Genome-wide studies of mRNA synthesis and degradation in eukaryotes

Abstract

Keywords:Transcription rate mRNA turnover RNA polymerase II Transcription elongation mRNA stabilityIn recent years, the use of genome-wide technologies has revolutionized the study of eukaryotic transcription producing results for thousands of genes at every step of mRNA life. The statistical analyses of the results for a single condition, different conditions, different transcription stages, or even between different techniques, is outlining a totally new landscape of the eukaryotic transcription process. Although most studies have been conducted in the yeast Saccharomyces cerevisiae as a model cell, others have also focused on higher eukaryotes, which can also be comparatively analyzed. The picture which emerges is that transcription is a more variable process than initially suspected, with large differences between genes at each stage of the process, from initiation to mRNA degradation, but with striking similarities for functionally related genes, indicating that all steps are coordinately regulated. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.

The Rpb4/7 Module of RNA Polymerase II Is Required for Carbon Catabolite Repressor Protein 4-Negative on TATA (Ccr4-Not) Complex to Promote Elongation

“…A prevailing model to explain the coordination between transcription and decay invokes the "imprinting" of RNAs with factors involved in transcription in the nucleus, which can then impart the regulation of decay in the cytoplasm (1,2). In particular, the imprinting of mRNAs with Rpb4/7 during the process of transcription was proposed (1).…”

“…transcription and translation). Furthermore, some pathways once thought to be antagonistic and distinct from each other, such as transcription and cytoplasmic mRNA decay, are now known to undergo crosstalk (1,2). However, the mechanism of how this occurs is unknown and is under intense investigation.…”

“…Ccr4 resides in a multisubunit complex called Ccr4-Not, which was first described as a transcriptional activator/ repressor (9,12). In addition to regulating the TATA-binding protein at the initiation stage, it directly associates with elongating RNA polymerase II (RNAPII) 2 and can reactivate arrested polymerase in vitro (13,14). Ccr4-Not has pivotal roles in both mRNA production and decay.…”

“…This buffering response may fine-tune gene expression and prepare the cell to adapt to changing environments. Buffering occurs during stress responses as well as during the course of yeast species evolution (2,5). The molecular players in gene buffering are largely unknown, but several studies have implicated candidates involved in transcription and decay (4, 6 -8).…”

RNA Polymerase II-Dependent Transcription in Fungi and Its Interplay with mRNA Decay

“…The comparison of the genomic patterns of run-on signals, reflecting elongationproficient RNA polymerases, with the genomic distribution of total RNA pol II measured by ChIP is an indirect way of detecting backtracked RNA polymerases (Perez-Ortin et al 2011). In general, a good correlation exists between the run-on and ChIP signals across the Saccharomyces genome, but some gene clusters exhibit lower run-on values than expected according to their ChIP signals (Pelechano et al 2009).…”