PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of tranLink to Publisher's site
 
Transcription. 2016 May-Jun; 7(3): 63–68.
Published online 2016 March 30. doi:  10.1080/21541264.2016.1168507
PMCID: PMC4984687

Chromatin structure and pre-mRNA processing work together

ABSTRACT

Chromatin is the natural context for transcription elongation. However, the elongating RNA polymerase II (RNAPII) is forced to pause by the positioned nucleosomes present in gene bodies. Here, we briefly discuss the current results suggesting that those pauses could serve as a mechanism to coordinate transcription elongation with pre-mRNA processing. Further, histone post-translational modifications have been found to regulate the recruitment of factors involved in pre-mRNA processing. This view highlights the important regulatory role of the chromatin context in the whole process of the mature mRNA synthesis.

KEYWORDS: mRNA capping, nucleosome, promoter proximal pausing, splicing, transcription termination

Introduction

Pre-mRNA processing and transcription are two interconnected processes that comprise several events with a very precise regulation. To obtain a final product of messenger ribonucleoproteins (mRNP) ready to be exported to the cytoplasm, each step in the production has to be precisely executed and to be coordinated with the surrounding functions. Thus, defective transcription directly interferes with the processing of the produced pre-mRNA and, conversely, problems in pre-mRNA processing affect transcription (reviewed in1). Adding to the complexity, transcription elongation takes place in the context of chromatin. We discuss here recent results from different groups that indicate that one of the functions of chromatin is in fact to coordinate these processes.

In vitro and in vivo experiments demonstrate that a nucleosome inside of a gene presents an obstacle for transcription elongation and promotes pausing of RNAPII.2-6 However, it is conceivable that pauses in transcription due to the presence of nucleosomes could also have a positive function. Several studies have described the genome-wide distribution of nucleosomes in different organisms,7-10 showing that, inside of genes, nucleosomes are preferentially positioned in certain regions (see below). RNAPII pause sites in transcription elongation often correlate with positioned nucleosomes8,11,12 and, strikingly, the transcription rate varies between genes and even in different regions of the same gene.13,14 It is not yet clear whether elongation rate differences between genes are due to differences in the nucleosome landscape, or whether the characteristic chromatin distribution inside of genes is important for regulating transcription elongation. New results from our laboratory point to an important role of chromatin in controlling the RNAPII elongation rate. Specifically, we have found that decreasing the levels of canonical histones in human cells, which creates a more open chromatin structure, results in faster RNAPII elongation, which strongly suggests that the density of nucleosomes affects the elongation rate.15

Nucleosome distribution and pre-mRNA capping

Most genes have a similar nucleosome distribution near the transcription start site: the promoter is nucleosome free, while the first (+1) nucleosome (with respect to the promoter element) is strongly positioned. Thus, the +1 nucleosome is located where two events—promoter-proximal pausing and pre-mRNA capping—take place, providing a good opportunity for coordination between transcription elongation, processing machineries and chromatin remodeling. RNAPII pausing has been proposed to act as a transcriptional checkpoint to ensure that all necessary elongation factors have been recruited.16 In an earlier work, Rasmussen and Lis proposed that capping and promoter-proximal pausing are linked processes.17 Later, Reinberg and co-workers demonstrated that DSIF, a factor involved in pausing, enhances capping of pre-mRNA in vitro.18 Maps of Drosophila nucleosomes and paused polymerases are consistent with the +1 nucleosome playing a role in promoter-proximal pausing in a subset of genes.11,19 Moreover, genes with a paused RNAPII have a shift in first nucleosome position, with a direct interaction between the +1 nucleosome and the RNAPII.8 Indeed, we have recently demonstrated by introducing strong nucleosome-positioning sequences that a well-positioned +1 nucleosome near the promoter of the c-Myc gene increases promoter-proximal pausing and pre-mRNA capping efficiency (Fig. 1A).20

Figure 1.
Chromatin structure and pre-mRNA processing work together. (A) Model showing the role of the +1 nucleosome in RNAPII promoter-proximal pausing and pre-mRNA capping. The +1 nucleosome-enhanced pausing provides a window of opportunity that might increase ...

Chromatin structure and pre-mRNA splicing

Most pre-mRNA splicing events occur co-transcriptionally,21-23 and it is clear that transcription elongation influences the splicing process.24 Two non-mutually exclusive mechanisms, the recruitment coupling and kinetic coupling models, have been postulated to explain how transcription and splicing are coordinated (these have been extensively described in several excellent reviews24-26). The mechanisms proposed depend on the interactions and kinetics of the elongating RNAPII, respectively. Since transcription takes place in chromatin, both the recruitment of factors to the transcription complex and the RNAPII transcription rate are influenced by the chromatin landscape. Numerous results have suggested that two main aspects are involved in chromatin-dependent control of splicing: nucleosome occupancy and histone posttranslational modifications.

In 2009, several laboratories reported biases in nucleosome occupancy in the gene bodies, with a stronger occupancy in exons than in introns, and more specifically, in constitutive exons than in alternative exons, and in exons with weak splice sites than in exons with strong splice sites.27-31 Overall, these results suggest that nucleosome positioning contributes to exon selection. It has been suggested that pausing or delaying of RNAPII, promoted by exonic nucleosome positioning, could help exon inclusion. Several data support this view. First, RNAPII accumulates at spliced exons,11,32-35 and its elongation rate is negatively correlated to the exon density.13,36 Second, changes in progesterone-dependent nucleosome occupancy correlate with alternative splicing and RNAPII accumulation.37 Third, as we have recently shown, perturbing the chromatin structure by depleting canonical histones leads to drastic alterations in splicing.15 In particular, histone depletion promotes skipping of the variable exons in the CD44 gene and leads to a reduction in the levels of RNAPII at that region. Interestingly, this defective phenotype can be rescued by a “slow” RNAPII mutant. Our data therefore suggest that the CD44 splicing defect is a direct consequence of an increased elongation rate caused by an aberrant chromatin organization (Fig. 1B).

Nucleosomes not only affect splicing due to their elongation barrier properties. For instance, some exon-specific histone post-translational modifications are involved in the recruitment of splicing factors. A paradigm for a histone modification that affects splicing is the trimethylation of H3 lysine 36 (H3K36me3), which is significantly enriched on exons.27,29,31,38 Silencing or mutating the H3K36 methyltransferase SETD2 has been associated with differential exon inclusion and intron retention.39,40 Moreover, H3K36me3 binding proteins, such as MRG1539 and Psip1/Ledgf,41 are able to recruit splicing factors to chromatin that regulate alternative splicing. Two recent studies have reported that the protein BS69/ZMYND11 is able to specifically bind K36me3 that occurs in the histone variant H3.3.42,43 BS69/ZMYND11 also interacts with a number of U5 snRNP components of the spliceosome.42 Strikingly, depletion of BS69/ZMYND11 strongly decreases intron retention, suggesting that BS69/ZMYND11 promotes retention of specific introns.42 We have reported that depletion of canonical histones increases the levels of the histone variant H3.3 at gene bodies and, intriguingly, promotes also intron retention.15 Therefore, higher levels of H3.3 at the body of transcribed genes under histone depletion could facilitate the recruitment of BS69/ZMYND11, which eventually would enhance intron retention. Other histone post-translational modifications, such as acetylation or methylation of H3K9, have also been found to be related to RNA splicing.44-46

In summary, many lines of evidence indicate that both alternative and constitutive splicing are affected by chromatin structure, which works either by modulating the RNAPII elongation rate or by promoting the recruitment of splicing factors (Fig. 1B). These two aspects may be two sides of the same coin, whose influence on splicing depends on the specific context of the exon.

Transcription termination, pre-mRNA 3′-end processing, polyadenylation and chromatin

Nucleosome occupancy around transcription termination sites is also well organized. In fact, polyadenylation (polyA) sites are strongly depleted of nucleosomes, whereas downstream regions are nucleosome enriched.27 It is well known that RNAPII pauses around the 3′ end of most mammalian and yeast genes,47-49 and that a forced pausing increases termination in vivo in an XRN2-dependent manner.50 Interestingly, a correlation between RNAPII accumulation and nucleosome organization around the polyA site has been reported.48,51 Moreover, a chromatin remodeling mutant of the ISWI sub-family in yeast shows termination defects.52 Based on these results, RNAPII pausing created by the positioned nucleosomes downstream of the polyA site has been proposed to help the termination process, although how the pausing affects 3′ pre-mRNA processing is still unclear.

Proudfoot and collaborators have recently reported a possible mechanism by which chromatin increases pausing at the termination region.53 They show that R-loop (RNA-DNA hybrids)–induced antisense transcription occurs after the polyA site promoting recruitment of DICER, AGO1, AGO2 and the G9a histone H3 lysine 9 methyltransferase. Following this, the level of the H3K9me2 repressive mark increases, and the heterochromatin protein 1γ (HP1γ) is recruited, to induce a heterochromatin-like structure that enhances RNAPII pausing and promotes termination. A role of facultative heterochromatin in controlling alternative polyA sites has been also reported in Arabidopsis thaliana (reviewed in54). In some cases, antisense transcription and RNA-interference machinery are also involved in alternative 3′-processing in plants.

Finally, consistent with the important role that chromatin plays in termination, our analyses of cells depleted of canonical histones have revealed defects in 3′-processing and polyA in some genes (S. Jimeno-González and J. C. Reyes, unpublished results).

Conclusions

Both the nucleosome organization and the combination of histone post-translational modifications at gene bodies strongly affect how pre-mRNA is processed. This mostly occurs through two interrelated mechanisms: by modulating the RNAPII elongation rate and by determining the recruitment of additional factors that directly affect RNA processing. A common aspect that arises from our data and the work from other groups is that the nucleosome-imposed slow progression of RNAPII provides windows of opportunities to recruit RNA processing factors. Hence, an “overly” permissive chromatin causes accumulation of pre-mRNA intermediaries (e.g., uncapped or unspliced pre-mRNA) that will eventually be degraded by the RNA quality control machinery. The cell can then use these chromatin-based mechanisms to change pre-mRNA processing efficiency in order to modulate gene expression, through the involvement of chromatin remodeling machineries and epigenetic factors far from their traditionally-studied working sites to promoters and enhancers. Finally, it is known that senescence and aging are characterized by changes in histone availability.55,56 Therefore, it is possible that RNA processing effects associated to senescence or aging are caused by chromatin alterations.

Disclosure of potential conflicts of interest

No potential conflicts of interest were disclosed.

Funding

Work in the Silvia Jimeno-González and José C. Reyes laboratory was supported by the Spanish Ministry of Economy and Competitiveness (MINECO) [Grants number BFU-2011-23442 and BFU2014-53543-P] and Andalusian Government [P06-CVI-4844].

References

[1] Moore MJ, Proudfoot NJ Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 2009; 136:688-700. [PubMed]
[2] Subtil-Rodriguez A, Reyes JC BRG1 helps RNA polymerase II to overcome a nucleosomal barrier during elongation, in vivo. EMBO Rep 2010; 11:751-757. [PubMed]
[3] Izban MG, Luse DS Transcription on nucleosomal templates by RNA polymerase II in vitro: inhibition of elongation with enhancement of sequence-specific pausing. Genes Dev 1991; 5:683-696. [PubMed]
[4] Kireeva ML, Hancock B, Cremona GH, Walter W, Studitsky VM, Kashlev M Nature of the nucleosomal barrier to RNA polymerase II. Mol Cell 2005; 18:97-108. [PubMed]
[5] Kwak H, Lis JT Control of Transcriptional Elongation. Annu Rev Genet 2013; 47:501-526.
[6] Hodges C, Bintu L, Lubkowska L, Kashlev M, Bustamante C Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. Science 2009; 325:626-628. [PMC free article] [PubMed]
[7] Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ Genome-scale identification of nucleosome positions in S. cerevisiae. Science 2005; 309:626-630. [PubMed]
[8] Mavrich TN, Jiang C, Ioshikhes IP, Li X, Venters BJ, Zanton SJ, Tomsho LP, Qi J, Glaser RL, Schuster SC et al. Nucleosome organization in the Drosophila genome. Nature 2008; 453:358-362. [PMC free article] [PubMed]
[9] Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K Dynamic regulation of nucleosome positioning in the human genome. Cell 2008; 132:887-898. [PubMed]
[10] Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 2008; 18:1051-1063. [PubMed]
[11] Kwak H, Fuda NJ, Core LJ, Lis JT Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 2013; 339:950-953. [PMC free article] [PubMed]
[12] Weber CM, Ramachandran S, Henikoff S Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase. Mol Cell 2014; 53:819-830. [PubMed]
[13] Jonkers I, Kwak H, Lis JT Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons. eLife 2014; 3:e02407. [PMC free article] [PubMed]
[14] Danko CG, Hah N, Luo X, Martins AL, Core L, Lis JT, Siepel A, Kraus WL Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol Cell 2013; 50:212-222. [PMC free article] [PubMed]
[15] Jimeno-Gonzalez S, Payan-Bravo L, Munoz-Cabello AM, Guijo M, Gutierrez G, Prado F, Reyes JC Defective histone supply causes changes in RNA polymerase II elongation rate and cotranscriptional pre-mRNA splicing. Proc Natl Acad Sci U S A 2015; 112:14840-14845. [PubMed]
[16] Henriques T, Gilchrist DA, Nechaev S, Bern M, Muse GW, Burkholder A, Fargo DC, Adelman K Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals. Mol Cell 2013; 52:517-528. [PMC free article] [PubMed]
[17] Rasmussen EB, Lis JT In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes. Proc Natl Acad Sci U S A 1993; 90:7923-7927. [PubMed]
[18] Mandal SS, Chu C, Wada T, Handa H, Shatkin AJ, Reinberg D Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II. Proc Natl Acad Sci U S A 2004; 101:7572-7577. [PubMed]
[19] Li J, Gilmour DS Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor. Embo J 2013; 32:1829-1841. [PubMed]
[20] Jimeno-Gonzalez S, Ceballos-Chavez M, Reyes JC A positioned +1 nucleosome enhances promoter-proximal pausing. Nucleic Acids Res 2015; 43:3068-3078. [PMC free article] [PubMed]
[21] Beyer AL, Osheim YN Splice site selection, rate of splicing, and alternative splicing on nascent transcripts. Genes Dev 1988; 2:754-765. [PubMed]
[22] Carrillo Oesterreich F, Preibisch S, Neugebauer KM Global analysis of nascent RNA reveals transcriptional pausing in terminal exons. Mol Cell 2010; 40:571-581. [PubMed]
[23] Tilgner H, Knowles DG, Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigo R Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res 2012; 22:1616-1625. [PubMed]
[24] Naftelberg S, Schor IE, Ast G, Kornblihtt AR Regulation of alternative splicing through coupling with transcription and chromatin structure. Annu Rev Biochem 2015; 84:165-198. [PubMed]
[25] Luco RF, Allo M, Schor IE, Kornblihtt AR, Misteli T Epigenetics in Alternative Pre-mRNA Splicing. Cell 2011; 144:16-26. [PMC free article] [PubMed]
[26] Dujardin G, Lafaille C, Petrillo E, Buggiano V, Gomez Acuna LI, Fiszbein A, Godoy Herz MA, Nieto Moreno N, Munoz MJ, Allo M et al. Transcriptional elongation and alternative splicing. Biochim Biophys Acta 2013; 1829:134-140. [PubMed]
[27] Spies N, Nielsen CB, Padgett RA, Burge CB Biased chromatin signatures around polyadenylation sites and exons. Mol Cell 2009; 36:245-254. [PMC free article] [PubMed]
[28] Andersson R, Enroth S, Rada-Iglesias A, Wadelius C, Komorowski J Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res 2009; 19:1732-1741. [PubMed]
[29] Tilgner H, Nikolaou C, Althammer S, Sammeth M, Beato M, Valcarcel J, Guigo R Nucleosome positioning as a determinant of exon recognition. Nat Struct Mol Biol 2009; 16:996-1001. [PubMed]
[30] Nahkuri S, Taft RJ, Mattick JS Nucleosomes are preferentially positioned at exons in somatic and sperm cells. Cell Cycle (Georgetown, Tex 2009; 8:3420-3424. [PubMed]
[31] Schwartz S, Meshorer E, Ast G Chromatin organization marks exon-intron structure. Nat Struct Mol Biol 2009; 16:990-995. [PubMed]
[32] Chodavarapu RK, Feng S, Bernatavichute YV, Chen PY, Stroud H, Yu Y, Hetzel JA, Kuo F, Kim J, Cokus SJ et al. Relationship between nucleosome positioning and DNA methylation. Nature 2010; 466:388-392. [PMC free article] [PubMed]
[33] Brodsky AS, Meyer CA, Swinburne IA, Hall G, Keenan BJ, Liu XS, Fox EA, Silver PA Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells. Genome Biol 2005; 6:R64. [PMC free article] [PubMed]
[34] Alexander RD, Innocente SA, Barrass JD, Beggs JD Splicing-dependent RNA polymerase pausing in yeast. Mol Cell 2010; 40:582-593. [PMC free article] [PubMed]
[35] Mayer A, di Iulio J, Maleri S, Eser U, Vierstra J, Reynolds A, Sandstrom R, Stamatoyannopoulos JA, Churchman LS Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution. Cell 2015; 161:541-554. [PMC free article] [PubMed]
[36] Veloso A, Kirkconnell KS, Magnuson B, Biewen B, Paulsen MT, Wilson TE, Ljungman M Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications. Genome Res 2014; 24:896-905. [PubMed]
[37] Iannone C, Pohl A, Papasaikas P, Soronellas D, Vicent GP, Beato M, ValcaRcel J Relationship between nucleosome positioning and progesterone-induced alternative splicing in breast cancer cells. RNA (New York, NY 2015; 21:360-374. [PubMed]
[38] Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 2009; 41:376-381. [PMC free article] [PubMed]
[39] Luco RF, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith OM, Misteli T Regulation of alternative splicing by histone modifications. Science 2010; 327:996-1000. [PMC free article] [PubMed]
[40] Simon JM, Hacker KE, Singh D, Brannon AR, Parker JS, Weiser M, Ho TH, Kuan PF, Jonasch E, Furey TS, Prins JF, Lieb JD, Rathmell WK, Davis IJ Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects. Genome Res 2013; 24:241-250. [PubMed]
[41] Pradeepa MM, Sutherland HG, Ule J, Grimes GR, Bickmore WA Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing. PLoS Genet 2012; 8:e1002717. [PMC free article] [PubMed]
[42] Guo R, Zheng L, Park JW, Lv R, Chen H, Jiao F, Xu W, Mu S, Wen H, Qiu J et al. BS69/ZMYND11 reads and connects histone H3.3 lysine 36 trimethylation-decorated chromatin to regulated pre-mRNA processing. Mol Cell 2014; 56:298-310. [PMC free article] [PubMed]
[43] Wen H, Li Y, Xi Y, Jiang S, Stratton S, Peng D, Tanaka K, Ren Y, Xia Z, Wu J et al. ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression. Nature 2014; 508:263-268. [PMC free article] [PubMed]
[44] Saint-Andre V, Batsche E, Rachez C, Muchardt C Histone H3 lysine 9 trimethylation and HP1gamma favor inclusion of alternative exons. Nat Struct Mol Biol 2011; 18:337-344. [PubMed]
[45] Schor IE, Rascovan N, Pelisch F, Allo M, Kornblihtt AR Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing. Proc Natl Acad Sci U S A 2009; 106:4325-4330. [PubMed]
[46] Curado J, Iannone C, Tilgner H, Valcarcel J, Guigo R Promoter-like epigenetic signatures in exons displaying cell type-specific splicing. Genome Biol 2015; 16:236. [PMC free article] [PubMed]
[47] Enriquez-Harris P, Levitt N, Briggs D, Proudfoot NJ A pause site for RNA polymerase II is associated with termination of transcription. Embo J 1991; 10:1833-1842. [PubMed]
[48] Grosso AR, de Almeida SF, Braga J, Carmo-Fonseca M Dynamic transitions in RNA polymerase II density profiles during transcription termination. Genome Res 2012; 22:1447-1456. [PubMed]
[49] Mayer A, Lidschreiber M, Siebert M, Leike K, Soding J, Cramer P Uniform transitions of the general RNA polymerase II transcription complex. Nat Struct Mol Biol 2010; 17:1272-1278. [PubMed]
[50] Gromak N, West S, Proudfoot NJ Pause sites promote transcriptional termination of mammalian RNA polymerase II. Mol Cell Biol 2006; 26:3986-3996. [PMC free article] [PubMed]
[51] Jordan-Pla A, Gupta I, de Miguel-Jimenez L, Steinmetz LM, Chavez S, Pelechano V, Perez-Ortin JE Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle. Nucleic Acids Res 2015; 43:787-802. [PMC free article] [PubMed]
[52] Morillon A, Karabetsou N, O'Sullivan J, Kent N, Proudfoot N, Mellor J Isw1 chromatin remodeling ATPase coordinates transcription elongation and termination by RNA polymerase II. Cell 2003; 115:425-435. [PubMed]
[53] Skourti-Stathaki K, Kamieniarz-Gdula K, Proudfoot NJ R-loops induce repressive chromatin marks over mammalian gene terminators. Nature 2014; 516:436-439. [PMC free article] [PubMed]
[54] Mathieu O, Bouche N Interplay between chromatin and RNA processing. Curr Opin Plant Biol 2014; 18:60-65. [PubMed]
[55] Hu Z, Chen K, Xia Z, Chavez M, Pal S, Seol JH, Chen CC, Li W, Tyler JK Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging. Genes Dev 2014; 28:396-408. [PubMed]
[56] O'Sullivan RJ, Kubicek S, Schreiber SL, Karlseder J Reduced histone biosynthesis and chromatin changes arising from a damage signal at telomeres. Nat Struct Mol Biol 2010; 17:1218-1225. [PMC free article] [PubMed]

Articles from Transcription are provided here courtesy of Taylor & Francis