Changes in elongation rate can also change the pattern of gene expression (Ip et al. 2011), which in turn could influence the synthesis and availability of elongation, termination, and processing proteins.
The variety of observed behaviors suggest that this collection of mutants will be a valuable resource for dissecting the mechanistic relationships between elongation rate, pausing, termination, and RNA processing events.
It is likely, therefore, that the two studies have located binding sites for different elongation, termination, or processing factors.
These localization patterns are related to the roles that the marks play in transcription: H3K4me3 regulates the efficiency of transcription initiation and early steps in transcription elongation, and H3K36me3 prevents the utilization of cryptic initiation sites in coding regions and controls aspects of transcription termination and processing [ 1- 4].
These Pol II catalytic activity mutants conferred various phenotypes both in vitro and in vivo, including altered TSS selection, RNA splicing, presumed termination or processing defects, and chromosome segregation defects (Kaplan et al. 2008; Kireeva et al. 2008; Kaplan et al. 2012; Larson et al. 2012; Braberg et al. 2013; Viktorovskaya et al. 2013).
We will also provide selected examples of how transcription termination and RNA 3′ end processing feed into the larger context of gene expression.
Gene expression program, rather than a simple assembly line to process mRNAs, is a complex network systematically coordinating many cellular pathways including transcription initiation-elongation-termination, RNA processing, transcription-coupled DNA repair, nuclear export of mRNAs, translation and RNA/protein degradation [1], [2], [3].
Conversely, inhibition of processing also blocks normal termination, further demonstrating the coupling of snRNA processing and transcription termination.
It is tightly integrated with transcription, particularly its termination, as well as other RNA processing events, i.e. capping and splicing.
Transcription termination occurs up to several hundred bases downstream of the 3′ end processing site even though both processes are intimately linked and mutation of many 3′ end processing factors results in transcription termination defects [48,76,93,98,102 105].
