Definition of RNA Polymerase II CoTC Terminator Elements in the Human Genome

Takayuki Nojima,Martin Dienstbier,Shona Murphy,Nicholas J Proudfoot,Michael J Dye

doi:10.1016/j.celrep.2013.03.012

Abstract

SummaryMammalian RNA polymerase II (Pol II) transcription termination is an essential step in protein-coding gene expression that is mediated by pre-mRNA processing activities and DNA-encoded terminator elements. Although much is known about the role of pre-mRNA processing in termination, our understanding of the characteristics and generality of terminator elements is limited. Whereas promoter databases list up to 40,000 known and potential Pol II promoter sequences, fewer than ten Pol II terminator sequences have been described. Using our knowledge of the human β-globin terminator mechanism, we have developed a selection strategy for mapping mammalian Pol II terminator elements. We report the identification of 78 cotranscriptional cleavage (CoTC)-type terminator elements at endogenous gene loci. The results of this analysis pave the way for the full understanding of Pol II termination pathways and their roles in gene expression.

Highlights

The transcription cycle consists of three stages
RNA degradation initiating at cotranscriptional cleavage (CoTC) sites leads to release of polymerase II (Pol II) and associated unprocessed pre-mRNA, from the DNA template (West et al, 2008)
CLIP-seq-Based CoTC Terminator Mapping Strategy Detailed transcriptional analysis of the human b-globin gene has shown that CoTC of b-globin 30 flanking region transcripts leads to release of Pol II and associated pre-mRNA, from the chromatin template prior to cleavage/polyadenylation at the poly(A) site

Summary

Introduction

The transcription cycle consists of three stages. Initiation, where RNA polymerase engages with the DNA template, followed by elongation where it translocates along the DNA template synthesizing the RNA copy of the gene and termination, where polymerase disengages from the DNA template. Pre-mRNA cleavage at the poly(A) site, mediated by the 30 end processing complex (Shi et al, 2009), generates two RNA products; a 50 cleavage product that is stabilized by polyadenylation as it is processed into mRNA and a 30 cleavage product that is subject to rapid degradation by the 50-30 exonuclease Xrn2 Such Xrn2-mediated transcript degradation has been shown to have a role in Pol II termination (West et al, 2004). RNA degradation initiating at cotranscriptional cleavage (CoTC) sites leads to release of Pol II and associated unprocessed pre-mRNA, from the DNA template (West et al, 2008) This distinguishing feature of CoTC-mediated termination is supported by electron microscopic studies in Drosophila that show that release of premRNA from transcription sites prior to 30 end processing is a common occurrence (Osheim et al, 2002)

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Discussion

Conclusion