Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0

Genome-wide localization of the RNA polymerase III transcription machinery in human cells


ABSTRACT: To characterize the pol III transcriptome in actively growing human cells, we used MR90hTeIrt lung fibroblasts, which are immortal but not transformed, with an intact Rb pathway. After formaldehyde cross-linking, chromatin was extracted and submitted to immunoprecipitation. To identify actively transcribed RNAP-III transcription units, we used antibodies directed against the RPC4 subunit of RNAP-III. To identify promoter regions, we used antibodies directed against Bdp1, which is part of both Brf1-TFIIIB and Brf2-TFIIIB, and thus should mark all types of active RNAP-III promoters. Antibodies directed against Brf1 were used to mark type 1 and 2 promoters. For type 3 promoters, we engineered an IMR90hTert cell line expressing the SNAPc subunit SNAP45 tagged at its C-terminal end with the biotin acceptor domain as well as the biotin ligase BirA and performed M-bM-^@M-^\chromatin affinity purificationM-bM-^@M-^] (ChAP) with streptavidin beads. In each case, the precipitated material was then processed for deep sequencing. ChIP-enriched DNA or ChAP-enriched DNA from MR90hTeIrt cells were analyzed by Illumina high-throughput sequencing. This analysis includes ChIP data done with antibodies against : RPC4, Bfr1, Bdp1 and SNAP45. Two lanes were run for RPC4, Brf1 and SNAP45, and three for Bdp1. One lane was run with Input DNA for control.

ORGANISM(S): Homo sapiens

SUBMITTER: Viviane Praz 

PROVIDER: E-GEOD-18184 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

altmetric image

Publications

Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells.

Canella Donatella D   Praz Viviane V   Reina Jaime H JH   Cousin Pascal P   Hernandez Nouria N  

Genome research 20100422 6


Our view of the RNA polymerase III (Pol III) transcription machinery in mammalian cells arises mostly from studies of the RN5S (5S) gene, the Ad2 VAI gene, and the RNU6 (U6) gene, as paradigms for genes with type 1, 2, and 3 promoters. Recruitment of Pol III onto these genes requires prior binding of well-characterized transcription factors. Technical limitations in dealing with repeated genomic units, typically found at mammalian Pol III genes, have so far hampered genome-wide studies of the Po  ...[more]

Similar Datasets

2010-02-11 | GSE18184 | GEO
2015-06-10 | GSE42239 | GEO
2015-06-10 | E-GEOD-42239 | biostudies-arrayexpress
2011-09-16 | E-MTAB-767 | biostudies-arrayexpress
2019-01-02 | PXD003748 | Pride
2010-04-14 | GSE20609 | GEO
2010-04-14 | GSE20309 | GEO
2010-04-14 | E-GEOD-20609 | biostudies-arrayexpress
2013-07-17 | E-GEOD-44586 | biostudies-arrayexpress
2024-01-16 | PXD045036 | Pride