impact of extreme temperatures, aiming at controlling microorganisms by cooking, on the physiology and the transcriptome of Escherichia coli. ABSTRACT: Because the genome of Escherichia coli K12 is well understood, this organism was used as a model to investigate physiological and molecular changes during cell adaptation and survival to cooking temperatures used in the food industry. Bacteria grown at 37Â°C to stationary phase in Brain Heart Infusion (BHI) broth, were heated at 58Â°C or 60Â°C to reach a process lethality value (F) of 2 and 3, or until an internal core temperature of 71Â°C was reached (control cooking temperature). Both growth recovery and cell membrane integrity were evaluated immediately after heating and a global transcription analysis was performed by using gene expression microarrays. Only cells heated at 58Â°C F = 2 were still able to grow on liquid or solid BHI after heat treatment. However, their transcriptome did not differ significantly compared to those of bacteria heated at 58Â°C F = 3 (P-FDR > 0.01) where no growth recovery was observed post treatment. Genome-wide transcriptomic data obtained at 71Â°C were distinct from the other treatments. Quantification of heat-shock genes expression by real-time PCR revealed that dnaK and groEL mRNA levels were significantly lower at 71Â°C than at 58Â°C and 60Â°C (P < 0.0001). Furthermore, despite of similar cell inactivation but growth on BHI media after heating, 132 and 8 genes were differentially expressed at 71Â°C when compared to 58Â°C and 60Â°C at F = 3 respectively (P-FDR < 0.01). Among them, genes like aroA, citE, glyS, oppB and asd, whose expression was up-regulated at 71Â°C, may be considered as good biomarkers to determine more accurately the efficiency of heat treatments. Bacteria were submitted to four different heat-treatments. Biological replicates: 5 Controls grown to an optimal temperature of 37Â°C (and used to prepare a common reference for each array hybridization), 5 Treatment 1 (58Â°C F = 2), 4 Treatment 2 (58Â°C F = 3), 4 Treatment 3 (60Â°C F = 3), 5 Treatment 4 (core temperature of 71Â°C). Treatment replicates were randomly hybridized on 3 microarray slides Agilent 8x15K (total of 24 array areas). Equal amounts of the labeled control cDNA pool and labeled cDNA from one of the heated groups were mixed and hybridized on each array.

Project description:Although majority of the genes linked to pediatric cataract exhibit lens fiber cell-enriched expression, our understanding of gene regulation in these cells is limited to function of just eight transcription factors and largely in the context of crystallins. Here, we identify small Maf transcription factors MafG and MafK as regulators of several non-crystallin human cataract genes in fiber cells and establish their significance to cataract. We applied a bioinformatics tool for cataract gene discovery iSyTE to identify MafG and its co-regulators in the lens, and generated various null-allelic combinations of MafG:MafK mouse mutants for phenotypic and molecular analysis. By age 4-months, MafG-/-:MafK+/- mutants exhibit lens defects that progressively develop into cataract. High-resolution phenotypic characterization of MafG-/-:MafK+/- lens reveals severe defects in fiber cells, while microarrays-based expression profiling identifies 97 differentially regulated genes (DRGs). Integrative analysis of MafG-/-:MafK+/- lens-DRGs with 1) binding-motifs and genomic targets of small Mafs and their regulatory partners, 2) iSyTE lens-expression data, and 3) interactions between DRGs in the String database, unravels a detailed small Maf regulatory network in the lens, several nodes of which are linked to human cataract. This analysis prioritizes 36 highly promising candidates from the original 97 DRGs. Significantly, 8/36 (22%) DRGs are associated with cataracts in human (GSTO1, MGST1, SC4MOL, UCHL1) or mouse (Aldh3a1, Crygf, Hspb1, Pcbd1), suggesting a multifactorial etiology that includes elevation of oxidative stress. These data identify MafG and MafK as new cataract-associated candidates and define their function in regulating largely non-crystallin genes linked to mouse and human cataract. Microarray comparision of lenses from mixed background (129Sv/J, C57BL/6J, and ICR) control (MafG+/-:MafK+/-; no-cataract) and compound (MafG-/-:MafK+/-; cataract) mouse mutants

Dataset Information

Chromatin isolation for mass spectrometry

Publications

MTHFD1 interaction with BRD4 links folate metabolism to transcriptional regulation.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure