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Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters.

Core LJ, Waterfall JJ, Lis JT.

Science. 2008 Dec 19;322(5909):1845-8. doi: 10.1126/science.1162228. Epub 2008 Dec 4.


Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome.

Flynn RA, Almada AE, Zamudio JR, Sharp PA.

Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10460-5. doi: 10.1073/pnas.1106630108. Epub 2011 Jun 13.


RNA exosome depletion reveals transcription upstream of active human promoters.

Preker P, Nielsen J, Kammler S, Lykke-Andersen S, Christensen MS, Mapendano CK, Schierup MH, Jensen TH.

Science. 2008 Dec 19;322(5909):1851-4. doi: 10.1126/science.1164096. Epub 2008 Dec 4.


Transcription. Gene expression--where to start?

Buratowski S.

Science. 2008 Dec 19;322(5909):1804-5. doi: 10.1126/science.1168805. No abstract available.


Precise maps of RNA polymerase reveal how promoters direct initiation and pausing.

Kwak H, Fuda NJ, Core LJ, Lis JT.

Science. 2013 Feb 22;339(6122):950-3. doi: 10.1126/science.1229386.


Pause & go: from the discovery of RNA polymerase pausing to its functional implications.

Mayer A, Landry HM, Churchman LS.

Curr Opin Cell Biol. 2017 Jun;46:72-80. doi: 10.1016/ Epub 2017 Mar 28. Review.


Nascent transcript sequencing visualizes transcription at nucleotide resolution.

Churchman LS, Weissman JS.

Nature. 2011 Jan 20;469(7330):368-73. doi: 10.1038/nature09652.


Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells.

Min IM, Waterfall JJ, Core LJ, Munroe RJ, Schimenti J, Lis JT.

Genes Dev. 2011 Apr 1;25(7):742-54. doi: 10.1101/gad.2005511.


Nascent RNA sequencing reveals distinct features in plant transcription.

Hetzel J, Duttke SH, Benner C, Chory J.

Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12316-12321. Epub 2016 Oct 11.


Divergent transcription is associated with promoters of transcriptional regulators.

Lepoivre C, Belhocine M, Bergon A, Griffon A, Yammine M, Vanhille L, Zacarias-Cabeza J, Garibal MA, Koch F, Maqbool MA, Fenouil R, Loriod B, Holota H, Gut M, Gut I, Imbert J, Andrau JC, Puthier D, Spicuglia S.

BMC Genomics. 2013 Dec 23;14:914. doi: 10.1186/1471-2164-14-914.


Defining the status of RNA polymerase at promoters.

Core LJ, Waterfall JJ, Gilchrist DA, Fargo DC, Kwak H, Adelman K, Lis JT.

Cell Rep. 2012 Oct 25;2(4):1025-35. doi: 10.1016/j.celrep.2012.08.034. Epub 2012 Oct 10.


Divergent transcription from active promoters.

Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, Flynn RA, Young RA, Sharp PA.

Science. 2008 Dec 19;322(5909):1849-51. doi: 10.1126/science.1162253. Epub 2008 Dec 4.


Global Run-On Sequencing (GRO-Seq).

Gardini A.

Methods Mol Biol. 2017;1468:111-20. doi: 10.1007/978-1-4939-4035-6_9.


Directing transcription to the right way.

Huang F, Workman JL.

Cell Res. 2013 Oct;23(10):1153-4. doi: 10.1038/cr.2013.100. Epub 2013 Jul 30.


Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers.

Tome JM, Tippens ND, Lis JT.

Nat Genet. 2018 Nov;50(11):1533-1541. doi: 10.1038/s41588-018-0234-5. Epub 2018 Oct 22.


Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq).

Mahat DB, Kwak H, Booth GT, Jonkers IH, Danko CG, Patel RK, Waters CT, Munson K, Core LJ, Lis JT.

Nat Protoc. 2016 Aug;11(8):1455-76. doi: 10.1038/nprot.2016.086. Epub 2016 Jul 21.


Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters.

Quinodoz M, Gobet C, Naef F, Gustafson KB.

Genome Biol. 2014 Jun 12;15(6):R85. doi: 10.1186/gb-2014-15-6-r85.


Divergent transcription: a new feature of active promoters.

Seila AC, Core LJ, Lis JT, Sharp PA.

Cell Cycle. 2009 Aug 15;8(16):2557-64. Epub 2009 Aug 19. Review.


Clusters of regulatory signals for RNA polymerase II transcription associated with Alu family repeats and CpG islands in human promoters.

Oei SL, Babich VS, Kazakov VI, Usmanova NM, Kropotov AV, Tomilin NV.

Genomics. 2004 May;83(5):873-82.


Relative efficiency of utilization of promoter and termination sites by bacteriophage T3 RNA polymerase.

Sengupta D, Chakravarti D, Maitra U.

J Biol Chem. 1989 Aug 25;264(24):14246-55.

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