Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

40 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq for monitoring expression changes in absence of chromatin anchoring

ABSTRACT: RNA-seq for monitoring expression levels in mutants that do not anchor chromatin at the nuclear periphery. RNA-seq of depleted rRNA samples of early embryo extracts for three different genotypes: wild-type, cec-4_delta and met-2 set-25_delta_delta, in two independent biological replicas

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Dimos Gaidatzis

PROVIDER: E-GEOD-74067 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Perinuclear Anchoring of H3K9-Methylated Chromatin Stabilizes Induced Cell Fate in C. elegans Embryos.

Gonzalez-Sandoval Adriana A Towbin Benjamin D BD Kalck Veronique V Cabianca Daphne S DS Gaidatzis Dimos D Hauer Michael H MH Geng Liqing L Wang Li L Yang Teddy T Wang Xinghao X Zhao Kehao K Gasser Susan M SM

Cell 20151119 6

Interphase chromatin is organized in distinct nuclear sub-compartments, reflecting its degree of compaction and transcriptional status. In Caenorhabditis elegans embryos, H3K9 methylation is necessary to silence and to anchor repeat-rich heterochromatin at the nuclear periphery. In a screen for perinuclear anchors of heterochromatin, we identified a previously uncharacterized C. elegans chromodomain protein, CEC-4. CEC-4 binds preferentially mono-, di-, or tri-methylated H3K9 and localizes at th ...[more]

PMID: 26607792

Similar Datasets

Defining soma-specific/enriched and germline-specific/enriched transcripts

Project description:To define what genes are predominantly or specifically expressed in either soma or germline in C. elegans adults, total RNA was extracted from germline-less glp-4 mutant animals or from dissected gonads, respectively. Total RNA sequencing was peformed in duplicates. Four samples in total.

2015-01-08 | E-GEOD-62857 | biostudies-arrayexpress

Developmental Timecourses total-RNA sequencing [Ribosome repleted total RNA]

Project description:We report the presence of extensive, transcriptionally controlled oscillations in the C. elegans, developmental transcriptome. Furthermore, using ribosome profiling, we show that these oscillating transcripts are actively translated. Examination of two timecourses that were collected over C. elegans development and analyzed by RNA-seq of "RiboMinus" libraries

2014-03-01 | E-GEOD-52864 | biostudies-arrayexpress

Functional characterization of C. elegans Y-box binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes (RNA-Seq)

Project description:We present a basic characterization of the function of Y-box binding proteins in C. elegans. Besides playing an important role for fertility in the germline (all four CEY proteins), we found that the presence of CEY-1 and CEY-4 is essential for the assembly of larger polysomes in the soma. We therefore performed ribosome-profiling in combination with total RNA sequencing in wild type and cey-1,-4 double mutant animals to globally compare mRNA levels and their translation status. Total RNA sequencing was peformed on RNA extacted from wild type and cey-1,-4 mutant animals in duplicates. Four samples in total.

2015-01-08 | E-GEOD-62858 | biostudies-arrayexpress

Functional characterization of C. elegans Y-box binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes (RIP-Seq)

Project description:We present a basic characterization of the function of Y-box binding proteins (YBPs) in C. elegans. YBPs in other organisms are known RNA-binding proteins. Our global analysis of associated mRNAs supports a role of YBPs as general mRNA binders in C.elegans. FLAG IPs were performed on transgenic animals expressing FLAG-tagged versions of either CEY-1, CEY-2, or CEY-4. MYC IPs served as controls. All IPs were performed in duplicates. 12 samples in total.

2015-01-08 | E-GEOD-62856 | biostudies-arrayexpress

Extensive oscillatory gene expression during C. elegans larval development [RNA-seq for polyA enriched mRNAs]

Project description:We report the presence of extensive, transcriptionally controlled oscillations in the C. elegans, developmental transcriptome. Furthermore, using ribosome profiling, we show that these oscillating transcripts are actively translated. Examination of three timecourses that were collected over C. elegans development and analyzed by RNA-seq of mRNA libraries

2014-03-01 | E-GEOD-52861 | biostudies-arrayexpress

Functional characterization of C. elegans Y-box binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes (ribosome)

Project description:We present a basic characterization of the function of Y-box binding proteins in C. elegans. Besides playing an important role for fertility in the germline (all four CEY proteins), we found that the presence of CEY-1 and CEY-4 is essential for the assembly of larger polysomes in the soma. We therefore performed ribosome-profiling in combination with total RNA sequencing in wild type and cey-1,-4 double mutant animals to globally compare mRNA levels and their translation status. Ribosome-profiling analysis was peformed on wild type and cey-1,-4 mutant animals in duplicates. Four samples in total.

2015-01-08 | E-GEOD-62859 | biostudies-arrayexpress

Extensive oscillatory gene expression during C. elegans larval development [Ribosome footprinting]

Project description:We report the presence of extensive, transcriptionally controlled oscillations in the C. elegans, developmental transcriptome. Furthermore, using ribosome profiling, we show that these oscillating transcripts are actively translated. Ribosome-profiling analysis of a timecourse that was collected over C. elegans development

2014-03-01 | E-GEOD-52905 | biostudies-arrayexpress

LEM-2 ChIP-seq to study chromatin anchoring

Project description:Chromatin Immunoprecipitation against the nuclear envelope protein LEM-2 to detect association to the nuclear periphery. LEM-2 ChIP was performed on early embryo fixed extracts for wild-type and two mutants that have altered position of a perinuclear chromatin reporter. LEM-2 ChIP on early embryo chromatin extracts of three different genotypes: wild-type, met-2 set-25_delta_delta and cec-4_delta, in two independent biological replicas

2015-12-11 | E-GEOD-74133 | biostudies-arrayexpress

Integral nuclear pore proteins bind to Pol III genes and are required for Pol III transcript processing in C. elegans [seq]

Project description:Nuclear pores associate with active protein-coding genes in yeast and have been implicated in transcriptional regulation. Here, we show that in addition to transcriptional regulation, key components of C. elegans nuclear pores are required for processing of a subset of small nucleolar RNAs (snoRNAs) and tRNAs transcribed by RNA Polymerase (Pol) III. Chromatin immunoprecipitation of NPP-13 and NPP-3, two integral nuclear pore components, and importin-M-CM-^_ IMB-1, provides strong evidence that this requirement is direct. All three proteins associate specifically with tRNA and snoRNA genes undergoing Pol III transcription. These pore components bind immediately downstream of the Pol III pre-initiation complex, but are not required for Pol III recruitment. Instead, NPP-13 is required for cleavage of tRNA and snoRNA precursors into mature RNAs, whereas Pol II transcript processing occurs normally. Our data suggest that integral nuclear pore proteins act to coordinate transcription and processing of Pol III transcripts in C. elegans. Genome-wide ChIP-seq and ChIP-chip were performed in mixed-stage C. elegans embryos for nuclear pore proteins NPP-13, NPP-3, IMB-1 and chromatin proteins Pol III (RPC-1), TBP-1, TFC-1 (SFC-1), TFC-4 (TAG-315), and Pol II (AMA-1). For RPC-1 and TBP-1 ChIP-seq, embryos depleted for NPP-13 were also used. Total RNAs from wild-type, NPP-13 RNAi, and IMB-1 RNAi embryos were analyzed by RNA-seq.

2013-09-05 | E-GEOD-42714 | biostudies-arrayexpress

Chromatin organization in NPP-13 knockdown C. elegans embryos [seq]

Project description:C. elegans nuclear pore protein NPP-13 associates with small RNA genes transcribed by RNA Polymerase III. To test if the nuclear pore-chromatin interactions play a role in large-scale chromatin organization, we determined nuclear membrane-genome interactions and RNA Polymerase II localization in C. elegans embryos depleted for NPP-13. Genome-wide ChIP-seq and ChIP-chip for nuclear membrane protein LEM-2, RNA Polymerase II (AMA-1) and H3K4me3 were performed in mixed-stage C. elegans embryos depleted for NPP-13. As a control, ChIP was also performed in wild-type embryos treated with empty vector.

2016-08-15 | E-GEOD-49903 | 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