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Cited by 203Genomics and Chromatin DynamicsRNA Research and SplicingRNA and protein synthesis mechanisms

4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells

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Fuchs, Gilad, Voichek, Yoav, Benjamin, Sima, Gilad, Shlomit, Amit, Ido, Oren, Moshe·2014·Genome Biology
DOI 10.1186/gb-2014-15-5-r69PMC PMC4072947
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Abstract

Although transcriptional elongation by RNA polymerase II is coupled with many RNA-related processes, genomewide elongation rates remain unknown. We describe a method, called 4sUDRB-seq, based on reversible inhibition of transcription elongation coupled with tagging newly transcribed RNA with 4-thiouridine and high throughput sequencing to measure simultaneously with high confidence genome-wide transcription elongation rates in cells. We find that most genes are transcribed at about 3.5 Kb/min, with elongation rates varying between 2 Kb/min and 6 Kb/min. 4sUDRB-seq can facilitate genomewide exploration of the involvement of specific elongation factors in transcription and the contribution of deregulated transcription elongation to various pathologies.

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  • Genome-wide techniques showed in various human cell lines that average RNA Pol II speed ranges between 1.25 kb/min and 3.5 kb/min.

    “All these techniques showed in various human cell lines that the average RNA Pol II speed ranges between 1.25 kb/min and 3.5 kb/min (Danko et al, 2013; Fuchs et al, 2014b; Jonkers et al, 2014; Saponaro et al, 2014; Veloso et al, 2014; Liang et al, 2018; Baluapuri et al, 2019; Gregersen et al, 2020).”

    From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Fuchs et al, 2014b

    The Results and discussion section (page unavailable) reports genome-wide measurements in 1,577 genes, with most transcribed at approximately 3.5 kb/min. The study used HeLa cells, but it does not establish an average of 1.25 kb/min or a range of average speeds across various human cell lines; its measured gene-level rates span 2–6 kb/min. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • RNA Pol II speed is highly variable within individual genes, as RNA Pol II accelerates while traveling throughout the gene body, starting at 0.5 kb/min in the first 10-15 kb and accelerating up to 2-4 kb/min downstream.

    “RNA Pol II speed was furthermore also shown to be highly variable within individual genes, as RNA Pol II accelerates while traveling throughout the gene body, starting at 0.5 kb/min in the first 10–15 kb and accelerating up to 2–4 kb/min downstream (Danko et al, 2013; Fuchs et al, 2014b; Jonkers et al, 2014; Saponaro et al, 2014).”

    From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Fuchs et al, 2014b

    The Results and discussion section reports that Pol II may move more slowly near the transcription start site and then accelerate, but also offers delayed transcription resumption after DRB removal as an alternative explanation. It does not establish a speed of 0.5 kb/min in the first 10–15 kb or 2–4 kb/min downstream; its reported 2–6 kb/min range describes rates across different genes. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

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References 45 · Cited by 203

Research works printed but not linked: 40

  1. 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 10.1073/pnas.90.17.7923 8367444 PMC47259 · DOI
  2. Proudfoot NJ Furger A Dye MJ Integrating mRNA processing with transcription Cell 2002 108 501 512 10.1016/S0092-8674(02)00617-7 11909521 · DOI
  3. Neugebauer KM On the importance of being co-transcriptional J Cell Sci 2002 115 3865 3871 10.1242/jcs.00073 12244124 · DOI
  4. Bentley DL Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors Curr Opin Cell Biol 2005 17 251 256 10.1016/j.ceb.2005.04.006 15901493 · DOI
  5. Hirose Y Manley JL RNA polymerase II is an essential mRNA polyadenylation factor Nature 1998 395 93 96 10.1038/25786 9738505 · DOI
  6. Hirose Y Tacke R Manley JL Phosphorylated RNA polymerase II stimulates pre-mRNA splicing Genes Dev 1999 13 1234 1239 10.1101/gad.13.10.1234 10346811 PMC316731 · DOI
  7. de la Mata M Alonso CR Kadener S Fededa JP Blaustein M Pelisch F Cramer P Bentley D Kornblihtt AR A slow RNA polymerase II affects alternative splicing in vivo Mol Cell 2003 12 525 532 10.1016/j.molcel.2003.08.001 14536091 · DOI · Paper page
  8. Core LJ Waterfall JJ Lis JT Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters Science 2008 322 1845 1848 10.1126/science.1162228 19056941 PMC2833333 · DOI
  9. Guenther MG Levine SS Boyer LA Jaenisch R Young RA A chromatin landmark and transcription initiation at most promoters in human cells Cell 2007 130 77 88 10.1016/j.cell.2007.05.042 17632057 PMC3200295 · DOI
  10. Muse GW Gilchrist DA Nechaev S Shah R Parker JS Grissom SF Zeitlinger J Adelman K RNA polymerase is poised for activation across the genome Nat Genet 2007 39 1507 1511 10.1038/ng.2007.21 17994021 PMC2365887 · DOI
  11. Nechaev S Fargo DC dos Santos G Liu L Gao Y Adelman K Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila Science 2010 327 335 338 10.1126/science.1181421 20007866 PMC3435875 · DOI · Paper page
  12. Bentley DL Groudine M A block to elongation is largely responsible for decreased transcription of c-myc in differentiated HL60 cells Nature 1986 321 702 706 10.1038/321702a0 3520340 · DOI
  13. Rougvie AE Lis JT The RNA polymerase II molecule at the 5' end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged Cell 1988 54 795 804 10.1016/S0092-8674(88)91087-2 3136931 · DOI
  14. Zeitlinger J Stark A Kellis M Hong JW Nechaev S Adelman K Levine M Young RA RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo Nat Genet 2007 39 1512 1516 10.1038/ng.2007.26 17994019 PMC2824921 · DOI
  15. 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 10.1073/pnas.0810666106 19251664 PMC2657401 · DOI · Paper page
  16. Ip JY Schmidt D Pan Q Ramani AK Fraser AG Odom DT Blencowe BJ Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation Genome Res 2011 21 390 401 10.1101/gr.111070.110 21163941 PMC3044853 · DOI
  17. 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 10.1126/science.1229386 23430654 PMC3974810 · DOI · Paper page
  18. Yin H Sweeney S Raha D Snyder M Lin H A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster PLoS Genet 2011 7 e1002380 10.1371/journal.pgen.1002380 22194694 PMC3240582 · DOI
  19. Pinto PA Henriques T Freitas MO Martins T Domingues RG Wyrzykowska PS Coelho PA Carmo AM Sunkel CE Proudfoot NJ Moreira A RNA polymerase II kinetics in polo polyadenylation signal selection EMBO J 2011 30 2431 2444 10.1038/emboj.2011.156 21602789 PMC3116286 · DOI · Paper page
  20. Lin C Smith ER Takahashi H Lai KC Martin-Brown S Florens L Washburn MP Conaway JW Conaway RC Shilatifard A AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia Mol Cell 2010 37 429 437 10.1016/j.molcel.2010.01.026 20159561 PMC2872029 · DOI
  21. Lin CY Loven J Rahl PB Paranal RM Burge CB Bradner JE Lee TI Young RA Transcriptional amplification in tumor cells with elevated c-Myc Cell 2012 151 56 67 10.1016/j.cell.2012.08.026 23021215 PMC3462372 · DOI
  22. Marazzi I Ho JS Kim J Manicassamy B Dewell S Albrecht RA Seibert CW Schaefer U Jeffrey KL Prinjha RK Lee K Garcia-Sastre A Roeder RG Tarakhovsky A Suppression of the antiviral response by an influenza histone mimic Nature 2012 483 428 433 10.1038/nature10892 22419161 PMC3598589 · DOI
  23. Sobhian B Laguette N Yatim A Nakamura M Levy Y Kiernan R Benkirane M HIV-1 Tat assembles a multifunctional transcription elongation complex and stably associates with the 7SK snRNP Mol Cell 2010 38 439 451 10.1016/j.molcel.2010.04.012 20471949 PMC3595998 · DOI
  24. He N Liu M Hsu J Xue Y Chou S Burlingame A Krogan NJ Alber T Zhou Q HIV-1 Tat and host AFF4 recruit two transcription elongation factors into a bifunctional complex for coordinated activation of HIV-1 transcription Mol Cell 2010 38 428 438 10.1016/j.molcel.2010.04.013 20471948 PMC3085314 · DOI
  25. He N Zhou Q New insights into the control of HIV-1 transcription: when Tat meets the 7SK snRNP and super elongation complex (SEC) J Neuroimmune Pharmacol 2011 6 260 268 10.1007/s11481-011-9267-6 21360054 PMC3087102 · DOI
  26. Ardehali MB Lis JT Tracking rates of transcription and splicing in vivo Nat Struct Mol Biol 2009 16 1123 1124 10.1038/nsmb1109-1123 19888309 · DOI
  27. Singh J Padgett RA Rates of in situ transcription and splicing in large human genes Nat Struct Mol Biol 2009 16 1128 1133 10.1038/nsmb.1666 19820712 PMC2783620 · DOI · Paper page
  28. Kim YJ Greer CB Cecchini KR Harris LN Tuck DP Kim TH HDAC inhibitors induce transcriptional repression of high copy number genes in breast cancer through elongation blockade Oncogene 2013 32 2828 2835 10.1038/onc.2013.32 23435418 PMC3676447 · DOI
  29. Saunders A Core LJ Sutcliffe C Lis JT Ashe HL Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription Genes Dev 2013 27 1146 1158 10.1101/gad.215459.113 23699410 PMC3672648 · DOI
  30. Luo X Chae M Krishnakumar R Danko CG Kraus WL Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFalpha signaling revealed by integrated genomic analyses BMC Genomics 2014 15 155 10.1186/1471-2164-15-155 24564208 PMC3945043 · DOI
  31. Dolken L Ruzsics Z Radle B Friedel CC Zimmer R Mages J Hoffmann R Dickinson P Forster T Ghazal P Koszinowski UH High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay RNA 2008 14 1959 1972 10.1261/rna.1136108 18658122 PMC2525961 · DOI
  32. Windhager L Bonfert T Burger K Ruzsics Z Krebs S Kaufmann S Malterer G L'Hernault A Schilhabel M Schreiber S Rosenstiel P Zimmer R Eick D Friedel CC Dolken L Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution Genome Res 2012 22 2031 2042 10.1101/gr.131847.111 22539649 PMC3460197 · DOI
  33. Fuchs G Shema E Vesterman R Kotler E Wolchinsky Z Wilder S Golomb L Pribluda A Zhang F Haj-Yahya M Feldmesser E Brik A Yu X Hanna J Aberdam D Domany E Oren M RNF20 and USP44 regulate stem cell differentiation by modulating H2B monoubiquitylation Mol Cell 2012 46 662 673 10.1016/j.molcel.2012.05.023 22681888 PMC3374598 · DOI
  34. Weinberger L Voichek Y Tirosh I Hornung G Amit I Barkai N Expression noise and acetylation profiles distinguish HDAC functions Mol Cell 2012 47 193 202 10.1016/j.molcel.2012.05.008 22683268 PMC3408861 · DOI
  35. Palangat M Larson DR Complexity of RNA polymerase II elongation dynamics Biochim Biophys Acta 1819 2012 667 672 PMC6310610 22480952
  36. Ehrensberger AH Kelly GP Svejstrup JQ Mechanistic interpretation of promoter-proximal peaks and RNAPII density maps Cell 2013 154 713 715 10.1016/j.cell.2013.07.032 23953103 · DOI
  37. 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 [Epub ahead of print] PMC4032854 24714810
  38. Rabani M Levin JZ Fan L Adiconis X Raychowdhury R Garber M Gnirke A Nusbaum C Hacohen N Friedman N Amit I Regev A Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells Nat Biotechnol 2011 29 436 442 10.1038/nbt.1861 21516085 PMC3114636 · DOI · Paper page
  39. Langmead B Trapnell C Pop M Salzberg SL Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol 2009 10 R25 10.1186/gb-2009-10-3-r25 19261174 PMC2690996 · DOI · Paper page
  40. Raney BJ Cline MS Rosenbloom KR Dreszer TR Learned K Barber GP Meyer LR Sloan CA Malladi VS Roskin KM Suh BB Hinrichs AS Clawson H Zweig AS Kirkup V Fujita PA Rhead B Smith KE Pohl A Kuhn RM Karolchik D Haussler D Kent WJ ENCODE whole-genome data in the UCSC genome browser (2011 update) Nucleic Acids Res 2011 39 D871 D875 10.1093/nar/gkq1017 21037257 PMC3013645 · DOI

Authors
Fuchs, G., Voichek, Y., Benjamin, S., Gilad, S., Amit, I., & Oren, M.
Affiliations
Weizmann Institute of Science (IL)
Corresponding author
  • Fuchs, Gilad
  • Oren, Moshe
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2014-05-09
Volume
15
Issue
5
Pages
R69-R69
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/gb-2014-15-5-r69
PMC
PMC4072947
OpenAlex
W2127652525
Cited by
203
References
45
Citations by year
2026: 9 · 2025: 17 · 2024: 30 · 2023: 10 · 2022: 14 · 2021: 27 · 2020: 20 · 2019: 21 · 2018: 12 · 2017: 14 · 2016: 12 · 2015: 15 · 2014: 2
FWCI
5.87
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome biology (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • Dr. Miriam and Sheldon G. Adelson Medical Research Foundation
  • FP7 Ideas: European Research Council (293438)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
RNA polymerase II, 4-thiouridine, elongation factors, gene expression regulation
MeSH terms
Dichlororibofuranosylbenzimidazole, HeLa Cells, Humans, RNA Polymerase II, Thiouridine, Genome, Human, Sequence Analysis, RNA, Transcription Elongation, Genetic

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