Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Circadian cycling of genome-wide histone methylation

ABSTRACT: Daily (circadian) clocks are essential for regulating and coordinating physiology in mammals. Modulation of local chromatin structure has been shown for only a small number of genes, principally thought to be directly modulated by Clock-mediated histone acetylation. Here we show that genome-wide changes of active and suppressive histone marks control global chromatin architecture over the day and night. Examination of mouse liver tissue at 4 time-points around the clock in "free-running", continuous conditions (constant darkness, temperature and food available ad libitum).

ORGANISM(S): Mus musculus

SUBMITTER: Akhilesh Reddy

PROVIDER: E-GEOD-23550 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Histone methyltransferase MLL3 contributes to genome-scale circadian transcription.

Valekunja Utham K UK Edgar Rachel S RS Oklejewicz Malgorzata M van der Horst Gijsbertus T J GT O'Neill John S JS Tamanini Filippo F Turner Daniel J DJ Reddy Akhilesh B AB

Proceedings of the National Academy of Sciences of the United States of America 20130107 4

Daily cyclical expression of thousands of genes in tissues such as the liver is orchestrated by the molecular circadian clock, the disruption of which is implicated in metabolic disorders and cancer. Although we understand much about the circadian transcription factors that can switch gene expression on and off, it is still unclear how global changes in rhythmic transcription are controlled at the genomic level. Here, we demonstrate circadian modification of an activating histone mark at a signi ...[more]

PMID: 23297224

Similar Datasets

The histone methyltransferase MLL3 regulates genome-scale circadian transcription

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

2013-01-01 | E-GEOD-37396 | biostudies-arrayexpress

Mouse embryonic RNA-seq

Project description:The study was aimed at interrogating the early stages of blood cell development within the embryo. Blood develops from mesoderm, which is specified at gastrulation. We therefore sorted cells from mouse embryos between E6.5 and E7.75 to capture gastrulation and the emergence of mesoderm, followed by specificiation of the first mature blood cells.

2016-07-08 | E-MTAB-4079 | biostudies-arrayexpress

ChIP-on-chip with anti-RBPj antibody from embryonic AGM E11.5

Project description:Hematopoietic Stem Cells (HSC) are originated during embryonic development from endothelial-like cells located in the ventral side of the dorsal aorta around day E10-12 of murine development. This region is called AGM for Aorta/Gonad/Mesonephros refering to the tissues around the hemogenic aorta. Hematopoiesis depends on the Notch pathway and the identification of Notch-targets is important for the understanding of blood origin. Hematopoietic Stem Cells (HSCs) specification occurs in the embryonic aorta and requires Notch activation, however which are the elements regulated by Notch that control this process are mainly unknown. Here, we took a genome-wide approach to identify putative direct Notch targets by precipitating the chromatin that binds to the Notch partner RBPj in the Aorta-Gonad-Mesonephros (AGM) tissue from E11.5 mouse embryos. This assay revealed 701 gene promoter regions as candidates to be regulated by Notch in the AGM. Chromatin was obtained from a pool of 40 dissected AGMs at E11.5. Chromatin immunoprecipitation (ChIP) was performed as previously described (Aguilera et al, PNAS 2004) with minor modifications. In brief, cross-linked chromatin was sonicated for 10 minutes, medium-power, 0.5-interval; with a Bioruptor (Diagenode) and precipitated with anti-RBPJ (Chu and Bresnick, 2004). After crosslinkage reversal, DNA was used as a template for PCR or for array hybridization. Mouse promoter chip on chip microarray SET (Agilent) was used to identify RBPj targets. It covers 70,000 best identified gene regions with a-5.5 kb to + 2.5 kb range, and has on average 25 probes per gene with an average probe to probe distance of 200 bp. The ChIP-on-chip was performed with dye swaps and one IgG control was brought along. Enrichment analysis was done by comparing the precipitation normalized dye swap signal with input control signal.

2014-10-22 | E-GEOD-52094 | biostudies-arrayexpress

Daily cycling of genome-wide histone methylation

Project description:Daily (circadian) clocks are essential for regulating and coordinating physiology in mammals. Modulation of local chromatin structure has been shown for only a small number of genes, principally thought to be directly modulated by Clock-mediated histone acetylation. Here we show that genome-wide changes of active and suppressive histone marks control global chromatin architecture over the day and night. Examination of mouse liver tissue at 4 time-points around the clock in "free-running", continuous conditions (constant darkness, temperature and food available ad libitum).

2013-01-01 | E-GEOD-37393 | biostudies-arrayexpress

Transcription profiling of S. cerevisiae unfolding response

Project description:The accumulation of unfolded proteins in the lumen of the endoplasmic reticulum (ER) causes stress and induces the unfolded protein response (UPR) which is characterised in part by the transcriptional induction of genes involved in assisting protein folding. Translational responses to ER stress have been less well described and here we report on a genome-wide analysis of translational regulation in the response to the ER stress-inducing agent dithiothreitol (DTT) in Saccharomyces cerevisiae. Although the observed polysome profiles were similar under control and ER stress conditions microarray analysis identified transcipt-specific translational regulation. Genes with functions in ribosomal biogenesis and assembly were translationally repressed under ER stress. In contrast mRNAs for known UPR genes, including the UPR transcription factor HAC1, the ER-oxidoreductase ERO1 and the ER-associated protein degradation (ERAD) gene DER1 were enriched in polysomal fractions under ER stress conditions. In addition, we show that splicing of HAC1 mRNA is required for efficient ribosomal loading and that Gcn2p is required for normal HAC1 splicing, so shedding light on the role of this protein kinase in the UPR pathway. Experiment Overall Design: Polyribosomes were extracted from S. cerevisiae cells treated with 2 mM DTT or water (control), and fractionated according to ribosome loading. Following RNA purification from these fractions, for each sub-polysomal and polysomal RNA sample, fractions from three independent extracts per treatment (DTT/control) were pooled.

2008-06-11 | E-GEOD-10091 | biostudies-arrayexpress

Sequestration of a two-component response regulator by a riboswitch regulated non-coding RNA

Project description:Riboswitches are ligand-binding elements contained within the 5M-bM-^@M-^Y untranslated regions of bacterial transcripts, which generally regulate expression of downstream open reading frames. Here we show that in Listeria monocytogenes, a Vitamin B12-binding (B12) riboswitch controls expression of a non-coding regulatory RNA, Rli55. Rli55 in turn controls expression of the eut genes, which enable ethanolamine utilization and require B12 as a cofactor. Defects in ethanolamine utilization, or in its regulation by Rli55, significantly attenuate Listeria virulence in mice. Rli55 functions by sequestering the two-component response regulator, EutV via a EutV binding-site contained within the RNA. Thus Rli55 is a riboswitch-regulated member of the small group of regulatory RNAs that function by sequestering a protein and reveals a unique mechanism of signal integration in bacterial gene regulation. RNA-Seq and CLIP-Seq to investigate the sequestration of EutV by rli55

2014-08-22 | E-GEOD-60363 | biostudies-arrayexpress

Arginine methylation and ubiquitylation crosstalk controls DNA end-resection and homologous recombination repair

Project description:Cross-talk between distinct protein post-translational modifications is critical for an effective DNA damage response. Arginine methylation plays an important role in maintaining genome stability, however how this modification integrates with other enzymatic activities is largely unknown. Here, we identify the deubiquitylating enzyme USP11 as a previously uncharacterised PRMT1 substrate, and that methylation of USP11 promotes DNA end-resection and the repair of DNA double strand breaks by homologous recombination (HR). In addition, we show that PRMT1 is a ubiquitylated protein that it is targeted for deubiquitylation by USP11, and that USP11 regulates the ability of PRMT1 to bind to and methylate MRE11. Interestingly, USP11 methylation by PRMT1 is not required for other USP11 activities during HR, such as PALB2 deubiquitylation. Taken together, our findings reveal a specific role for USP11 during the early stages of DSB repair, which is mediated through its ability to regulate the activity of the PRMT1-MRE11 pathway.

2021-11-02 | PXD028324 | Pride

The effect of inhibition of receptor tyrosine kinase AXL on DNA damage response in ovarian cancer

Project description:AXL is a receptor tyrosine kinase that is often overexpressed in cancers. It contributes to pathophysiology in cancer progression and therapeutic resistance, making it an emerging therapeutic target. The first-in-class AXL inhibitor bemcentinib (R428/BGB324) has been granted fast track designation by the U.S. Food and Drug Administration (FDA) in STK11-mutated advanced metastatic non-small cell lung cancer and was also reported to show selective sensitivity towards ovarian cancers (OC) with a Mesenchymal molecular subtype. In this study, we further explored AXL’s role in mediating DNA damage responses by using OC as a disease model. AXL inhibition using R428 resulted in the increase of DNA damage with the concurrent upregulation of DNA damage response signalling molecules. Furthermore, AXL inhibition rendered cells more sensitive to the inhibition of ATR, a crucial mediator for replication stress. Combinatory use of AXL and ATR inhibitors showed additive effects in OC. Through SILAC co-immunoprecipitation mass spectrometry, we identified a novel binding partner of AXL, SAM68, whose loss in OC cells harboured phenotypes in DNA damage responses similar to AXL inhibition. In addition, AXL- and SAM68-deficiency or R428 treatment induced elevated levels of cholesterol and upregulated genes in the cholesterol biosynthesis pathway. There might be a novel protective role of cholesterol in shielding cancer cells against DNA damage induced by AXL inhibition or SMA68 deficiency.

2023-06-22 | PXD042572 | Pride

Mammalian NET-seq reveals genome-wide nascent transcription coupled to RNA processing

Project description:We have generated single-nucleotide resolution, nascent transcription profiles from HeLa cells by developing Native Elongation Transcript sequencing technology for mammalian chromatin (mNET-seq). Our extensive data sets provide a substantial resource to study mammalian nascent transcript profiles. We reveal unanticipated phosphorylation states for RNA polymerase II C-terminal domain (Pol II CTD) at both gene ends. We also observe that following 5’ splice site cleavage by the spliceosome, upstream exon transcripts are tethered to Pol II CTD phosphorylated on the serine 5 position (S5P) which is accumulated over downstream exons. We further show that depletion of termination factors substantially reduces Pol II pausing at gene ends leading to termination defects. Remarkably termination factors play an additional promoter role by restricting non-productive RNA synthesis and redistributing Pol II CTD S2P to promoters. These data demonstrate that CTD phosphorylation is more dynamic and variably distributed across mammalian transcription units than previously envisaged. To monitor nascent RNA within the mammalian Pol II complex, and its association with different CTD phosphorylation states, we employed mNET-seq methodology on HeLa cells, complemented with direct sequencing of chromatin-bound RNA (ChrRNA-seq). mNET-seq was preformed using the antibodies 8WG16, CMA602, CMA603 and CMA601, which are specific for unphosphorylated CTD, Ser2 phosphorylation, Ser5 phosphorylation and all CTD isoforms, respectively. In another experiment, to evaluate the effect of transcription termination factors in nascent RNA production by Pol II, mNET-seq and complemented with ChrRNA-seq was preformed on HeLa cells transfected with siRNA against PTBP1, CPSF73, CstF64+CstF64tau or Xrn2, and the gene profiles were compared with profiles from HeLa transfected with siRNA for Luciferase generated by the same protocol.

2015-04-23 | E-GEOD-60358 | biostudies-arrayexpress

Transcription profiling of wild type, waaG mutant and rfaH mutant Salmonella enterica serovar Enteritidis PT4 and serovar Typhimurium to investigate live-attenuated vacine candidates

Project description:Effect of mutation of rfaH on gene expression in Salmonella enterica serovar Enteritidis PT4 and Salmonella enterica serovar Typhimurium 4/74

2006-11-13 | E-MEXP-844 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data