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Series GSE42714 Query DataSets for GSE42714
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
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.
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.
Contributor(s) Ikegami K, Lieb JD
Citation(s) 24011592
Submission date Dec 04, 2012
Last update date May 15, 2019
Contact name Kohta Ikegami
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
Platforms (2)
GPL9269 Illumina Genome Analyzer II (Caenorhabditis elegans)
GPL13657 Illumina HiSeq 2000 (Caenorhabditis elegans)
Samples (21)
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)
This SubSeries is part of SuperSeries:
GSE42741 Chromatin Immunoprecipitation of Nuclear Pore Proteins in C. elegans
BioProject PRJNA182987
SRA SRP017438

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Supplementary file Size Download File type/resource
GSE42714_RAW.tar 445.3 Mb (http)(custom) TAR (of BEDGRAPH, WIG)
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Raw data are available in SRA
Processed data provided as supplementary file

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