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Items: 23

1.

tRNA Genes Affect Chromosome Structure and Function via Local Effects.

Hamdani O, Dhillon N, Hsieh TS, Fujita T, Ocampo J, Kirkland JG, Lawrimore J, Kobayashi TJ, Friedman B, Fulton D, Wu KY, Chereji RV, Oki M, Bloom K, Clark DJ, Rando OJ, Kamakaka RT.

Mol Cell Biol. 2019 Apr 2;39(8). pii: e00432-18. doi: 10.1128/MCB.00432-18. Print 2019 Apr 15.

2.

Contrasting roles of the RSC and ISW1/CHD1 chromatin remodelers in RNA polymerase II elongation and termination.

Ocampo J, Chereji RV, Eriksson PR, Clark DJ.

Genome Res. 2019 Mar;29(3):407-417. doi: 10.1101/gr.242032.118. Epub 2019 Jan 25.

PMID:
30683752
3.

Mechanism of FACT removal from transcribed genes by anticancer drugs curaxins.

Chang HW, Valieva ME, Safina A, Chereji RV, Wang J, Kulaeva OI, Morozov AV, Kirpichnikov MP, Feofanov AV, Gurova KV, Studitsky VM.

Sci Adv. 2018 Nov 7;4(11):eaav2131. doi: 10.1126/sciadv.aav2131. eCollection 2018 Nov.

4.

Single-Molecule Analysis Reveals Linked Cycles of RSC Chromatin Remodeling and Ace1p Transcription Factor Binding in Yeast.

Mehta GD, Ball DA, Eriksson PR, Chereji RV, Clark DJ, McNally JG, Karpova TS.

Mol Cell. 2018 Dec 6;72(5):875-887.e9. doi: 10.1016/j.molcel.2018.09.009. Epub 2018 Oct 11.

PMID:
30318444
5.

SWI/SNF and RSC cooperate to reposition and evict promoter nucleosomes at highly expressed genes in yeast.

Rawal Y, Chereji RV, Qiu H, Ananthakrishnan S, Govind CK, Clark DJ, Hinnebusch AG.

Genes Dev. 2018 May 1;32(9-10):695-710. doi: 10.1101/gad.312850.118. Epub 2018 May 21.

6.

SPT6 interacts with NSD2 and facilitates interferon-induced transcription.

Ouda R, Sarai N, Nehru V, Patel MC, Debrosse M, Bachu M, Chereji RV, Eriksson PR, Clark DJ, Ozato K.

FEBS Lett. 2018 May;592(10):1681-1692. doi: 10.1002/1873-3468.13069. Epub 2018 May 20.

7.

Gcn4 Binding in Coding Regions Can Activate Internal and Canonical 5' Promoters in Yeast.

Rawal Y, Chereji RV, Valabhoju V, Qiu H, Ocampo J, Clark DJ, Hinnebusch AG.

Mol Cell. 2018 Apr 19;70(2):297-311.e4. doi: 10.1016/j.molcel.2018.03.007. Epub 2018 Apr 5.

8.

Major Determinants of Nucleosome Positioning.

Chereji RV, Clark DJ.

Biophys J. 2018 May 22;114(10):2279-2289. doi: 10.1016/j.bpj.2018.03.015. Epub 2018 Apr 6. Review.

9.

Precise genome-wide mapping of single nucleosomes and linkers in vivo.

Chereji RV, Ramachandran S, Bryson TD, Henikoff S.

Genome Biol. 2018 Feb 9;19(1):19. doi: 10.1186/s13059-018-1398-0.

10.

Conventional and pioneer modes of glucocorticoid receptor interaction with enhancer chromatin in vivo.

Johnson TA, Chereji RV, Stavreva DA, Morris SA, Hager GL, Clark DJ.

Nucleic Acids Res. 2018 Jan 9;46(1):203-214. doi: 10.1093/nar/gkx1044.

11.

Mediator binds to boundaries of chromosomal interaction domains and to proteins involved in DNA looping, RNA metabolism, chromatin remodeling, and actin assembly.

Chereji RV, Bharatula V, Elfving N, Blomberg J, Larsson M, Morozov AV, Broach JR, Björklund S.

Nucleic Acids Res. 2017 Sep 6;45(15):8806-8821. doi: 10.1093/nar/gkx491.

12.

MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers.

Chereji RV, Ocampo J, Clark DJ.

Mol Cell. 2017 Feb 2;65(3):565-577.e3. doi: 10.1016/j.molcel.2016.12.009.

13.

The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo.

Ocampo J, Chereji RV, Eriksson PR, Clark DJ.

Nucleic Acids Res. 2016 Jun 2;44(10):4625-35. doi: 10.1093/nar/gkw068. Epub 2016 Feb 9.

14.

Genome-wide cooperation by HAT Gcn5, remodeler SWI/SNF, and chaperone Ydj1 in promoter nucleosome eviction and transcriptional activation.

Qiu H, Chereji RV, Hu C, Cole HA, Rawal Y, Clark DJ, Hinnebusch AG.

Genome Res. 2016 Feb;26(2):211-25. doi: 10.1101/gr.196337.115. Epub 2015 Nov 24.

15.

Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster.

Chereji RV, Kan TW, Grudniewska MK, Romashchenko AV, Berezikov E, Zhimulev IF, Guryev V, Morozov AV, Moshkin YM.

Nucleic Acids Res. 2016 Feb 18;44(3):1036-51. doi: 10.1093/nar/gkv978. Epub 2015 Oct 1.

16.

Heavy transcription of yeast genes correlates with differential loss of histone H2B relative to H4 and queued RNA polymerases.

Cole HA, Ocampo J, Iben JR, Chereji RV, Clark DJ.

Nucleic Acids Res. 2014 Nov 10;42(20):12512-22. doi: 10.1093/nar/gku1013. Epub 2014 Oct 27.

17.

Functional roles of nucleosome stability and dynamics.

Chereji RV, Morozov AV.

Brief Funct Genomics. 2015 Jan;14(1):50-60. doi: 10.1093/bfgp/elu038. Epub 2014 Sep 30. Review.

18.

RSC-dependent constructive and destructive interference between opposing arrays of phased nucleosomes in yeast.

Ganguli D, Chereji RV, Iben JR, Cole HA, Clark DJ.

Genome Res. 2014 Oct;24(10):1637-49. doi: 10.1101/gr.177014.114. Epub 2014 Jul 11.

19.

Ubiquitous nucleosome crowding in the yeast genome.

Chereji RV, Morozov AV.

Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5236-41. doi: 10.1073/pnas.1321001111. Epub 2014 Mar 24.

20.

A dynamic interplay of nucleosome and Msn2 binding regulates kinetics of gene activation and repression following stress.

Elfving N, Chereji RV, Bharatula V, Björklund S, Morozov AV, Broach JR.

Nucleic Acids Res. 2014 May;42(9):5468-82. doi: 10.1093/nar/gku176. Epub 2014 Mar 5.

21.

Noise and interlocking signaling pathways promote distinct transcription factor dynamics in response to different stresses.

Petrenko N, Chereji RV, McClean MN, Morozov AV, Broach JR.

Mol Biol Cell. 2013 Jun;24(12):2045-57. doi: 10.1091/mbc.E12-12-0870. Epub 2013 Apr 24.

22.

Statistical Mechanics of Nucleosomes Constrained by Higher-Order Chromatin Structure.

Chereji RV, Morozov AV.

J Stat Phys. 2011 Jul 1;144(2):379-404.

23.

Statistical mechanics of nucleosome ordering by chromatin-structure-induced two-body interactions.

Chereji RV, Tolkunov D, Locke G, Morozov AV.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 May;83(5 Pt 1):050903. Epub 2011 May 13.

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