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| Status |
Public on Sep 05, 2013 |
| Title |
Integral nuclear pore proteins bind to Pol III genes and are required for Pol III transcript processing in C. elegans [seq] |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
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-ß 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.
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| Overall design |
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.
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| Contributor(s) |
Ikegami K, Lieb JD |
| Citation(s) |
24011592 |
| |
| Submission date |
Dec 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Kohta Ikegami |
| E-mail(s) |
kohta.ikegami@cchmc.org
|
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
Division of Molecular Cardiovascular Biology
|
| Lab |
Ikegami Lab
|
| Street address |
240 Albert Sabin Way, Cincinnati, OH 45229
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
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| Platforms (2) |
| GPL9269 |
Illumina Genome Analyzer II (Caenorhabditis elegans) |
| GPL13657 |
Illumina HiSeq 2000 (Caenorhabditis elegans) |
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| Samples (21)
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| GSM1048401 |
AMA-1 ChIP-seq in N2 mixed-stage embryos (BC085) |
| GSM1048402 |
AMA-1 ChIP-seq in N2 mixed-stage embryos (BC002) |
| GSM1048409 |
IMB-1 ChIP-seq in N2 mixed-stage embryos (BC166) |
| GSM1048410 |
IMB-1 ChIP-seq in N2 mixed-stage embryos (KI026) |
| GSM1048411 |
Input-seq in N2 mixed-stage embryos (BC071) |
| GSM1048412 |
Input-seq in N2 mixed-stage embryos (BC089) |
| GSM1048413 |
NPP-13 ChIP-seq in N2 mixed-stage embryos (KI024) |
| GSM1048414 |
NPP-3 ChIP-seq in N2 mixed-stage embryos (BC075) |
| GSM1048415 |
NPP-3 ChIP-seq in N2 mixed-stage embryos (BC076) |
| GSM1048416 |
NPP-3 ChIP-seq in N2 mixed-stage embryos (BC164) |
| GSM1048417 |
Pol III RPC-1 ChIP-seq in N2 mixed-stage embryos treated with empty vector (BC177) |
| GSM1048418 |
Pol III RPC-1 ChIP-seq in N2 mixed-stage embryos treated with NPP-13 RNAi (BC178) |
| GSM1048419 |
Pol III RPC-1 ChIP-seq in N2 mixed-stage embryos treated with empty vector (BC179) |
| GSM1048420 |
Pol III RPC-1 ChIP-seq in N2 mixed-stage embryos treated with NPP-13 RNAi (BC180) |
| GSM1048421 |
TBP-1 ChIP-seq in N2 mixed-stage embryos (BC057) |
| GSM1048422 |
TBP-1 ChIP-seq in N2 mixed-stage embryos treated with empty vector (BC257) |
| GSM1048423 |
TBP-1 ChIP-seq in N2 mixed-stage embryos treated with NPP-13 RNAi (BC258) |
| GSM1048424 |
TBP-1 ChIP-seq in N2 mixed-stage embryos (FW002) |
| GSM1048425 |
RNA-seq in N2 mixed-stage embryos treated with empty vector (BC183) |
| GSM1048426 |
RNA-seq in N2 mixed-stage embryos treated with NPP-13 RNAi (BC184) |
| GSM1048427 |
RNA-seq in N2 mixed-stage embryos treated with IMB-1 RNAi (BC185) |
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| This SubSeries is part of SuperSeries: |
| GSE42741 |
Chromatin Immunoprecipitation of Nuclear Pore Proteins in C. elegans |
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| Relations |
| BioProject |
PRJNA182987 |
| SRA |
SRP017438 |
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