Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells

Danko, Charles G.; Hah, Nasun; Luo, Xin; Martins, André L.; Core, Leighton J.; Lis, John T.; Siepel, Adam; Kraus, W. Lee

doi:10.1016/j.molcel.2013.05.025

Cited by 30 publications

(61 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This finding begs the question of whether physiological regulation of elongation rate exerts a significant influence on alternative splicing. In favor of this possibility, elongation rates vary between genes and within genes (Danko et al 2013;Jonkers et al 2014;Veloso et al 2014) over a range (;0.5-4 kb/min) that overlaps the average rates of the slow C4/R749H and fast E1126G mutants used here (0.5-1.9 kb/min) ( Fig. 1D; Supplemental Fig.…”

Section: Discussionmentioning

confidence: 84%

“…2A). Furthermore, elongation rates have been reported to change in response to physiological stimuli (Danko et al 2013) that could thereby regulate alternative splicing. Intriguingly, many elongation ratesensitive cassette exons in our HEK293 cell lines are also abnormally included or skipped in breast and ovarian tumors (Figs.…”

Section: Discussionmentioning

confidence: 99%

“…It is also unclear whether faster elongation has the opposite effect on splicing of slower elongation as predicted by the model. In vivo elongation rates of wild-type Pol II vary between ;0.5 and >4 kb/min and may be regulated (Danko et al 2013;Veloso et al 2014), but it is not known whether cotranscriptional alternative splicing decisions are sensitive to changes in elongation rate within this range. We examined splicing in human cells expressing Rpb1 point mutants that either accelerate or decelerate average rates of elongation.…”

mentioning

confidence: 99%

See 2 more Smart Citations

Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate

et al. 2014

View full text Add to dashboard Cite

Alternative splicing modulates expression of most human genes. The kinetic model of cotranscriptional splicing suggests that slow elongation expands and that fast elongation compresses the "window of opportunity" for recognition of upstream splice sites, thereby increasing or decreasing inclusion of alternative exons. We tested the model using RNA polymerase II mutants that change average elongation rates genome-wide. Slow and fast elongation affected constitutive and alternative splicing, frequently altering exon inclusion and intron retention in ways not predicted by the model. Cassette exons included by slow and excluded by fast elongation (type I) have weaker splice sites, shorter flanking introns, and distinct sequence motifs relative to "slow-excluded" and "fast-included" exons (type II). Many rate-sensitive exons are misspliced in tumors. Unexpectedly, slow and fast elongation often both increased or both decreased inclusion of a particular exon or retained intron. These results suggest that an optimal rate of transcriptional elongation is required for normal cotranscriptional pre-mRNA splicing.

show abstract

Section: Discussionmentioning

confidence: 84%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate

et al. 2014

View full text Add to dashboard Cite

show abstract

“…Cells were collected at ∼70%-80% confluence, and nuclei were isolated as described previously (Luo et al 2014). Nuclear run-on and GRO-seq library preparation were performed as previously described (Hah et al 2011), with modifications (Danko et al 2013;Luo et al 2014). After library quality control assessment using a Bioanalyzer (Agilent), the samples were subjected to 50-bp single-end sequencing using an Illumina HiSeq 2000 Sequencing System.…”

Section: Global Run-on Sequencing (Gro-seq)mentioning

confidence: 99%

Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis

et al. 2017

View full text Add to dashboard Cite

Noncoding transcription is a defining feature of active enhancers, linking transcription factor (TF) binding to the molecular mechanisms controlling gene expression. To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 11 different human breast cancer cell lines representing five major molecular subtypes of breast cancer, as well as two immortalized ("normal") human breast cell lines. In addition, we developed a robust and unbiased computational pipeline that simultaneously identifies putative subtype-specific enhancers and their cognate TFs by integrating the magnitude of enhancer transcription, TF mRNA expression levels, TF motif -values, and enrichment of H3K4me1 and H3K27ac. When applied across the 13 different cell lines noted above, the Total Functional Score of Enhancer Elements (TFSEE) identified key breast cancer subtype-specific TFs that act at transcribed enhancers to dictate gene expression patterns determining growth outcomes, including Forkhead TFs, FOSL1, and PLAG1. FOSL1, a Fos family TF, (1) is highly enriched at the enhancers of triple negative breast cancer (TNBC) cells, (2) acts as a key regulator of the proliferation and viability of TNBC cells, but not Luminal A cells, and (3) is associated with a poor prognosis in TNBC breast cancer patients. Taken together, our results validate our enhancer identification pipeline and reveal that enhancers transcribed in breast cancer cells direct critical gene regulatory networks that promote pathogenesis.

show abstract

“…We can hypothesize that this might be a crucial region for the dystrophin transcriptional dynamics regulation, requiring a pausing site and then restarting elongation downstream. Since R-loops also promote chromatin architecture shaping, which controls termination region, this region might also be implicated in gene transcription termination and polyadenylation regulation [32,33]. Very recently ultra-deep transcript sequencing analyses have shown that dystrophin pre-mRNA undergoes multi-step non-sequential splicing thus suggesting a highly regulated process in which control of RNA pol II processivity may be critical [34].…”

Section: A New Dmd Rna Pol II Pausing Sitementioning

confidence: 99%

Transcriptional and epigenetic analyses of the DMD locus reveal novel cis ‑acting DNA elements that govern muscle dystrophin expression

Gherardi

Bovolenta

Passarelli

et al. 2017

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

View full text Add to dashboard Cite

The dystrophin gene (DMD) is the largest gene in the human genome, mapping on the Xp21 chromosome locus. It spans 2.2Mb and accounts for approximately 0,1% of the entire human genome. Mutations in this gene cause Duchenne and Becker Muscular Dystrophy, X-linked Dilated Cardiomyopathy, and other milder muscle phenotypes. Beside the remarkable number of reports describing dystrophin gene expression and the pathogenic consequences of the gene mutations in dystrophinopathies, the full scenario of the DMD transcription dynamics remains however, poorly understood. Considering that the full transcription of the DMD gene requires about 16h, we have investigated the activity of RNA Polymerase II along the entire DMD locus within the context of specific chromatin modifications using a variety of chromatin-based techniques. Our results unveil a surprisingly powerful processivity of the RNA polymerase II along the entire 2.2Mb of the DMD locus with just one site of pausing around intron 52. We also discovered epigenetic marks highlighting the existence of four novel cis‑DNA elements, two of which, located within intron 34 and exon 45, appear to govern the architecture of the DMD chromatin with implications on the expression levels of the muscle dystrophin mRNA. Overall, our findings provide a global view on how the entire DMD locus is dynamically transcribed by the RNA pol II and shed light on the mechanisms involved in dystrophin gene expression control, which can positively impact on the optimization of the novel ongoing therapeutic strategies for dystrophinopathies.

show abstract

Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells

Cited by 30 publications

References 0 publications

Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate

Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate

Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis

Transcriptional and epigenetic analyses of the DMD locus reveal novel cis ‑acting DNA elements that govern muscle dystrophin expression

Contact Info

Product

Resources

About