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Items: 1 to 50 of 177

1.

Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment.

Dileep V, Wilson KA, Marchal C, Lyu X, Zhao PA, Li B, Poulet A, Bartlett DA, Rivera-Mulia JC, Qin ZS, Robins AJ, Schulz TC, Kulik MJ, McCord RP, Dekker J, Dalton S, Corces VG, Gilbert DM.

Stem Cell Reports. 2019 Jul 9;13(1):193-206. doi: 10.1016/j.stemcr.2019.05.021. Epub 2019 Jun 20.

2.

Maintenance of CTCF- and Transcription Factor-Mediated Interactions from the Gametes to the Early Mouse Embryo.

Jung YH, Kremsky I, Gold HB, Rowley MJ, Punyawai K, Buonanotte A, Lyu X, Bixler BJ, Chan AWS, Corces VG.

Mol Cell. 2019 Jul 11;75(1):154-171.e5. doi: 10.1016/j.molcel.2019.04.014. Epub 2019 May 2.

PMID:
31056445
3.

Condensin II Counteracts Cohesin and RNA Polymerase II in the Establishment of 3D Chromatin Organization.

Rowley MJ, Lyu X, Rana V, Ando-Kuri M, Karns R, Bosco G, Corces VG.

Cell Rep. 2019 Mar 12;26(11):2890-2903.e3. doi: 10.1016/j.celrep.2019.01.116.

4.

Pach-ing It in: The Peculiar Organization of Mammalian Pachytene Chromosomes.

Jung YH, Corces VG.

Mol Cell. 2019 Feb 7;73(3):392-394. doi: 10.1016/j.molcel.2019.01.030.

PMID:
30735652
5.

Chromatin changes in Anopheles gambiae induced by Plasmodium falciparum infection.

Ruiz JL, Yerbanga RS, Lefèvre T, Ouedraogo JB, Corces VG, Gómez-Díaz E.

Epigenetics Chromatin. 2019 Jan 7;12(1):5. doi: 10.1186/s13072-018-0250-9.

6.

Resolution of the DNA methylation state of single CpG dyads using in silico strand annealing and WGBS data.

Xu C, Corces VG.

Nat Protoc. 2019 Jan;14(1):202-216. doi: 10.1038/s41596-018-0090-x.

PMID:
30542058
7.

Engineering 3D genome organization.

Lyu X, Corces VG.

Cell Res. 2019 Jan;29(1):1-3. doi: 10.1038/s41422-018-0116-5. No abstract available.

PMID:
30514898
8.

Organizational principles of 3D genome architecture.

Rowley MJ, Corces VG.

Nat Rev Genet. 2018 Dec;19(12):789-800. doi: 10.1038/s41576-018-0060-8. Review.

PMID:
30367165
9.

A tethered-inchworm model of SMC DNA translocation.

Nichols MH, Corces VG.

Nat Struct Mol Biol. 2018 Oct;25(10):906-910. doi: 10.1038/s41594-018-0135-4. Epub 2018 Sep 24. Review.

PMID:
30250225
10.

Architectural Proteins and Pluripotency Factors Cooperate to Orchestrate the Transcriptional Response of hESCs to Temperature Stress.

Lyu X, Rowley MJ, Corces VG.

Mol Cell. 2018 Sep 20;71(6):940-955.e7. doi: 10.1016/j.molcel.2018.07.012. Epub 2018 Aug 16.

PMID:
30122536
11.

Analysis of Chromatin Interactions Mediated by Specific Architectural Proteins in Drosophila Cells.

Ando-Kuri M, Rivera ISM, Rowley MJ, Corces VG.

Methods Mol Biol. 2018;1766:239-256. doi: 10.1007/978-1-4939-7768-0_14.

12.

Genome-Wide Mapping of Protein-DNA Interactions on Nascent Chromatin.

Xu C, Corces VG.

Methods Mol Biol. 2018;1766:231-238. doi: 10.1007/978-1-4939-7768-0_13.

13.

Nascent DNA methylome mapping reveals inheritance of hemimethylation at CTCF/cohesin sites.

Xu C, Corces VG.

Science. 2018 Mar 9;359(6380):1166-1170. doi: 10.1126/science.aan5480.

14.

Developing in 3D: the role of CTCF in cell differentiation.

Arzate-Mejía RG, Recillas-Targa F, Corces VG.

Development. 2018 Mar 22;145(6). pii: dev137729. doi: 10.1242/dev.137729. Review.

15.

Not just heads and tails: The complexity of the sperm epigenome.

Gold HB, Jung YH, Corces VG.

J Biol Chem. 2018 Sep 7;293(36):13815-13820. doi: 10.1074/jbc.R117.001561. Epub 2018 Mar 5. Review.

PMID:
29507096
16.

Evolutionarily Conserved Principles Predict 3D Chromatin Organization.

Rowley MJ, Nichols MH, Lyu X, Ando-Kuri M, Rivera ISM, Hermetz K, Wang P, Ruan Y, Corces VG.

Mol Cell. 2017 Sep 7;67(5):837-852.e7. doi: 10.1016/j.molcel.2017.07.022. Epub 2017 Aug 17.

17.

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA.

Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG, Cheng X.

Mol Cell. 2017 Jun 1;66(5):711-720.e3. doi: 10.1016/j.molcel.2017.05.004. Epub 2017 May 18.

18.

Chromatin States in Mouse Sperm Correlate with Embryonic and Adult Regulatory Landscapes.

Jung YH, Sauria MEG, Lyu X, Cheema MS, Ausio J, Taylor J, Corces VG.

Cell Rep. 2017 Feb 7;18(6):1366-1382. doi: 10.1016/j.celrep.2017.01.034.

19.

Epigenetic regulation of Plasmodium falciparum clonally variant gene expression during development in Anopheles gambiae.

Gómez-Díaz E, Yerbanga RS, Lefèvre T, Cohuet A, Rowley MJ, Ouedraogo JB, Corces VG.

Sci Rep. 2017 Jan 16;7:40655. doi: 10.1038/srep40655.

20.

Capturing native interactions: intrinsic methods to study chromatin conformation.

Rowley MJ, Corces VG.

Mol Syst Biol. 2016 Dec 9;12(12):897. doi: 10.15252/msb.20167438. No abstract available.

21.

Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture.

Cubeñas-Potts C, Rowley MJ, Lyu X, Li G, Lei EP, Corces VG.

Nucleic Acids Res. 2017 Feb 28;45(4):1714-1730. doi: 10.1093/nar/gkw1114.

22.

Minute-Made Data Analysis: Tools for Rapid Interrogation of Hi-C Contacts.

Rowley MJ, Corces VG.

Mol Cell. 2016 Oct 6;64(1):9-11. doi: 10.1016/j.molcel.2016.09.029.

23.

Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming.

Beagan JA, Gilgenast TG, Kim J, Plona Z, Norton HK, Hu G, Hsu SC, Shields EJ, Lyu X, Apostolou E, Hochedlinger K, Corces VG, Dekker J, Phillips-Cremins JE.

Cell Stem Cell. 2016 May 5;18(5):611-24. doi: 10.1016/j.stem.2016.04.004.

24.

The three-dimensional cancer genome.

Corces MR, Corces VG.

Curr Opin Genet Dev. 2016 Feb;36:1-7. doi: 10.1016/j.gde.2016.01.002. Epub 2016 Feb 6. Review.

25.

The three-dimensional genome: principles and roles of long-distance interactions.

Rowley MJ, Corces VG.

Curr Opin Cell Biol. 2016 Jun;40:8-14. doi: 10.1016/j.ceb.2016.01.009. Epub 2016 Feb 4. Review.

26.

Towards a predictive model of chromatin 3D organization.

Xu C, Corces VG.

Semin Cell Dev Biol. 2016 Sep;57:24-30. doi: 10.1016/j.semcdb.2015.11.013. Epub 2015 Dec 3. Review.

27.

HiFive: a tool suite for easy and efficient HiC and 5C data analysis.

Sauria ME, Phillips-Cremins JE, Corces VG, Taylor J.

Genome Biol. 2015 Oct 24;16:237. doi: 10.1186/s13059-015-0806-y.

28.

Topologically Associating Domains: An invariant framework or a dynamic scaffold?

Cubeñas-Potts C, Corces VG.

Nucleus. 2015;6(6):430-4. doi: 10.1080/19491034.2015.1096467. Epub 2015 Sep 29.

29.

Integrated tRNA, transcript, and protein profiles in response to steroid hormone signaling.

Van Bortle K, Nichols MH, Ramos E, Corces VG.

RNA. 2015 Oct;21(10):1807-17. doi: 10.1261/rna.052126.115. Epub 2015 Aug 19.

30.

A CTCF Code for 3D Genome Architecture.

Nichols MH, Corces VG.

Cell. 2015 Aug 13;162(4):703-5. doi: 10.1016/j.cell.2015.07.053.

31.

CTCF-dependent co-localization of canonical Smad signaling factors at architectural protein binding sites in D. melanogaster.

Van Bortle K, Peterson AJ, Takenaka N, O'Connor MB, Corces VG.

Cell Cycle. 2015;14(16):2677-87. doi: 10.1080/15384101.2015.1053670.

32.

Architectural proteins, transcription, and the three-dimensional organization of the genome.

Cubeñas-Potts C, Corces VG.

FEBS Lett. 2015 Oct 7;589(20 Pt A):2923-30. doi: 10.1016/j.febslet.2015.05.025. Epub 2015 May 22. Review.

33.

Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing.

Li L, Lyu X, Hou C, Takenaka N, Nguyen HQ, Ong CT, Cubeñas-Potts C, Hu M, Lei EP, Bosco G, Qin ZS, Corces VG.

Mol Cell. 2015 Apr 16;58(2):216-31. doi: 10.1016/j.molcel.2015.02.023. Epub 2015 Mar 26.

34.

Architectural proteins: regulators of 3D genome organization in cell fate.

Gómez-Díaz E, Corces VG.

Trends Cell Biol. 2014 Nov;24(11):703-11. doi: 10.1016/j.tcb.2014.08.003. Epub 2014 Sep 10. Review.

35.

Insights into the epigenomic landscape of the human malaria vector Anopheles gambiae.

Gómez-Díaz E, Rivero A, Chandre F, Corces VG.

Front Genet. 2014 Aug 15;5:277. doi: 10.3389/fgene.2014.00277. eCollection 2014.

36.

Insulator function and topological domain border strength scale with architectural protein occupancy.

Van Bortle K, Nichols MH, Li L, Ong CT, Takenaka N, Qin ZS, Corces VG.

Genome Biol. 2014 Jun 30;15(6):R82. doi: 10.1186/gb-2014-15-5-r82.

37.

Lost in transition: dynamic enhancer organization across naive and primed stem cell states.

Van Bortle K, Corces VG.

Cell Stem Cell. 2014 Jun 5;14(6):693-4. doi: 10.1016/j.stem.2014.05.004.

38.

Editorial overview: Genome architecture and expression: the nucleus, top and bottom.

Levens D, Corces V.

Curr Opin Genet Dev. 2014 Apr;25:v-vii. doi: 10.1016/j.gde.2014.04.001. Epub 2014 Apr 19. No abstract available.

PMID:
24755367
39.

CTCF: an architectural protein bridging genome topology and function.

Ong CT, Corces VG.

Nat Rev Genet. 2014 Apr;15(4):234-46. doi: 10.1038/nrg3663. Epub 2014 Mar 11. Review.

40.

Poly(ADP-ribosyl)ation regulates insulator function and intrachromosomal interactions in Drosophila.

Ong CT, Van Bortle K, Ramos E, Corces VG.

Cell. 2013 Sep 26;155(1):148-59. doi: 10.1016/j.cell.2013.08.052. Epub 2013 Sep 19.

41.

Distinct isoforms of the Drosophila Brd4 homologue are present at enhancers, promoters and insulator sites.

Kellner WA, Van Bortle K, Li L, Ramos E, Takenaka N, Corces VG.

Nucleic Acids Res. 2013 Nov;41(20):9274-83. doi: 10.1093/nar/gkt722. Epub 2013 Aug 13.

42.

The Drosophila transcription factor Adf-1 (nalyot) regulates dendrite growth by controlling FasII and Staufen expression downstream of CaMKII and neural activity.

Timmerman C, Suppiah S, Gurudatta BV, Yang J, Banerjee C, Sandstrom DJ, Corces VG, Sanyal S.

J Neurosci. 2013 Jul 17;33(29):11916-31. doi: 10.1523/JNEUROSCI.1760-13.2013.

43.

Chromatin insulators: linking genome organization to cellular function.

Phillips-Cremins JE, Corces VG.

Mol Cell. 2013 May 23;50(4):461-74. doi: 10.1016/j.molcel.2013.04.018. Review.

44.

Architectural protein subclasses shape 3D organization of genomes during lineage commitment.

Phillips-Cremins JE, Sauria ME, Sanyal A, Gerasimova TI, Lajoie BR, Bell JS, Ong CT, Hookway TA, Guo C, Sun Y, Bland MJ, Wagstaff W, Dalton S, McDevitt TC, Sen R, Dekker J, Taylor J, Corces VG.

Cell. 2013 Jun 6;153(6):1281-95. doi: 10.1016/j.cell.2013.04.053. Epub 2013 May 23.

45.

Dynamic changes in the genomic localization of DNA replication-related element binding factor during the cell cycle.

Gurudatta BV, Yang J, Van Bortle K, Donlin-Asp PG, Corces VG.

Cell Cycle. 2013 May 15;12(10):1605-15. doi: 10.4161/cc.24742. Epub 2013 Apr 25.

46.

Spinning the web of cell fate.

Van Bortle K, Corces VG.

Cell. 2013 Mar 14;152(6):1213-7. doi: 10.1016/j.cell.2013.02.052. Review.

47.

A subset of Drosophila Myc sites remain associated with mitotic chromosomes colocalized with insulator proteins.

Yang J, Sung E, Donlin-Asp PG, Corces VG.

Nat Commun. 2013;4:1464. doi: 10.1038/ncomms2469.

48.

Identification and characterization of proteins involved in nuclear organization using Drosophila GFP protein trap lines.

Rohrbaugh M, Clore A, Davis J, Johnson S, Jones B, Jones K, Kim J, Kithuka B, Lunsford K, Mitchell J, Mott B, Ramos E, Tchedou MR, Acosta G, Araujo M, Cushing S, Duffy G, Graves F, Griffin K, Gurudatta BV, Jackson D, Jaimes D, Jamison K, Jones K, Kelley D, Kilgore M, Laramore D, Le T, Mazhar B, Mazhar MM, McCrary B, Miller T, Moreland C, Mullins A, Munye E, Okoorie S, Pittman E, Roberts N, Rose D, Rowland A, Shagarabi A, Smith J, Stallworth T, Stroud N, Sung E, Sung K, Takenaka N, Torre E, Veira J, Vu K, Wagstaff W, Wood AM, Wu K, Yang J, Corces VG.

PLoS One. 2013;8(1):e53091. doi: 10.1371/journal.pone.0053091. Epub 2013 Jan 16.

49.

The role of chromatin insulators in nuclear architecture and genome function.

Van Bortle K, Corces VG.

Curr Opin Genet Dev. 2013 Apr;23(2):212-8. doi: 10.1016/j.gde.2012.11.003. Epub 2013 Jan 5. Review.

50.

Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains.

Hou C, Li L, Qin ZS, Corces VG.

Mol Cell. 2012 Nov 9;48(3):471-84. doi: 10.1016/j.molcel.2012.08.031. Epub 2012 Oct 4.

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