Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

36 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

M1A marks translation initiation sites in human and mouse messenger RNA [Sequencing]

ABSTRACT: We developed a novel approach, m1A-seq, for high-resolution mapping of the transcriptome-wide m1A landscape, based on antibody-mediated capture followed by massively parallel sequencing Identification of m1A modified sequences in human, mouse and yeast cell lines

ORGANISM(S): Homo sapiens

SUBMITTER: Sharon Moshitch-Moshkovitz

PROVIDER: E-GEOD-70485 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA.

Dominissini Dan D Nachtergaele Sigrid S Moshitch-Moshkovitz Sharon S Peer Eyal E Kol Nitzan N Ben-Haim Moshe Shay MS Dai Qing Q Di Segni Ayelet A Salmon-Divon Mali M Clark Wesley C WC Zheng Guanqun G Pan Tao T Solomon Oz O Eyal Eran E Hershkovitz Vera V Han Dali D Doré Louis C LC Amariglio Ninette N Rechavi Gideon G He Chuan C

Nature 20160210 7591

Gene expression can be regulated post-transcriptionally through dynamic and reversible RNA modifications. A recent noteworthy example is N(6)-methyladenosine (m(6)A), which affects messenger RNA (mRNA) localization, stability, translation and splicing. Here we report on a new mRNA modification, N(1)-methyladenosine (m(1)A), that occurs on thousands of different gene transcripts in eukaryotic cells, from yeast to mammals, at an estimated average transcript stoichiometry of 20% in humans. Employin ...[more]

PMID: 26863196

Similar Datasets

Genome-wide identification of PIF3-binding sites and direct-target genes of PIF3 transcriptional regulation in skotomorphogenesis

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

2013-02-01 | E-GEOD-39217 | biostudies-arrayexpress

Synergistic Activation of Inflammatory Cytokine Genes by Priming of Regulatory DNA Elements for Increased Transcription in Response to TLR Signaling

Project description:Synergistic activation of inflammatory cytokine genes by IFN-gamma and TLR signaling is important for innate immunity and inflammatory disease pathogenesis, but underlying mechanisms are not known. By obtaining over three billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of human primary monocytes under IFN-gamma-priming and TLR stimulation. We found that IFN-gamma induced genome-wide sustained occupancy of STAT1, IRF-1 and associated histone acetylation at TSS-proximal and distal regulatory elements and provided a synergy mechanism whereby IFN-gamma creates a primed chromatin environment to augment TLR-induced gene transcription, which suggest therapeutic approaches that selectively target priming mechanisms. Examination and comparison of the changes in TF binding and histone modification in human primary monocytes under different conditions.

2013-09-20 | E-GEOD-43036 | biostudies-arrayexpress

MMSET alters EZH2 Binding in Myeloma Cells

Project description:We investigated EZH2 binding in the presence and absence of MMSET protein. MMSET overexpression in t(4;14)+ myeloma leads to global loss of H3K27 methylation and redistribution of EZH2 binding throughout the genome ChIP-seq for EZH2 in two cell types

2014-09-01 | E-GEOD-57632 | biostudies-arrayexpress

Orphan nuclear receptor TR4 uses non-equivalent binding sites to regulate gene targets from proximal and distal transcriptional regulatory elements during human definitive erythropoiesis [ChIP-seq]

Project description:In this study, we resolved the genome-wide binding of TR4 in differentiating human erythroid cells by performing chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq). We found that TR4 preferentially binds to DR1 elements in the promoters of its target genes, and that the majority of these genes encode proteins that participate in fundamental biological functions such as mRNA processing, translation, RNA splicing and primary metabolic process. Interestingly, we also found an increased occurrence of other repeat element motifs (such as DR4, IR1 and ER6) at TR4-bound distal sites that are located more than 10 Kbp away from the nearest gene. This raises the tantalizing possibility that TR4 may heterodimerize with unique partners, including other nuclear receptors such as RXR, thus allowing TR4 to elicit unique transcriptional responses when acting at proximal (promoter) and distal (enhancer and silencer) regulatory sites during human erythropoiesis. Examination of TR4 genome wild binding in human erythroid cells, which are harvested at day 8, 11 and 14 during in vitro differentiation. Two replicates were included for each differentiation stage.

2015-02-04 | E-GEOD-54759 | biostudies-arrayexpress

Androgen Receptor (AR) targets in a cell line from the mouse proximal caput epididymus

Project description:Sequence data represent a profile of AR network targets in proliferating and non-proliferating P17 cells without cross linking AR to DNA prior to purification. P17 cells were derived from the mouse epididymal cell line PC1 by genetic modification to express a tagged wild type mouse AR cDNA (N-TAP-mAR). N-TAP-mAR allows purification of multi-protein complexes and their genomic targets with FLAG antibody coupled magnetic beads under native conditions. comparison of AR targets in proliferating versus non-proliferating cells using the PC1 WT cell line (not expressing a tagged AR) as a negative control.

2015-06-11 | E-GEOD-38656 | biostudies-arrayexpress

Genome-wide maps of HIF1a binding sites in ccRCC cell line under hypoxia condition

Project description:We report the application of chromatin immunoprecipitation and next generation sequencing technology for HIF1a binding sites at genome wide level in a RCC (renal cell carcinoma) cell line under hypoxia conditions. We found HIF1a binding sites in Caki-2 cell line under hypoxia conditions. Especially, we found HIF1a bind to SPOP under hypoxia condition, which was further validated. Examination of HIF1a binding sites in Caki-2 cell line under hypoxia condition

2014-03-27 | E-GEOD-54327 | biostudies-arrayexpress

Genome-wide identification of PIF1-binding sites and direct-target genes of PIF1 transcriptional regulation in skotomorphogenesis

Project description:Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF1, 3, 4 and 5) are critically necessary to maintaining this developmental state, and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using combined ChIP-seq and RNA-seq analyses, we have identified genes that are direct targets of PIF1 transcriptional regulation, and we provide evidence that the quartet collectively regulate these genes by shared, direct binding to the target promoters in promoting skotomorphogenesis. Three biological replicates data of PIF1-binding sites were collected by comparing the parallel ChIP samples from Myc-epitope-tagged-PIF1 (P1M) overexpressing transgenic seedlings and the wild-type (WT) control.

2014-10-02 | E-GEOD-43283 | biostudies-arrayexpress

Genome-wide identification of PIF4-binding sites and direct-target genes of PIF4 transcriptional regulation in skotomorphogenesis

Project description:Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF4, 3, 4 and 5) are critically necessary to maintaining this developmental state, and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using combined ChIP-seq and RNA-seq analyses, we have identified genes that are direct targets of PIF4 transcriptional regulation, and we provide evidence that the quartet collectively regulate these genes by shared, direct binding to the target promoters in promoting skotomorphogenesis. Three biological replicates data of PIF4-binding sites were collected by comparing the parallel ChIP samples from Myc-epitope-tagged-PIF4 (P1M) overexpressing transgenic seedlings and the wild-type (WT) control.

2014-10-02 | E-GEOD-43284 | biostudies-arrayexpress

Genome-wide identification of PIF3-binding sites and direct-target genes of PIF3 transcriptional regulation in skotomorphogenesis [ChIP-Seq]

Project description:Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF1, 3, 4 and 5) are critically necessary to maintaining this developmental state, and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using combined ChIP-seq and RNA-seq analyses, we have identified genes that are direct targets of PIF3 transcriptional regulation, and we provide evidence that the quartet collectively regulate these genes by shared, direct binding to the target promoters in promoting skotomorphogenesis. Four biological replicates data of PIF3-binding sites were collected by comparing the parallel ChIP samples from transgenic seedlings overexpressing Myc-epitope-tagged PIF3 (35S:PIF3-5xMyc, P3M) in pif3-3 null mutant background and the wild-type (WT) control.

2013-02-01 | E-GEOD-39215 | biostudies-arrayexpress

RGA binding sites in Arabidopsis thaliana seedlings

Project description:DELLA proteins act as hubs that relay environmental information to the multiple transcriptional circuits that control growth and development through physical interaction with transcription factors from different families. We have analyzed the presence of one DELLA protein at the Arabidopsis genome by chromatin immunoprecipitation coupled to large-scale sequencing and we find that it binds at the promoters of multiple genes. Enrichment analysis shows a strong preference for cis elements recognized by specific transcription factor families. In particular, we demonstrate that DELLA proteins are recruited by type-B ARABIDOPSIS RESPONSE REGULATORS (ARR) to the promoters of cytokinin-regulated genes, where they act as transcriptional co-activators. The biological relevance of this mechanism is underpinned by the necessity of simultaneous presence of DELLAs and ARRs to restrict root meristem growth and to promote photomorphogenesis. Provided are 3 biological replicates analysing RGA binding sites in Arabidopsis seedlings. ChIP-seq was performed on plants expressing RGA-GFP under the native RGA promoter and on non-transgenic control plants as reference

2015-07-23 | E-GEOD-59187 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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