U.S. Department of Health and Human Services

Laboratory of Cellular and Developmental Biology

Jurrien Dean, M.D., Chief

​Publications

A selection of recent and significant publications can be viewed below.

Publications
Dale RK, Matzat LH, Lei EP. metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA. Nucleic Acids Res. 2014 Oct 1; 42 (14):9158-70. [Full Text/Abstract]
Deng W, Rupon JW, Krivega I, Breda L, Motta I, Jahn KS, Reik A, Gregory PD, Rivella S, Dean A, Blobel GA. Reactivation of developmentally silenced globin genes by forced chromatin looping. Cell. 2014 Aug 14; 158 (4):849-60. [Full Text/Abstract]
Plank JL, Dean A. Enhancer Function: Mechanistic and Genome-Wide Insights Come Together. Mol Cell. 2014 Jul 3; 55 (1):5-14. [Full Text/Abstract]
King MR, Matzat LH, Dale RK, Lim SJ, Lei EP. The RNA-binding protein Rumpelstiltskin antagonizes gypsy chromatin insulator function in a tissue-specific manner. J Cell Sci. 2014 Jul 1; 127 (Pt 13):2956-66. [Full Text/Abstract]
Chen ZX, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AM, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, Clough E, Dasgupta A, Gubbala S, Han Y, Jayaseelan JC, Kalra D, Kim YA, Kovar CL, Lee SL, Li M, Malley JD, Malone JH, Mathew T, Mattiuzzo NR, Munidasa M, Muzny DM, Ongeri F, Perales L, Przytycka TM, Pu LL, Robinson G, Thornton RL, Saada N, Scherer SE, Smith HE, Vinson C, Warner CB, Worley KC, Wu YQ, Zou X, Cherbas P, Kellis M, Eisen MB, Piano F, Kionte K, Fitch DH, Sternberg PW, Cutter AD, Duff MO, Hoskins RA, Graveley BR, Gibbs RA, Bickel PJ, Kopp A, Carninci P, Celniker SE, Oliver B, Richards S. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res. 2014 Jul; 24 (7):1209-23. [Full Text/Abstract]
Avella MA, Baibakov B, Dean J. A single domain of the ZP2 zona pellucida protein mediates gamete recognition in mice and humans. J Cell Biol. 2014 Jun 23; 205 (6):801-9. [Full Text/Abstract]
Krivega I, Dale RK, Dean A. Role of LDB1 in the transition from chromatin looping to transcription activation. Genes Dev. 2014 Jun 15; 28 (12):1278-90. [Full Text/Abstract]
Yun WJ, Kim YW, Kang Y, Lee J, Dean A, Kim A. The hematopoietic regulator TAL1 is required for chromatin looping between the β-globin LCR and human γ-globin genes to activate transcription. Nucleic Acids Res. 2014 Apr; 42 (7):4283-93. [Full Text/Abstract]
Názer E, Lei EP. Modulation of chromatin modifying complexes by noncoding RNAs in trans. Curr Opin Genet Dev. 2014 Apr; 25 :68-73. [Full Text/Abstract]
Brown JB, Boley N, Eisman R, May GE, Stoiber MH, Duff MO, Booth BW, Wen J, Park S, Suzuki AM, Wan KH, Yu C, Zhang D, Carlson JW, Cherbas L, Eads BD, Miller D, Mockaitis K, Roberts J, Davis CA, Frise E, Hammonds AS, Olson S, Shenker S, Sturgill D, Samsonova AA, Weiszmann R, Robinson G, Hernandez J, Andrews J, Bickel PJ, Carninci P, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Lai EC, Oliver B, Perrimon N, Graveley BR, Celniker SE. Diversity and dynamics of the Drosophila transcriptome. Nature. 2014 Mar 16; 512 (7515):393-399. [Full Text/Abstract]
Matzat LH, Lei EP. Surviving an identity crisis: A revised view of chromatin insulators in the genomics era. Biochim Biophys Acta. 2014 Mar; 1839 (3):203-14. [Full Text/Abstract]
Lei EP. The regulation of gene expression is fundamental to development and disease. Introduction. Biochim Biophys Acta. 2014 Mar; 1839 (3):117. [Full Text/Abstract]
Sturgill D, Malone JH, Sun X, Smith HE, Rabinow L, Samson ML, Oliver B. Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki). BMC Bioinformatics. 2013 Nov 9; 14 :320. [Full Text/Abstract]
Li L, Lu X, Dean J. The maternal to zygotic transition in mammals. Mol Aspects Med. 2013 Oct; 34 (5):919-38. [Full Text/Abstract]
Matzat LH, Dale RK, Lei EP. Messenger RNA is a functional component of a chromatin insulator complex. EMBO Rep. 2013 Oct; 14 (10):916-22. [Full Text/Abstract]
Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M, Matzat LH, Dale RK, Smith SA, Yarosh CA, Kelly SM, Nabet B, Mecenas D, Li W, Laishram RS, Qiao M, Lipshitz HD, Piano F, Corbett AH, Carstens RP, Frey BJ, Anderson RA, Lynch KW, Penalva LO, Lei EP, Fraser AG, Blencowe BJ, Morris QD, Hughes TR. A compendium of RNA-binding motifs for decoding gene regulation. Nature. 2013 Jul 11; 499 (7457):172-7. [Full Text/Abstract]
Li L, Freudenberg J, Cui K, Dale R, Song SH, Dean A, Zhao K, Jothi R, Love PE. Ldb1-nucleated transcription complexes function as primary mediators of global erythroid gene activation. Blood. 2013 May 30; 121 (22):4575-85. [Full Text/Abstract]
Avella MA, Xiong B, Dean J. The molecular basis of gamete recognition in mice and humans. Mol Hum Reprod. 2013 May; 19 (5):279-89. [Full Text/Abstract]
Pennacchio LA, Bickmore W, Dean A, Nobrega MA, Bejerano G. Enhancers: five essential questions. Nat Rev Genet. 2013 Apr; 14 (4):288-95. [Full Text/Abstract]
Lim SJ, Boyle PJ, Chinen M, Dale RK, Lei EP. Genome-wide localization of exosome components to active promoters and chromatin insulators in Drosophila. Nucleic Acids Res. 2013 Mar 1; 41 (5):2963-80. [Full Text/Abstract]
Thomas CG, Li R, Smith HE, Woodruff GC, Oliver B, Haag ES. Simplification and desexualization of gene expression in self-fertile nematodes. Curr Biol. 2012 Nov 20; 22 (22):2167-72. [Full Text/Abstract]
Clough E, Oliver B. Genomics of sex determination in Drosophila. Brief Funct Genomics. 2012 Sep; 11 (5):387-94. [Full Text/Abstract]
Junier I, Dale RK, Hou C, Képès F, Dean A. CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the β-globin locus. Nucleic Acids Res. 2012 Sep; 40 (16):7718-27. [Full Text/Abstract]
Baibakov B, Boggs NA, Yauger B, Baibakov G, Dean J. Human sperm bind to the N-terminal domain of ZP2 in humanized zonae pellucidae in transgenic mice. J Cell Biol. 2012 Jun 25; 197 (7):897-905. [Full Text/Abstract]
Deng W, Lee J, Wang H, Miller J, Reik A, Gregory PD, Dean A, Blobel GA. Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell. 2012 Jun 8; 149 (6):1233-44. [Full Text/Abstract]
Malone JH, Cho DY, Mattiuzzo NR, Artieri CG, Jiang L, Dale RK, Smith HE, McDaniel J, Munro S, Salit M, Andrews J, Przytycka TM, Oliver B. Mediation of Drosophila autosomal dosage effects and compensation by network interactions. Genome Biol. 2012 Apr 24; 13 (4):r28. [Full Text/Abstract]
Bender MA, Ragoczy T, Lee J, Byron R, Telling A, Dean A, Groudine M. The hypersensitive sites of the murine β-globin locus control region act independently to affect nuclear localization and transcriptional elongation. Blood. 2012 Apr 19; 119 (16):3820-7. [Full Text/Abstract]
Burkart AD, Xiong B, Baibakov B, Jiménez-Movilla M, Dean J. Ovastacin, a cortical granule protease, cleaves ZP2 in the zona pellucida to prevent polyspermy. J Cell Biol. 2012 Apr 2; 197 (1):37-44. [Full Text/Abstract]
Krivega I, Dean A. Enhancer and promoter interactions-long distance calls. Curr Opin Genet Dev. 2012 Apr; 22 (2):79-85. [Full Text/Abstract]
Matzat LH, Dale RK, Moshkovich N, Lei EP. Tissue-specific regulation of chromatin insulator function. PLoS Genet. 2012; 8 (11):e1003069. [Full Text/Abstract]