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Items: 26

1.

An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells.

Zhang Z, Chng KR, Lingadahalli S, Chen Z, Liu MH, Do HH, Cai S, Rinaldi N, Poh HM, Li G, Sung YY, Heng CL, Core LJ, Tan SK, Ruan X, Lis JT, Kellis M, Ruan Y, Sung WK, Cheung E.

Genome Res. 2019 Feb;29(2):223-235. doi: 10.1101/gr.230243.117. Epub 2019 Jan 3.

2.

Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme.

Chu T, Rice EJ, Booth GT, Salamanca HH, Wang Z, Core LJ, Longo SL, Corona RJ, Chin LS, Lis JT, Kwak H, Danko CG.

Nat Genet. 2018 Nov;50(11):1553-1564. doi: 10.1038/s41588-018-0244-3. Epub 2018 Oct 22.

3.

Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation.

Duarte FM, Fuda NJ, Mahat DB, Core LJ, Guertin MJ, Lis JT.

Genes Dev. 2016 Aug 1;30(15):1731-46. doi: 10.1101/gad.284430.116. Epub 2016 Aug 4.

4.

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.

5.

Identification of active transcriptional regulatory elements from GRO-seq data.

Danko CG, Hyland SL, Core LJ, Martins AL, Waters CT, Lee HW, Cheung VG, Kraus WL, Lis JT, Siepel A.

Nat Methods. 2015 May;12(5):433-8. doi: 10.1038/nmeth.3329. Epub 2015 Mar 23.

6.

Nuclear stability and transcriptional directionality separate functionally distinct RNA species.

Andersson R, Refsing Andersen P, Valen E, Core LJ, Bornholdt J, Boyd M, Heick Jensen T, Sandelin A.

Nat Commun. 2014 Nov 12;5:5336. doi: 10.1038/ncomms6336.

PMID:
25387874
7.

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.

Core LJ, Martins AL, Danko CG, Waters CT, Siepel A, Lis JT.

Nat Genet. 2014 Dec;46(12):1311-20. doi: 10.1038/ng.3142. Epub 2014 Nov 10.

8.

RNA-DNA differences are generated in human cells within seconds after RNA exits polymerase II.

Wang IX, Core LJ, Kwak H, Brady L, Bruzel A, McDaniel L, Richards AL, Wu M, Grunseich C, Lis JT, Cheung VG.

Cell Rep. 2014 Mar 13;6(5):906-15. doi: 10.1016/j.celrep.2014.01.037. Epub 2014 Feb 20.

9.

Pol II docking and pausing at growth and stress genes in C. elegans.

Maxwell CS, Kruesi WS, Core LJ, Kurhanewicz N, Waters CT, Lewarch CL, Antoshechkin I, Lis JT, Meyer BJ, Baugh LR.

Cell Rep. 2014 Feb 13;6(3):455-66. doi: 10.1016/j.celrep.2014.01.008. Epub 2014 Jan 30.

10.

Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription.

Kilpinen H, Waszak SM, Gschwind AR, Raghav SK, Witwicki RM, Orioli A, Migliavacca E, Wiederkehr M, Gutierrez-Arcelus M, Panousis NI, Yurovsky A, Lappalainen T, Romano-Palumbo L, Planchon A, Bielser D, Bryois J, Padioleau I, Udin G, Thurnheer S, Hacker D, Core LJ, Lis JT, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET.

Science. 2013 Nov 8;342(6159):744-7. doi: 10.1126/science.1242463. Epub 2013 Oct 17.

11.

Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation.

Kruesi WS, Core LJ, Waters CT, Lis JT, Meyer BJ.

Elife. 2013 Jun 18;2:e00808. doi: 10.7554/eLife.00808.

12.

Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription.

Saunders A, Core LJ, Sutcliffe C, Lis JT, Ashe HL.

Genes Dev. 2013 May 15;27(10):1146-58. doi: 10.1101/gad.215459.113.

13.

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.

14.

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.

15.

Fcp1 dephosphorylation of the RNA polymerase II C-terminal domain is required for efficient transcription of heat shock genes.

Fuda NJ, Buckley MS, Wei W, Core LJ, Waters CT, Reinberg D, Lis JT.

Mol Cell Biol. 2012 Sep;32(17):3428-37. doi: 10.1128/MCB.00247-12. Epub 2012 Jun 25.

16.

Bacillus subtilis RapA phosphatase domain interaction with its substrate, phosphorylated Spo0F, and its inhibitor, the PhrA peptide.

Diaz AR, Core LJ, Jiang M, Morelli M, Chiang CH, Szurmant H, Perego M.

J Bacteriol. 2012 Mar;194(6):1378-88. doi: 10.1128/JB.06747-11. Epub 2012 Jan 20.

17.

The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo.

Chopra VS, Hendrix DA, Core LJ, Tsui C, Lis JT, Levine M.

Mol Cell. 2011 Jun 24;42(6):837-44. doi: 10.1016/j.molcel.2011.05.009.

18.

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.

19.

X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila.

Larschan E, Bishop EP, Kharchenko PV, Core LJ, Lis JT, Park PJ, Kuroda MI.

Nature. 2011 Mar 3;471(7336):115-8. doi: 10.1038/nature09757.

20.

Paused Pol II captures enhancer activity and acts as a potent insulator.

Core LJ, Lis JT.

Genes Dev. 2009 Jul 15;23(14):1606-12. doi: 10.1101/gad.1827709.

21.

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.

PMID:
19597342
22.

Postrecruitment regulation of RNA polymerase II directs rapid signaling responses at the promoters of estrogen target genes.

Kininis M, Isaacs GD, Core LJ, Hah N, Kraus WL.

Mol Cell Biol. 2009 Mar;29(5):1123-33. doi: 10.1128/MCB.00841-08. Epub 2008 Dec 22.

23.

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.

24.

Transcription regulation through promoter-proximal pausing of RNA polymerase II.

Core LJ, Lis JT.

Science. 2008 Mar 28;319(5871):1791-2. doi: 10.1126/science.1150843.

25.

Breaking barriers to transcription elongation.

Saunders A, Core LJ, Lis JT.

Nat Rev Mol Cell Biol. 2006 Aug;7(8):557-67. Review. No abstract available.

PMID:
16936696
26.

A free terminal carboxylate group is required for PhrA pentapeptide inhibition of RapA phosphatase.

Core LJ, Ishikawa S, Perego M.

Peptides. 2001 Oct;22(10):1549-53.

PMID:
11587784

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