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Items: 39

1.

Revealing a human p53 universe.

Nguyen TT, Grimm SA, Bushel PR, Li J, Li Y, Bennett BD, Lavender CA, Ward JM, Fargo DC, Anderson CW, Li L, Resnick MA, Menendez D.

Nucleic Acids Res. 2018 Sep 19;46(16):8153-8167. doi: 10.1093/nar/gky720.

PMID:
30107566
2.

Muver, a computational framework for accurately calling accumulated mutations.

Burkholder AB, Lujan SA, Lavender CA, Grimm SA, Kunkel TA, Fargo DC.

BMC Genomics. 2018 May 9;19(1):345. doi: 10.1186/s12864-018-4753-3.

3.

Widespread transcriptional pausing and elongation control at enhancers.

Henriques T, Scruggs BS, Inouye MO, Muse GW, Williams LH, Burkholder AB, Lavender CA, Fargo DC, Adelman K.

Genes Dev. 2018 Jan 1;32(1):26-41. doi: 10.1101/gad.309351.117. Epub 2018 Jan 29.

4.

Methionine metabolism is essential for SIRT1-regulated mouse embryonic stem cell maintenance and embryonic development.

Tang S, Fang Y, Huang G, Xu X, Padilla-Banks E, Fan W, Xu Q, Sanderson SM, Foley JF, Dowdy S, McBurney MW, Fargo DC, Williams CJ, Locasale JW, Guan Z, Li X.

EMBO J. 2017 Nov 2;36(21):3175-3193. doi: 10.15252/embj.201796708. Epub 2017 Oct 11.

PMID:
29021282
5.

Intestinal Epithelial Sirtuin 1 Regulates Intestinal Inflammation During Aging in Mice by Altering the Intestinal Microbiota.

Wellman AS, Metukuri MR, Kazgan N, Xu X, Xu Q, Ren NSX, Czopik A, Shanahan MT, Kang A, Chen W, Azcarate-Peril MA, Gulati AS, Fargo DC, Guarente L, Li X.

Gastroenterology. 2017 Sep;153(3):772-786. doi: 10.1053/j.gastro.2017.05.022. Epub 2017 May 26.

6.

ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data.

Lavender CA, Shapiro AJ, Burkholder AB, Bennett BD, Adelman K, Fargo DC.

Nucleic Acids Res. 2017 Jun 2;45(10):5678-5690. doi: 10.1093/nar/gkx270.

7.

The phosphorylation status of T522 modulates tissue-specific functions of SIRT1 in energy metabolism in mice.

Lu J, Xu Q, Ji M, Guo X, Xu X, Fargo DC, Li X.

EMBO Rep. 2017 May;18(5):841-857. doi: 10.15252/embr.201643803. Epub 2017 Mar 31.

8.

Haploinsufficiency of SIRT1 Enhances Glutamine Metabolism and Promotes Cancer Development.

Ren NSX, Ji M, Tokar EJ, Busch EL, Xu X, Lewis D, Li X, Jin A, Zhang Y, Wu WKK, Huang W, Li L, Fargo DC, Keku TO, Sandler RS, Li X.

Curr Biol. 2017 Feb 20;27(4):483-494. doi: 10.1016/j.cub.2016.12.047. Epub 2017 Feb 2.

9.

The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts.

Saini N, Roberts SA, Klimczak LJ, Chan K, Grimm SA, Dai S, Fargo DC, Boyer JC, Kaufmann WK, Taylor JA, Lee E, Cortes-Ciriano I, Park PJ, Schurman SH, Malc EP, Mieczkowski PA, Gordenin DA.

PLoS Genet. 2016 Oct 27;12(10):e1006385. doi: 10.1371/journal.pgen.1006385. eCollection 2016 Oct.

10.

CNOT3-Dependent mRNA Deadenylation Safeguards the Pluripotent State.

Zheng X, Yang P, Lackford B, Bennett BD, Wang L, Li H, Wang Y, Miao Y, Foley JF, Fargo DC, Jin Y, Williams CJ, Jothi R, Hu G.

Stem Cell Reports. 2016 Nov 8;7(5):897-910. doi: 10.1016/j.stemcr.2016.09.007. Epub 2016 Oct 13.

11.

INO80 is required for oncogenic transcription and tumor growth in non-small cell lung cancer.

Zhang S, Zhou B, Wang L, Li P, Bennett BD, Snyder R, Garantziotis S, Fargo DC, Cox AD, Chen L, Hu G.

Oncogene. 2017 Mar;36(10):1430-1439. doi: 10.1038/onc.2016.311. Epub 2016 Sep 19.

PMID:
27641337
12.

Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters.

Lavender CA, Cannady KR, Hoffman JA, Trotter KW, Gilchrist DA, Bennett BD, Burkholder AB, Burd CJ, Fargo DC, Archer TK.

PLoS Genet. 2016 Aug 3;12(8):e1006224. doi: 10.1371/journal.pgen.1006224. eCollection 2016 Aug.

13.

RNA polymerase II promoter-proximal pausing in mammalian long non-coding genes.

Bunch H, Lawney BP, Burkholder A, Ma D, Zheng X, Motola S, Fargo DC, Levine SS, Wang YE, Hu G.

Genomics. 2016 Aug;108(2):64-77. doi: 10.1016/j.ygeno.2016.07.003. Epub 2016 Jul 16.

PMID:
27432546
14.

A Novel Analytical Strategy to Identify Fusion Transcripts between Repetitive Elements and Protein Coding-Exons Using RNA-Seq.

Wang T, Santos JH, Feng J, Fargo DC, Shen L, Riadi G, Keeley E, Rosh ZS, Nestler EJ, Woychik RP.

PLoS One. 2016 Jul 14;11(7):e0159028. doi: 10.1371/journal.pone.0159028. eCollection 2016.

15.

INO80 governs superenhancer-mediated oncogenic transcription and tumor growth in melanoma.

Zhou B, Wang L, Zhang S, Bennett BD, He F, Zhang Y, Xiong C, Han L, Diao L, Li P, Fargo DC, Cox AD, Hu G.

Genes Dev. 2016 Jun 15;30(12):1440-53. doi: 10.1101/gad.277178.115.

16.

A Serial shRNA Screen for Roadblocks to Reprogramming Identifies the Protein Modifier SUMO2.

Borkent M, Bennett BD, Lackford B, Bar-Nur O, Brumbaugh J, Wang L, Du Y, Fargo DC, Apostolou E, Cheloufi S, Maherali N, Elledge SJ, Hu G, Hochedlinger K.

Stem Cell Reports. 2016 May 10;6(5):704-716. doi: 10.1016/j.stemcr.2016.02.004. Epub 2016 Mar 3.

17.

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers.

Chan K, Roberts SA, Klimczak LJ, Sterling JF, Saini N, Malc EP, Kim J, Kwiatkowski DJ, Fargo DC, Mieczkowski PA, Getz G, Gordenin DA.

Nat Genet. 2015 Sep;47(9):1067-72. doi: 10.1038/ng.3378. Epub 2015 Aug 10.

18.

Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin.

Scruggs BS, Gilchrist DA, Nechaev S, Muse GW, Burkholder A, Fargo DC, Adelman K.

Mol Cell. 2015 Jun 18;58(6):1101-12. doi: 10.1016/j.molcel.2015.04.006. Epub 2015 May 28.

19.

Pausing of RNA polymerase II regulates mammalian developmental potential through control of signaling networks.

Williams LH, Fromm G, Gokey NG, Henriques T, Muse GW, Burkholder A, Fargo DC, Hu G, Adelman K.

Mol Cell. 2015 Apr 16;58(2):311-322. doi: 10.1016/j.molcel.2015.02.003. Epub 2015 Mar 12.

20.

Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation.

Clausen AR, Lujan SA, Burkholder AB, Orebaugh CD, Williams JS, Clausen MF, Malc EP, Mieczkowski PA, Fargo DC, Smith DJ, Kunkel TA.

Nat Struct Mol Biol. 2015 Mar;22(3):185-91. doi: 10.1038/nsmb.2957. Epub 2015 Jan 26.

21.

Post-transcriptional regulation of transcript abundance by a conserved member of the tristetraprolin family in Candida albicans.

Wells ML, Washington OL, Hicks SN, Nobile CJ, Hartooni N, Wilson GM, Zucconi BE, Huang W, Li L, Fargo DC, Blackshear PJ.

Mol Microbiol. 2015 Mar;95(6):1036-53. doi: 10.1111/mmi.12913. Epub 2015 Jan 30.

22.

Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition.

Lujan SA, Clausen AR, Clark AB, MacAlpine HK, MacAlpine DM, Malc EP, Mieczkowski PA, Burkholder AB, Fargo DC, Gordenin DA, Kunkel TA.

Genome Res. 2014 Nov;24(11):1751-64. doi: 10.1101/gr.178335.114. Epub 2014 Sep 12.

23.

SIRT1-mediated deacetylation of CRABPII regulates cellular retinoic acid signaling and modulates embryonic stem cell differentiation.

Tang S, Huang G, Fan W, Chen Y, Ward JM, Xu X, Xu Q, Kang A, McBurney MW, Fargo DC, Hu G, Baumgart-Vogt E, Zhao Y, Li X.

Mol Cell. 2014 Sep 18;55(6):843-855. doi: 10.1016/j.molcel.2014.07.011. Epub 2014 Aug 21.

24.

INO80 facilitates pluripotency gene activation in embryonic stem cell self-renewal, reprogramming, and blastocyst development.

Wang L, Du Y, Ward JM, Shimbo T, Lackford B, Zheng X, Miao YL, Zhou B, Han L, Fargo DC, Jothi R, Williams CJ, Wade PA, Hu G.

Cell Stem Cell. 2014 May 1;14(5):575-91. doi: 10.1016/j.stem.2014.02.013.

25.

The THO complex regulates pluripotency gene mRNA export and controls embryonic stem cell self-renewal and somatic cell reprogramming.

Wang L, Miao YL, Zheng X, Lackford B, Zhou B, Han L, Yao C, Ward JM, Burkholder A, Lipchina I, Fargo DC, Hochedlinger K, Shi Y, Williams CJ, Hu G.

Cell Stem Cell. 2013 Dec 5;13(6):676-90. doi: 10.1016/j.stem.2013.10.008.

26.

Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals.

Henriques T, Gilchrist DA, Nechaev S, Bern M, Muse GW, Burkholder A, Fargo DC, Adelman K.

Mol Cell. 2013 Nov 21;52(4):517-28. doi: 10.1016/j.molcel.2013.10.001. Epub 2013 Oct 31.

27.

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.

28.

Posttranscriptional regulation of cell-cell interaction protein-encoding transcripts by Zfs1p in Schizosaccharomyces pombe.

Wells ML, Huang W, Li L, Gerrish KE, Fargo DC, Ozsolak F, Blackshear PJ.

Mol Cell Biol. 2012 Oct;32(20):4206-14. Epub 2012 Aug 20.

29.

Regulating the regulators: the pervasive effects of Pol II pausing on stimulus-responsive gene networks.

Gilchrist DA, Fromm G, dos Santos G, Pham LN, McDaniel IE, Burkholder A, Fargo DC, Adelman K.

Genes Dev. 2012 May 1;26(9):933-44. doi: 10.1101/gad.187781.112.

30.

Rapid activity-induced transcription of Arc and other IEGs relies on poised RNA polymerase II.

Saha RN, Wissink EM, Bailey ER, Zhao M, Fargo DC, Hwang JY, Daigle KR, Fenn JD, Adelman K, Dudek SM.

Nat Neurosci. 2011 May 29;14(7):848-56. doi: 10.1038/nn.2839.

31.

Expanded methyl-sensitive cut counting reveals hypomethylation as an epigenetic state that highlights functional sequences of the genome.

Colaneri A, Staffa N, Fargo DC, Gao Y, Wang T, Peddada SD, Birnbaumer L.

Proc Natl Acad Sci U S A. 2011 Jun 7;108(23):9715-20. doi: 10.1073/pnas.1105713108. Epub 2011 May 20. Erratum in: Proc Natl Acad Sci U S A. 2013 Mar 19;110(12):4853.

32.

Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation.

Gilchrist DA, Dos Santos G, Fargo DC, Xie B, Gao Y, Li L, Adelman K.

Cell. 2010 Nov 12;143(4):540-51. doi: 10.1016/j.cell.2010.10.004.

33.

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus).

Stajich JE, Wilke SK, Ahrén D, Au CH, Birren BW, Borodovsky M, Burns C, Canbäck B, Casselton LA, Cheng CK, Deng J, Dietrich FS, Fargo DC, Farman ML, Gathman AC, Goldberg J, Guigó R, Hoegger PJ, Hooker JB, Huggins A, James TY, Kamada T, Kilaru S, Kodira C, Kües U, Kupfer D, Kwan HS, Lomsadze A, Li W, Lilly WW, Ma LJ, Mackey AJ, Manning G, Martin F, Muraguchi H, Natvig DO, Palmerini H, Ramesh MA, Rehmeyer CJ, Roe BA, Shenoy N, Stanke M, Ter-Hovhannisyan V, Tunlid A, Velagapudi R, Vision TJ, Zeng Q, Zolan ME, Pukkila PJ.

Proc Natl Acad Sci U S A. 2010 Jun 29;107(26):11889-94. doi: 10.1073/pnas.1003391107. Epub 2010 Jun 14.

34.

Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila.

Nechaev S, Fargo DC, dos Santos G, Liu L, Gao Y, Adelman K.

Science. 2010 Jan 15;327(5963):335-8. doi: 10.1126/science.1181421. Epub 2009 Dec 10.

35.

Using ChIP-chip and ChIP-seq to study the regulation of gene expression: genome-wide localization studies reveal widespread regulation of transcription elongation.

Gilchrist DA, Fargo DC, Adelman K.

Methods. 2009 Aug;48(4):398-408. doi: 10.1016/j.ymeth.2009.02.024. Epub 2009 Mar 9. Review.

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