Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A conserved factor Dhp1/Rat1/Xrn2 triggers premature transcription termination and nucleates heterochromatin to promote gene silencing

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

ORGANISM(S): Schizosaccharomyces pombe

SUBMITTER: Shiv Grewal

PROVIDER: E-GEOD-74741 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Conserved factor Dhp1/Rat1/Xrn2 triggers premature transcription termination and nucleates heterochromatin to promote gene silencing.

Chalamcharla Venkata R VR Folco H Diego HD Dhakshnamoorthy Jothy J Grewal Shiv I S SI

Proceedings of the National Academy of Sciences of the United States of America 20151202 51

Cotranscriptional RNA processing and surveillance factors mediate heterochromatin formation in diverse eukaryotes. In fission yeast, RNAi machinery and RNA elimination factors including the Mtl1-Red1 core and the exosome are involved in facultative heterochromatin assembly; however, the exact mechanisms remain unclear. Here we show that RNA elimination factors cooperate with the conserved exoribonuclease Dhp1/Rat1/Xrn2, which couples pre-mRNA 3'-end processing to transcription termination, to pr ...[more]

PMID: 26631744

Similar Datasets

A conserved factor Dhp1/Rat1/Xrn2 triggers premature transcription termination and nucleates heterochromatin to promote gene silencing [ChIP-chip]

Project description:Occupancy profiling of lysine 9 dimethylated histone H3 in fission yeast. Occupancy profiling of Red1, Mtl1, and Mmi1 proteins in fission yeast. Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of lysine 9 dimethylated histone H3, Red1, Mtl1, and Mmi1 proteins from asynchronous culture of fission yeast.

2016-01-05 | E-GEOD-74740 | biostudies-arrayexpress

Taz1-Shelterin promotes facultative heterochromatin assembly at chromosome-internal sites containing late replication origins [Taz1]

Project description:Occupancy profiling of Shelterin components in fission yeast. Facultative heterochromatin regulates gene expression, but its assembly is poorly understood. Previously, we identified facultative heterochromatin islands in the fission yeast genome and found that RNA elimination machinery promotes island assembly at meiotic genes. Here, we report that Taz1, a component of the telomere protection complex Shelterin, is required to assemble heterochromatin islands at regions corresponding to late replication origins that are sites of double-strand break formation during meiosis. The loss of Taz1 and other Shelterin subunits, including Ccq1 that interacts with Clr4/Suv39h, abolishes heterochromatin at late origins and causes defective silencing of associated genes. Moreover, the late origin regulator Rif1 affects heterochromatin at Taz1-dependent islands and subtelomeric regions. We uncover a connection between heterochromatin and replication control, and show that heterochromatin factors affect timing of replication. These analyses implicate Shelterin in facultative heterochromatin assembly at late origins, which has important implications for the maintenance of genome stability and gene regulation. Whole cell extract DNA and DNA recovered from Taz1 or Rif1-immunoprecipitated chromatin of fission yeast were random-prime PCR amplified and labeled with Cy3 (whole cell extract DNA) or with Cy5 (IP DNA) and analyzed using custom 60mer Agilent array that tiles Schizosaccharomyces pombe genome in 300bp intervals alternately on both strands.

2016-06-09 | E-GEOD-78822 | biostudies-arrayexpress

Taz1-Shelterin promotes facultative heterochromatin assembly at chromosome-internal sites containing late replication origins

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

2016-06-09 | E-GEOD-78823 | biostudies-arrayexpress

Taz1-Shelterin promotes facultative heterochromatin assembly at chromosome-internal sites containing late replication origins [H3K9me2]

Project description:ChIP-chip analyses of lysine 9 dimethylated histone H3 in Shelterin mutants. Facultative heterochromatin regulates gene expression, but its assembly is poorly understood. Previously, we identified facultative heterochromatin islands in the fission yeast genome and found that RNA elimination machinery promotes island assembly at meiotic genes. Here, we report that Taz1, a component of the telomere protection complex Shelterin, is required to assemble heterochromatin islands at regions corresponding to late replication origins that are sites of double-strand break formation during meiosis. The loss of Taz1 and other Shelterin subunits, including Ccq1 that interacts with Clr4/Suv39h, abolishes heterochromatin at late origins and causes defective silencing of associated genes. Moreover, the late origin regulator Rif1 affects heterochromatin at Taz1-dependent islands and subtelomeric regions. We uncover a connection between heterochromatin and replication control, and show that heterochromatin factors affect timing of replication. These analyses implicate Shelterin in facultative heterochromatin assembly at late origins, which has important implications for the maintenance of genome stability and gene regulation. Whole cell extract DNA and DNA recovered from H3K9 dimethylated chromatin of fission yeast were random-prime PCR amplified and labeled with Cy3 (whole cell extract) or Cy5 (IP DNA) and analyzed using custom 60mer Agilent array that tiles Schizosaccharomyces pombe genome in 300bp intervals alternately on both strands.

2016-06-09 | E-GEOD-78820 | biostudies-arrayexpress

Expression profiling and ChIP-chip of Schizosaccharomyces pombe strains wildtype, erh1â??, and ccr4â??

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

2016-06-15 | E-GEOD-76114 | biostudies-arrayexpress

The fission yeast Schizosaccharomyces pombe: H3K9me2, Erh1-GFP and CFP-Mmi1 ChIP-chip

Project description:ChIP-chip analyses of H3K9me2 (in WT, erh1â??, mmi1â?? and ccr4â??), Erh1-GFP (in WT and mmi1â??) and CFP-Mmi1 (in WT) H3K9me2: WT vs erh1â??, WT vs mmi1â?? and WT vs ccr4â??; Erh1-GFP: WT vs mmi1â??; CFP-Mmi1 in WT, Biological replicates: 2

2016-06-15 | E-GEOD-76111 | biostudies-arrayexpress

Taz1-Shelterin promotes facultative heterochromatin assembly at chromosome-internal sites containing late replication origins [Rec12]

Project description:Occupancy profiling of Rec12 during fission yeast meiosis. Facultative heterochromatin regulates gene expression, but its assembly is poorly understood. Previously, we identified facultative heterochromatin islands in the fission yeast genome and found that RNA elimination machinery promotes island assembly at meiotic genes. Here, we report that Taz1, a component of the telomere protection complex Shelterin, is required to assemble heterochromatin islands at regions corresponding to late replication origins that are sites of double-strand break formation during meiosis. The loss of Taz1 and other Shelterin subunits, including Ccq1 that interacts with Clr4/Suv39h, abolishes heterochromatin at late origins and causes defective silencing of associated genes. Moreover, the late origin regulator Rif1 affects heterochromatin at Taz1-dependent islands and subtelomeric regions. We uncover a connection between heterochromatin and replication control, and show that heterochromatin factors affect timing of replication. These analyses implicate Shelterin in facultative heterochromatin assembly at late origins, which has important implications for the maintenance of genome stability and gene regulation. Whole cell extract DNA and DNA recovered by Rec12 ChIP from fission yeast undergoing synchronous meiosis were random-prime PCR amplified and labeled with Cy3 (whole cell extract) or Cy5 (IP DNA) and analyzed using custom 60mer Agilent array that tiles Schizosaccharomyces pombe genome in 300bp intervals alternately on both strands.

2016-06-09 | E-GEOD-78821 | biostudies-arrayexpress

A conserved factor Dhp1/Rat1/Xrn2 triggers premature transcription termination and nucleates heterochromatin to promote gene silencing [sRNA-seq]

Project description:Co-transcriptional RNA processing and surveillance factors mediate heterochromatin formation in fission yeast. In addition to RNAi, RNA elimination machinery including MTREC (Mtl1-Red1 core) and the exosome are involved in facultative heterochromatin assembly, however, the exact mechanisms remain unclear. Here we show that RNA elimination factors cooperate with the conserved exoribonuclease Dhp1/Rat1/Xrn2, which couples pre-mRNA 3â-end processing to transcription termination, to promote premature termination and facultative heterochromatin formation at meiotic genes. Dhp1 also affects termination of transcripts at genes that are targets of RNAi-mediated heterochromatin assembly. Moreover, Dhp1 facilitates constitutive heterochromatin formation and silencing at centromeric and mating-type loci. Remarkably, we find that Dhp1 interacts with the Clr4/Suv39h methyltransferase complex and acts directly to nucleate heterochromatin. Our results uncover a novel role for 3â-end processing and termination machinery in gene silencing through premature termination and suggest that non-canonical termination by Dhp1 and RNA elimination factors is linked to heterochromatin assembly. These findings have important implications for understanding mechanisms of gene silencing in higher eukaryotes. Sequencing and analysis of small RNA in two S. pombe mutants

2016-01-05 | E-GEOD-74739 | biostudies-arrayexpress

Msn2p occupancy dynamics in yeast BY4741 responding to 0.4mM H2O2 over time (0-60 min)

Project description:Numerous factors have been implicated in regulating gene expression changes, including changes to nucleosome occupancy. Here we followed dynamic changes to nucleosome occupancy, gene expression and DNA binding of the transcription factor Msn2p genome-wide in yeast cells responding to hydrogen peroxide. and reveal new relationships between regulators of stress-dependent gene expression in yeast. Msn2p occupancy was measured in response to 0.4mM H2O2 in the S288c derivative BY4741 with an integrated myc-tagged Msn2p. A single replicate of the time course was performed with time points at 0, 4, 12, 20, 40 and 60 minutes after treatment.

2012-06-17 | E-GEOD-30898 | biostudies-arrayexpress

Taz1-Shelterin promotes facultative heterochromatin assembly at chromosome-internal sites containing late replication origins [BrdU]

Project description:BrdU profiling of replication activity in hydroxyurea treated synchronous culture of fission yeast. Facultative heterochromatin regulates gene expression, but its assembly is poorly understood. Previously, we identified facultative heterochromatin islands in the fission yeast genome and found that RNA elimination machinery promotes island assembly at meiotic genes. Here, we report that Taz1, a component of the telomere protection complex Shelterin, is required to assemble heterochromatin islands at regions corresponding to late replication origins that are sites of double-strand break formation during meiosis. The loss of Taz1 and other Shelterin subunits, including Ccq1 that interacts with Clr4/Suv39h, abolishes heterochromatin at late origins and causes defective silencing of associated genes. Moreover, the late origin regulator Rif1 affects heterochromatin at Taz1-dependent islands and subtelomeric regions. We uncover a connection between heterochromatin and replication control, and show that heterochromatin factors affect timing of replication. These analyses implicate Shelterin in facultative heterochromatin assembly at late origins, which has important implications for the maintenance of genome stability and gene regulation. Cdc25-22 cells carrying thymidine kinase and human nucleoside transporter expression modules were arrested at the G2/M boundary. After release into the cell cycle in minimal medium supplemented with hydroxyurea and 5â-bromo-2â-deoxyuridine (BrdU) cells were collected at time corresponding to maximal septation index and fixed by treatment with sodium azide. BrdU labeled DNA was recovered by immunoprecipitation, amplified by random-primed PCR and after conjugation with Cy5 (IP) or Cy3 (input DNA) analyzed on Agilent 60mer array.

2016-06-09 | E-GEOD-78819 | 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