Control of Cell Identity Genes Occurs in Insulated Neighborhoods

The following articles are publications of the Jill Dowen Lab

Histone H3K18 & H3K23 acetylation directs establishment of MLL-mediated H3K4 methylation. Fox GC, Poncha KF, Smith BR, van der Maas LN, Robbins NN, Graham B, Dowen JM, Strahl BD, Young NL, and Jain K. J Biol.Chem. 2024 Jul 1:107527. doi: 10.1016/j.jbc.2024.107527. PMID:38960040.

Heterochromatic 3D genome organization is directed by HP1a- and H3K9-dependent and independent mechanisms. Stutzman AV, Hill CA. Armstrong RA, Gohil R, Duronio RJ, Dowen JM and McKay DJ. Molecular Cell. 2024 May 18:S1097-2765(24)00395-2. doi: 10.1016/j.molcel.2024.05.002. PMID:38795706.

Cohesin regulation and roles in chromosome structure and function. Rittehouse NL and Dowen JM. Current Opinion in Genetics & Development. 2024 Apr:85:102159. doi: 10.1016/j.gde.2024.102159. PMID:38382406.

Proximity-dependent recruitment of Polycomb repressive complexes by the lndRNA Airn. Braceros, AK, Schertzer MG, Omer A, Trotman JB, Davis ES, Dowen JM, Phanstiel DH, Liederman-Aiden E, Calabrese MJ. Cell Reports. 2023 Jul 25;42(7):112803. doi: 10.1016/j.celrep.2023.112803. PMID:37436897.

PDS5A and PDS5B differentially affect gene expression without altering cohesin localization across the genome. Arruda NL, Bryan AF, Dowen JM. Epigenetics & Chromatin. 2022 Aug19;15(1):30. doi: 10.1186/s13072-022-00463-6. PMID: 35986423.

Chromosomal localization of cohesin is differentially regulated by WIZ, WAPL, and G9a. Justice M, Bryan AF, Limas JC, Cook JG, Dowen JM. BMC Genomics. 2022 Apr30;23(1):337. doi: 10.1186/s12864-022-08574-w. PMID: 35501690.

Functional impact of cancer-associated cohesin variants on gene expression and cellular identity. Rittenhouse NL, Carico ZM, Liu YF, Stefan HC, Arruda NL, Zhou J, Dowen JM. Genetics. 2021 Apr15;217(4):iyab025. doi: 10.1093/genetics/iyab025. PMID: 33704438.

A cohesin cancer mutation reveals a role for the hinge domain in genome organization and gene expression. Carico ZM, Stefan HC, Justice M, Yimit A, Dowen JM. PLoS Genetics. 2021 Mar 24;17(3):e1009435. doi: 10.1371/journal.pgen.1009435 PMID: 33760811. PMCID: PMC7990204.

Distinct and overlapping roles of STAG1 and STAG2 in cohesin localization and gene expression in embryonic stem cells. Arruda NL, Carico ZM, Justice M, Liu YF, Zhou J, Stefan HC, Dowen JM. Epigenetics & Chromatin. 2020 Aug 10;13(1);32. doi: 10.1186/s13072-020-00353-9. PMCID: PMC7418333

A WIZ/Cohesin/CTCF Complex Anchors DNA Loops to Define Gene Expression and Cell Identity. Justice M, Carico ZM, Stefan HC, Dowen JM. 2020 Apr 14;31(2):107503. doi: 10.1016/j.celrep.2020.03.067. PMCID: PMC7212317

lncRNA-Induced Spread of Polycomb Controlled by Genome Architecture, RNA Abundance, and CpG Island DNA. Schertzer MD, Braceros KCA, Starmer J, Cherney RE, Lee DM, Salazar G, Justice M, Bischoff SR, Cowley DO, Ariel P, Zylka MJ, Dowen JM, Magnuson T, Calabrese JM. Molecular Cell. 2019 Aug 8;75(3):523-537.e10. doi: 10.1016/j.molcel.2019.05.028. Epub 2019 Jun 27. PMCID: PMC6688959

Advancements in mapping 3D genome architecture. McKay DJ, Stutzman AV, Dowen JM. Methods. 2019 Jun 12. pii: S1046-2023(18)30496-1. PMCID: PMC7391055 Peer-reviewed Review Article.

Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Dowen JM, Fan ZP, Hnisz D, Ren G, Abraham BJ, Zhang LN, Weintraub AS, Schuijers J, Lee TI, Zhao K, Young RA. Cell. 2014 Oct 9;159(2):374-87. doi: 10.1016/j.cell.2014.09.030. PMCID: PMC4197132

SMC complexes link gene expression and genome architecture. Dowen JM, Young RA. Curr Opin Genet Dev. 2014 Apr;25:131-7. doi: 10.1016/j.gde.2013.11.009. Epub 2014 May 8. PMCID: PMC4045092 Peer-reviewed Review Article.

Multiple structural maintenance of chromosome complexes at transcriptional regulatory elements. Dowen JM, Bilodeau S, Orlando DA, Hübner MR, Abraham BJ, Spector DL, Young RA. Stem Cell Reports. 2013 Oct 24;1(5):371-8. doi: 10.1016/j.stemcr.2013.09.002. eCollection 2013. PMCID: PMC3841252

Widespread dynamic DNA methylation in response to biotic stress. Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR. Proc Natl Acad Sci U S A. 2012 Aug 7;109(32):E2183-91. doi: 10.1073/pnas.1209329109. Epub 2012 Jun 25. PMCID: PMC3420206

Functional studies and homology modeling of Msh2-Msh3 predict that mispair recognition involves DNA bending and strand separation. Dowen JM, Putnam CD, Kolodner RD. Mol Cell Biol. 2010 Jul;30(13):3321-8. doi: 10.1128/MCB.01558-09. Epub 2010 Apr 26. PMCID: PMC2897569

Saccharomyces cerevisiae Msh2-Msh3 acts in repair of base-base mispairs. Harrington JM, Kolodner RD. Mol Cell Biol. 2007 Sep;27(18):6546-54. doi: 10.1128/MCB.00855-07. Epub 2007 Jul 16. PMCID: PMC2099603

Medical sequencing of candidate genes for nonsyndromic cleft lip and palate. Vieira AR, Avila JR, Daack-Hirsch S, Dragan E, Félix TM, Rahimov F, Harrington J, Schultz RR, Watanabe Y, Johnson M, Fang J, O’Brien SE, Orioli IM, Castilla EE, Fitzpatrick DR, Jiang R, Marazita ML, Murray JC.. PLoS Genet. 2005 Dec;1(6):e64. doi: 10.1371/journal.pgen.0010064. Epub 2005 Dec 2. PMCID: PMC1298935