Close association of RNA polymerase II and many transcription factors with Pol III genes.
Transcription of the eukaryotic genomes is carried out by three distinct RNA polymerases I, II, and III, whereby each polymerase is thought to independently transcribe a distinct set of genes. To investigate a possible relationship of RNA polymerases II and III, we mapped their in vivo binding sites throughout the human genome by using ChIP-Seq in two different cell lines, GM12878 and K562 cells. Pol III was found to bind near many known genes as well as several previously unidentified target genes. RNA-Seq studies indicate that a majority of the bound genes are expressed, although a subset are not suggestive of stalling by RNA polymerase III. Pol II was found to bind near many known Pol III genes, including tRNA, U6, HVG, hY, 7SK and previously unidentified Pol III target genes. Similarly, in vivo binding studies also reveal that a number of transcription factors normally associated with Pol II transcription, including c-Fos, c-Jun and c-Myc, also tightly associate with most Pol III-transcribed genes. Inhibition of Pol II activity using alpha-amanitin reduced expression of a number of Pol III genes (e.g., U6, hY, HVG), suggesting that Pol II plays an important role in regulating their transcription. These results indicate that, contrary to previous expectations, polymerases can often work with one another to globally coordinate gene expression.
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.
Debasish
D
Raha
Zhong
Z
Wang
Zarmik
Z
Moqtaderi
Linfeng
L
Wu
Guoneng
G
Zhong
Mark
M
Gerstein
Kevin
K
Struhl
Michael
M
Snyder
D053959:Alpha-Amanitin / Q000494:pharmacology; D001665:Binding Sites / Q000235:genetics; D004258:DNA Polymerase III / Q000378:metabolism*; D005786:Gene Expression Regulation; D015894:Genome, Human; D055106:Genome-Wide Association Study; D006801:Humans; D019384:Nucleic Acid Synthesis Inhibitors / Q000494:pharmacology; D011544:Pseudogenes; D012319:RNA Polymerase II / Q000037:antagonists & inhibitors / Q000378:metabolism*; D012343:RNA, Transfer / Q000235:genetics; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic
D053959:Alpha-Amanitin; D019384:Nucleic Acid Synthesis Inhibitors; D014157:Transcription Factors; D012343:RNA, Transfer; D012319:RNA Polymerase II; D004258:DNA Polymerase III