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Items: 28

1.

Characterization of novel primary miRNA transcription units in human cells using Bru-seq nascent RNA sequencing.

Bedi K, Paulsen MT, Wilson TE, Ljungman M.

NAR Genom Bioinform. 2020 Mar;2(1):lqz014. doi: 10.1093/nargab/lqz014. Epub 2019 Oct 30.

2.

Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication.

Sima J, Chakraborty A, Dileep V, Michalski M, Klein KN, Holcomb NP, Turner JL, Paulsen MT, Rivera-Mulia JC, Trevilla-Garcia C, Bartlett DA, Zhao PA, Washburn BK, Nora EP, Kraft K, Mundlos S, Bruneau BG, Ljungman M, Fraser P, Ay F, Gilbert DM.

Cell. 2019 Feb 7;176(4):816-830.e18. doi: 10.1016/j.cell.2018.11.036. Epub 2018 Dec 27.

PMID:
30595451
3.

Abnormal RNA stability in amyotrophic lateral sclerosis.

Tank EM, Figueroa-Romero C, Hinder LM, Bedi K, Archbold HC, Li X, Weskamp K, Safren N, Paez-Colasante X, Pacut C, Thumma S, Paulsen MT, Guo K, Hur J, Ljungman M, Feldman EL, Barmada SJ.

Nat Commun. 2018 Jul 20;9(1):2845. doi: 10.1038/s41467-018-05049-z.

4.

Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression.

Zhang Y, Pitchiaya S, Cieślik M, Niknafs YS, Tien JC, Hosono Y, Iyer MK, Yazdani S, Subramaniam S, Shukla SK, Jiang X, Wang L, Liu TY, Uhl M, Gawronski AR, Qiao Y, Xiao L, Dhanasekaran SM, Juckette KM, Kunju LP, Cao X, Patel U, Batish M, Shukla GC, Paulsen MT, Ljungman M, Jiang H, Mehra R, Backofen R, Sahinalp CS, Freier SM, Watt AT, Guo S, Wei JT, Feng FY, Malik R, Chinnaiyan AM.

Nat Genet. 2018 Jun;50(6):814-824. doi: 10.1038/s41588-018-0120-1. Epub 2018 May 28.

5.

Transcriptional and post-transcriptional regulation of the ionizing radiation response by ATM and p53.

Venkata Narayanan I, Paulsen MT, Bedi K, Berg N, Ljungman EA, Francia S, Veloso A, Magnuson B, di Fagagna FD, Wilson TE, Ljungman M.

Sci Rep. 2017 Mar 3;7:43598. doi: 10.1038/srep43598.

6.

Gene length as a biological timer to establish temporal transcriptional regulation.

Kirkconnell KS, Magnuson B, Paulsen MT, Lu B, Bedi K, Ljungman M.

Cell Cycle. 2017 Feb;16(3):259-270. doi: 10.1080/15384101.2016.1234550. Epub 2017 Jan 5.

7.

Capturing the dynamic nascent transcriptome during acute cellular responses: The serum response.

Kirkconnell KS, Paulsen MT, Magnuson B, Bedi K, Ljungman M.

Biol Open. 2016 Jun 15;5(6):837-47. doi: 10.1242/bio.019323.

8.

Identifying transcription start sites and active enhancer elements using BruUV-seq.

Magnuson B, Veloso A, Kirkconnell KS, de Andrade Lima LC, Paulsen MT, Ljungman EA, Bedi K, Prasad J, Wilson TE, Ljungman M.

Sci Rep. 2015 Dec 11;5:17978. doi: 10.1038/srep17978.

9.

Oncogenic fusion protein EWS-FLI1 is a network hub that regulates alternative splicing.

Selvanathan SP, Graham GT, Erkizan HV, Dirksen U, Natarajan TG, Dakic A, Yu S, Liu X, Paulsen MT, Ljungman ME, Wu CH, Lawlor ER, Üren A, Toretsky JA.

Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):E1307-16. doi: 10.1073/pnas.1500536112. Epub 2015 Mar 3.

10.

DNA repair and recovery of RNA synthesis following exposure to ultraviolet light are delayed in long genes.

Andrade-Lima LC, Veloso A, Paulsen MT, Menck CF, Ljungman M.

Nucleic Acids Res. 2015 Mar 11;43(5):2744-56. doi: 10.1093/nar/gkv148. Epub 2015 Feb 26.

11.

Effects of physiological and synthetic IAP antagonism on c-IAP-dependent signaling.

Kocab AJ, Veloso A, Paulsen MT, Ljungman M, Duckett CS.

Oncogene. 2015 Oct;34(43):5472-81. doi: 10.1038/onc.2015.3. Epub 2015 Feb 9.

12.

Zinc finger protein 407 (ZFP407) regulates insulin-stimulated glucose uptake and glucose transporter 4 (Glut4) mRNA.

Buchner DA, Charrier A, Srinivasan E, Wang L, Paulsen MT, Ljungman M, Bridges D, Saltiel AR.

J Biol Chem. 2015 Mar 6;290(10):6376-86. doi: 10.1074/jbc.M114.623736. Epub 2015 Jan 16.

13.

The long non-coding RNA PCAT-1 promotes prostate cancer cell proliferation through cMyc.

Prensner JR, Chen W, Han S, Iyer MK, Cao Q, Kothari V, Evans JR, Knudsen KE, Paulsen MT, Ljungman M, Lawrence TS, Chinnaiyan AM, Feng FY.

Neoplasia. 2014 Nov 20;16(11):900-8. doi: 10.1016/j.neo.2014.09.001. eCollection 2014 Nov.

14.

Effects of NaCl substitution on the sensory properties of sausages: temporal aspects.

Paulsen MT, Nys A, Kvarberg R, Hersleth M.

Meat Sci. 2014 Oct;98(2):164-70. doi: 10.1016/j.meatsci.2014.05.020. Epub 2014 Jun 2.

PMID:
24960637
15.

Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications.

Veloso A, Kirkconnell KS, Magnuson B, Biewen B, Paulsen MT, Wilson TE, Ljungman M.

Genome Res. 2014 Jun;24(6):896-905. doi: 10.1101/gr.171405.113. Epub 2014 Apr 8.

16.

Genome-wide transcriptional effects of the anti-cancer agent camptothecin.

Veloso A, Biewen B, Paulsen MT, Berg N, Carmo de Andrade Lima L, Prasad J, Bedi K, Magnuson B, Wilson TE, Ljungman M.

PLoS One. 2013 Oct 23;8(10):e78190. doi: 10.1371/journal.pone.0078190. eCollection 2013.

17.

Use of Bru-Seq and BruChase-Seq for genome-wide assessment of the synthesis and stability of RNA.

Paulsen MT, Veloso A, Prasad J, Bedi K, Ljungman EA, Magnuson B, Wilson TE, Ljungman M.

Methods. 2014 May 1;67(1):45-54. doi: 10.1016/j.ymeth.2013.08.015. Epub 2013 Aug 21.

18.

Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response.

Paulsen MT, Veloso A, Prasad J, Bedi K, Ljungman EA, Tsan YC, Chang CW, Tarrier B, Washburn JG, Lyons R, Robinson DR, Kumar-Sinha C, Wilson TE, Ljungman M.

Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2240-5. doi: 10.1073/pnas.1219192110. Epub 2013 Jan 23.

19.

Chfr and RNF8 synergistically regulate ATM activation.

Wu J, Chen Y, Lu LY, Wu Y, Paulsen MT, Ljungman M, Ferguson DO, Yu X.

Nat Struct Mol Biol. 2011 Jun 26;18(7):761-8. doi: 10.1038/nsmb.2078.

20.

Differential roles for DNA polymerases eta, zeta, and REV1 in lesion bypass of intrastrand versus interstrand DNA cross-links.

Hicks JK, Chute CL, Paulsen MT, Ragland RL, Howlett NG, Guéranger Q, Glover TW, Canman CE.

Mol Cell Biol. 2010 Mar;30(5):1217-30. doi: 10.1128/MCB.00993-09. Epub 2009 Dec 22.

21.

Psoralen-induced DNA interstrand cross-links block transcription and induce p53 in an ataxia-telangiectasia and rad3-related-dependent manner.

Derheimer FA, Hicks JK, Paulsen MT, Canman CE, Ljungman M.

Mol Pharmacol. 2009 Mar;75(3):599-607. doi: 10.1124/mol.108.051698. Epub 2008 Dec 8.

22.

RPA and ATR link transcriptional stress to p53.

Derheimer FA, O'Hagan HM, Krueger HM, Hanasoge S, Paulsen MT, Ljungman M.

Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12778-83. Epub 2007 Jul 6.

23.

The p53-targeting human phosphatase hCdc14A interacts with the Cdk1/cyclin B complex and is differentially expressed in human cancers.

Paulsen MT, Starks AM, Derheimer FA, Hanasoge S, Li L, Dixon JE, Ljungman M.

Mol Cancer. 2006 Jun 19;5:25.

24.
25.

Phenylbutyrate inhibits the invasive properties of prostate and breast cancer cell lines in the sea urchin embryo basement membrane invasion assay.

Dyer ES, Paulsen MT, Markwart SM, Goh M, Livant DL, Ljungman M.

Int J Cancer. 2002 Oct 10;101(5):496-9.

26.

Induction of ser15 and lys382 modifications of p53 by blockage of transcription elongation.

Ljungman M, O'Hagan HM, Paulsen MT.

Oncogene. 2001 Sep 20;20(42):5964-71.

27.

Phenylbutyrate attenuates the expression of Bcl-X(L), DNA-PK, caveolin-1, and VEGF in prostate cancer cells.

Goh M, Chen F, Paulsen MT, Yeager AM, Dyer ES, Ljungman M.

Neoplasia. 2001 Jul-Aug;3(4):331-8.

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