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Determining cellular CTCF and cohesin abundances to constrain 3D genome models.

Cattoglio C, Pustova I, Walther N, Ho JJ, Hantsche-Grininger M, Inouye CJ, Hossain MJ, Dailey GM, Ellenberg J, Darzacq X, Tjian R, Hansen AS.

Elife. 2019 Jun 17;8. pii: e40164. doi: 10.7554/eLife.40164.


Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation.

McSwiggen DT, Hansen AS, Teves SS, Marie-Nelly H, Hao Y, Heckert AB, Umemoto KK, Dugast-Darzacq C, Tjian R, Darzacq X.

Elife. 2019 May 7;8. pii: e47098. doi: 10.7554/eLife.47098.


Evidence for an Integrated Gene Repression Mechanism Based on mRNA Isoform Toggling in Human Cells.

Hollerer I, Barker JC, Jorgensen V, Tresenrider A, Dugast-Darzacq C, Chan LY, Darzacq X, Tjian R, Ünal E, Brar GA.

G3 (Bethesda). 2019 Apr 9;9(4):1045-1053. doi: 10.1534/g3.118.200802.


A stable mode of bookmarking by TBP recruits RNA polymerase II to mitotic chromosomes.

Teves SS, An L, Bhargava-Shah A, Xie L, Darzacq X, Tjian R.

Elife. 2018 Jun 25;7. pii: e35621. doi: 10.7554/eLife.35621.


Imaging dynamic and selective low-complexity domain interactions that control gene transcription.

Chong S, Dugast-Darzacq C, Liu Z, Dong P, Dailey GM, Cattoglio C, Heckert A, Banala S, Lavis L, Darzacq X, Tjian R.

Science. 2018 Jul 27;361(6400). pii: eaar2555. doi: 10.1126/science.aar2555. Epub 2018 Jun 21.


dCas9-targeted locus-specific protein isolation method identifies histone gene regulators.

Tsui C, Inouye C, Levy M, Lu A, Florens L, Washburn MP, Tjian R.

Proc Natl Acad Sci U S A. 2018 Mar 20;115(12):E2734-E2741. doi: 10.1073/pnas.1718844115. Epub 2018 Mar 5.


Visualizing transcription factor dynamics in living cells.

Liu Z, Tjian R.

J Cell Biol. 2018 Apr 2;217(4):1181-1191. doi: 10.1083/jcb.201710038. Epub 2018 Jan 29. Review.


Robust model-based analysis of single-particle tracking experiments with Spot-On.

Hansen AS, Woringer M, Grimm JB, Lavis LD, Tjian R, Darzacq X.

Elife. 2018 Jan 4;7. pii: e33125. doi: 10.7554/eLife.33125.


Genomes in Focus: Development and Applications of CRISPR-Cas9 Imaging Technologies.

Knight SC, Tjian R, Doudna JA.

Angew Chem Int Ed Engl. 2018 Apr 9;57(16):4329-4337. doi: 10.1002/anie.201709201. Epub 2018 Feb 28. Review.


Recent evidence that TADs and chromatin loops are dynamic structures.

Hansen AS, Cattoglio C, Darzacq X, Tjian R.

Nucleus. 2018 Jan 1;9(1):20-32. doi: 10.1080/19491034.2017.1389365. Epub 2017 Dec 14.


A dynamic interplay of enhancer elements regulates Klf4 expression in naïve pluripotency.

Xie L, Torigoe SE, Xiao J, Mai DH, Li L, Davis FP, Dong P, Marie-Nelly H, Grimm J, Lavis L, Darzacq X, Cattoglio C, Liu Z, Tjian R.

Genes Dev. 2017 Sep 1;31(17):1795-1808. doi: 10.1101/gad.303321.117.


Measuring dynamics of eukaryotic transcription initiation: Challenges, insights and opportunities.

Zhang Z, Tjian R.

Transcription. 2018;9(3):159-165. doi: 10.1080/21541264.2017.1363017. Epub 2017 Oct 9.


Not just Salk.

Greider C, Hopkins N, Steitz J, Amon A, Asai D, Barres B, Bass B, Bassler B, Birgeneau R, Bjorkman P, Botchan M, Brugge J, Cech T, Colwell R, Craig N, deLange T, Eisen M, Gottesman S, Green R, Handelsman J, Kimble J, King MC, Lehmann R, Marder E, Mullins D, O'Shea E, Schmid S, Seydoux G, Spradling A, Storz G, Szostak J, Telesnitsky A, Tilghman S, Tjian R, Vale R, Wolberger C, Zakian V.

Science. 2017 Sep 15;357(6356):1105-1106. doi: 10.1126/science.aao6221. No abstract available.


Regulation of DNA demethylation by the XPC DNA repair complex in somatic and pluripotent stem cells.

Ho JJ, Cattoglio C, McSwiggen DT, Tjian R, Fong YW.

Genes Dev. 2017 Apr 15;31(8):830-844. doi: 10.1101/gad.295741.116.


CTCF and cohesin regulate chromatin loop stability with distinct dynamics.

Hansen AS, Pustova I, Cattoglio C, Tjian R, Darzacq X.

Elife. 2017 May 3;6. pii: e25776. doi: 10.7554/eLife.25776.


Dual Mechanism of Rag Gene Repression by c-Myb during Pre-B Cell Proliferation.

Timblin GA, Xie L, Tjian R, Schlissel MS.

Mol Cell Biol. 2017 May 31;37(12). pii: e00437-16. doi: 10.1128/MCB.00437-16. Print 2017 Jun 15.


A dynamic mode of mitotic bookmarking by transcription factors.

Teves SS, An L, Hansen AS, Xie L, Darzacq X, Tjian R.

Elife. 2016 Nov 19;5. pii: e22280. doi: 10.7554/eLife.22280.


Rapid dynamics of general transcription factor TFIIB binding during preinitiation complex assembly revealed by single-molecule analysis.

Zhang Z, English BP, Grimm JB, Kazane SA, Hu W, Tsai A, Inouye C, You C, Piehler J, Schultz PG, Lavis LD, Revyakin A, Tjian R.

Genes Dev. 2016 Sep 15;30(18):2106-2118.


Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection.

East-Seletsky A, O'Connell MR, Knight SC, Burstein D, Cate JH, Tjian R, Doudna JA.

Nature. 2016 Oct 13;538(7624):270-273. doi: 10.1038/nature19802. Epub 2016 Sep 26.


Real-time imaging of Huntingtin aggregates diverting target search and gene transcription.

Li L, Liu H, Dong P, Li D, Legant WR, Grimm JB, Lavis LD, Betzig E, Tjian R, Liu Z.

Elife. 2016 Aug 3;5. pii: e17056. doi: 10.7554/eLife.17056.


Near-atomic resolution visualization of human transcription promoter opening.

He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E.

Nature. 2016 May 19;533(7603):359-65. doi: 10.1038/nature17970. Epub 2016 May 11.


Nucleosomes impede Cas9 access to DNA in vivo and in vitro.

Horlbeck MA, Witkowsky LB, Guglielmi B, Replogle JM, Gilbert LA, Villalta JE, Torigoe SE, Tjian R, Weissman JS.

Elife. 2016 Mar 17;5. pii: e12677. doi: 10.7554/eLife.12677.


MEF2C and EBF1 Co-regulate B Cell-Specific Transcription.

Kong NR, Davis M, Chai L, Winoto A, Tjian R.

PLoS Genet. 2016 Feb 22;12(2):e1005845. doi: 10.1371/journal.pgen.1005845. eCollection 2016 Feb.


Imaging Transcription: Past, Present, and Future.

Coleman RA, Liu Z, Darzacq X, Tjian R, Singer RH, Lionnet T.

Cold Spring Harb Symp Quant Biol. 2015;80:1-8. doi: 10.1101/sqb.2015.80.027201. Epub 2016 Jan 13. Review.


Architecture of the human XPC DNA repair and stem cell coactivator complex.

Zhang ET, He Y, Grob P, Fong YW, Nogales E, Tjian R.

Proc Natl Acad Sci U S A. 2015 Dec 1;112(48):14817-22. doi: 10.1073/pnas.1520104112. Epub 2015 Nov 16.


Dynamics of CRISPR-Cas9 genome interrogation in living cells.

Knight SC, Xie L, Deng W, Guglielmi B, Witkowsky LB, Bosanac L, Zhang ET, El Beheiry M, Masson JB, Dahan M, Liu Z, Doudna JA, Tjian R.

Science. 2015 Nov 13;350(6262):823-6. doi: 10.1126/science.aac6572.


A specific E3 ligase/deubiquitinase pair modulates TBP protein levels during muscle differentiation.

Li L, Martinez SS, Hu W, Liu Z, Tjian R.

Elife. 2015 Sep 22;4:e08536. doi: 10.7554/eLife.08536.


CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells.

Deng W, Shi X, Tjian R, Lionnet T, Singer RH.

Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):11870-5. doi: 10.1073/pnas.1515692112. Epub 2015 Aug 31.


Chemical perturbation of an intrinsically disordered region of TFIID distinguishes two modes of transcription initiation.

Zhang Z, Boskovic Z, Hussain MM, Hu W, Inouye C, Kim HJ, Abole AK, Doud MK, Lewis TA, Koehler AN, Schreiber SL, Tjian R.

Elife. 2015 Aug 28;4. doi: 10.7554/eLife.07777.


Functional and mechanistic studies of XPC DNA-repair complex as transcriptional coactivator in embryonic stem cells.

Cattoglio C, Zhang ET, Grubisic I, Chiba K, Fong YW, Tjian R.

Proc Natl Acad Sci U S A. 2015 May 5;112(18):E2317-26. doi: 10.1073/pnas.1505569112. Epub 2015 Apr 21.


Supporting biomedical research: meeting challenges and opportunities at HHMI.

Tjian R.

JAMA. 2015 Jan 13;313(2):133-4. doi: 10.1001/jama.2014.16543. No abstract available.


3D imaging of Sox2 enhancer clusters in embryonic stem cells.

Liu Z, Legant WR, Chen BC, Li L, Grimm JB, Lavis LD, Betzig E, Tjian R.

Elife. 2014 Dec 24;3:e04236. doi: 10.7554/eLife.04236.


The dyskerin ribonucleoprotein complex as an OCT4/SOX2 coactivator in embryonic stem cells.

Fong YW, Ho JJ, Inouye C, Tjian R.

Elife. 2014 Nov 19;3. doi: 10.7554/eLife.03573.


Core promoter factor TAF9B regulates neuronal gene expression.

Herrera FJ, Yamaguchi T, Roelink H, Tjian R.

Elife. 2014 Jul 8;3:e02559. doi: 10.7554/eLife.02559.


TAF7L modulates brown adipose tissue formation.

Zhou H, Wan B, Grubisic I, Kaplan T, Tjian R.

Elife. 2014 May 29;3. doi: 10.7554/eLife.02811.


Looping back to leap forward: transcription enters a new era.

Levine M, Cattoglio C, Tjian R.

Cell. 2014 Mar 27;157(1):13-25. doi: 10.1016/j.cell.2014.02.009. Review.


Single-molecule dynamics of enhanceosome assembly in embryonic stem cells.

Chen J, Zhang Z, Li L, Chen BC, Revyakin A, Hajj B, Legant W, Dahan M, Lionnet T, Betzig E, Tjian R, Liu Z.

Cell. 2014 Mar 13;156(6):1274-1285. doi: 10.1016/j.cell.2014.01.062.


Charting Brachyury-mediated developmental pathways during early mouse embryogenesis.

Lolas M, Valenzuela PD, Tjian R, Liu Z.

Proc Natl Acad Sci U S A. 2014 Mar 25;111(12):4478-83. doi: 10.1073/pnas.1402612111. Epub 2014 Mar 10.


Single-molecule tracking of the transcription cycle by sub-second RNA detection.

Zhang Z, Revyakin A, Grimm JB, Lavis LD, Tjian R.

Elife. 2014;3:e01775. doi: 10.7554/eLife.01775. Epub 2014 Jan 28.


The intertwined roles of transcription and repair proteins.

Fong YW, Cattoglio C, Tjian R.

Mol Cell. 2013 Nov 7;52(3):291-302. doi: 10.1016/j.molcel.2013.10.018. Review.


Taf7l cooperates with Trf2 to regulate spermiogenesis.

Zhou H, Grubisic I, Zheng K, He Y, Wang PJ, Kaplan T, Tjian R.

Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):16886-91. doi: 10.1073/pnas.1317034110. Epub 2013 Sep 30.


Gene-specific transcriptional mechanisms at the histone gene cluster revealed by single-cell imaging.

Guglielmi B, La Rochelle N, Tjian R.

Mol Cell. 2013 Aug 22;51(4):480-92. doi: 10.1016/j.molcel.2013.08.009.


Dual functions of TAF7L in adipocyte differentiation.

Zhou H, Kaplan T, Li Y, Grubisic I, Zhang Z, Wang PJ, Eisen MB, Tjian R.

Elife. 2013 Jan 8;2:e00170. doi: 10.7554/eLife.00170.


Transcription initiation by human RNA polymerase II visualized at single-molecule resolution.

Revyakin A, Zhang Z, Coleman RA, Li Y, Inouye C, Lucas JK, Park SR, Chu S, Tjian R.

Genes Dev. 2012 Aug 1;26(15):1691-702. doi: 10.1101/gad.194936.112. Epub 2012 Jul 18.


Transcriptional regulation by coactivators in embryonic stem cells.

Fong YW, Cattoglio C, Yamaguchi T, Tjian R.

Trends Cell Biol. 2012 Jun;22(6):292-8. doi: 10.1016/j.tcb.2012.04.002. Epub 2012 May 7. Review.


A DNA repair complex functions as an Oct4/Sox2 coactivator in embryonic stem cells.

Fong YW, Inouye C, Yamaguchi T, Cattoglio C, Grubisic I, Tjian R.

Cell. 2011 Sep 30;147(1):120-31. doi: 10.1016/j.cell.2011.08.038.


Control of embryonic stem cell lineage commitment by core promoter factor, TAF3.

Liu Z, Scannell DR, Eisen MB, Tjian R.

Cell. 2011 Sep 2;146(5):720-31. doi: 10.1016/j.cell.2011.08.005.


Sub-nuclear compartmentalization of core promoter factors and target genes.

Yao J, Tjian R.

Cell Cycle. 2011 Aug 1;10(15):2405-6. Epub 2011 Aug 1. No abstract available.


Core promoter recognition complex changes accompany liver development.

D'Alessio JA, Ng R, Willenbring H, Tjian R.

Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):3906-11. doi: 10.1073/pnas.1100640108. Epub 2011 Feb 22.


Subnuclear segregation of genes and core promoter factors in myogenesis.

Yao J, Fetter RD, Hu P, Betzig E, Tjian R.

Genes Dev. 2011 Mar 15;25(6):569-80. doi: 10.1101/gad.2021411. Epub 2011 Feb 28.

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