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
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 (2014 Mar 16; 7515; 512):393-399. [Full Text/Abstract]
Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R. Comparative analysis of the transcriptome across distant species. Nature. 2014 Aug 28; 512 (2014 Aug 28; 7515; 512):445-8. [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 (2014 Aug 14; 4; 158):849-60. [Full Text/Abstract]
Plank JL, Dean A. Enhancer function: mechanistic and genome-wide insights come together. Mol Cell. 2014 Jul 3; 55 (55; 1; 2014 Jul 3):5-14. [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; 2014 Jul; 24):1209-23. [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 (127; 2014 Jul 1; Pt 13):2956-66. [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 (2014 Jun 23; 6; 205):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 (28; 2014 Jun 15; 12):1278-90. [Full Text/Abstract]
Kimmel AR, Sztalryd C. Perilipin 5, a lipid droplet protein adapted to mitochondrial energy utilization. Curr Opin Lipidol. 2014 Apr; 25 (25; 2; 2014 Apr):110-7. [Full Text/Abstract]
Ludtmann MH, Otto GP, Schilde C, Chen ZH, Allan CY, Brace S, Beesley PW, Kimmel AR, Fisher P, Killick R, Williams RS. An ancestral non-proteolytic role for presenilin proteins in multicellular development of the social amoeba Dictyostelium discoideum. J Cell Sci. 2014 Apr 1; 127 (127; Pt 7; 2014 Apr 1):1576-84. [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; 42; 2014 Apr):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 (25; 2014 Apr):68-73. [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 (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 (2014 Mar; 1839; 3):117. [Full Text/Abstract]
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; 42; 2014 Oct 1):9158-70. [Full Text/Abstract]
Sztalryd C, Kimmel AR. Perilipins: Lipid droplet coat proteins adapted for tissue-specific energy storage and utilization, and lipid cytoprotection. Biochimie. 2014 Jan; 96 (2014 Jan; 96):96-101. [Full Text/Abstract]
Platt JL, Rogers BJ, Rogers KC, Harwood AJ, Kimmel AR. Different CHD chromatin remodelers are required for expression of distinct gene sets and specific stages during development of Dictyostelium discoideum. Development. 2013 Dec; 140 (2013 Dec; 140; 24):4926-36. [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 (2013 Nov 9; 14):320. [Full Text/Abstract]
Brzostowski JA, Sawai S, Rozov O, Liao XH, Imoto D, Parent CA, Kimmel AR. Phosphorylation of chemoattractant receptors regulates chemotaxis, actin re-organization, and signal-relay. J Cell Sci. 2013 Oct 15; 126 (126; Pt 20; 2013 Oct 15):4614-26. [Full Text/Abstract]
Li L, Lu X, Dean J. The maternal to zygotic transition in mammals. Mol Aspects Med. 2013 Oct; 34 (2013 Oct; 5; 34):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 (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; 2013 Jul 11; 499):172-7. [Full Text/Abstract]
Liao XH, Buggey J, Lee YK, Kimmel AR. Chemoattractant stimulation of TORC2 is regulated by receptor/G protein-targeted inhibitory mechanisms that function upstream and independently of an essential GEF/Ras activation pathway in Dictyostelium. Mol Biol Cell. 2013 Jul; 24 (13; 24; 2013 Jul):2146-55. [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 (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 (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 (14; 4; 2013 Apr):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 (2013 Mar 1; 41; 5):2963-80. [Full Text/Abstract]
Faix J, Linkner J, Nordholz B, Platt JL, Liao XH, Kimmel AR. The application of the Cre-loxP system for generating multiple knock-out and knock-in targeted loci. Methods Mol Biol. 2013; 983 (983; 2013):249-67. [Full Text/Abstract]
Platt JL, Kent NA, Harwood AJ, Kimmel AR. Analysis of chromatin organization by deep sequencing technologies. Methods Mol Biol. 2013; 983 (983; 2013):173-83. [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 (2012 Nov 20; 22):2167-72. [Full Text/Abstract]
Clough E, Oliver B. Genomics of sex determination in Drosophila. Brief Funct Genomics. 2012 Sep; 11 (2012 Sep; 5; 11):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 (40; 2012 Sep; 16):7718-27. [Full Text/Abstract]
Hsieh K, Lee YK, Londos C, Raaka BM, Dalen KT, Kimmel AR. Perilipin family members preferentially sequester to either triacylglycerol-specific or cholesteryl-ester-specific intracellular lipid storage droplets. J Cell Sci. 2012 Sep 1; 125 (Pt 17; 125; 2012 Sep 1):4067-76. [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 (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 (149; 6; 2012 Jun 8):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 (2012 Apr 24; 4; 13):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; 119; 2012 Apr 19):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 (197; 2012 Apr 2; 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; 2012 Apr; 22):79-85. [Full Text/Abstract]
Rosel D, Khurana T, Majithia A, Huang X, Bhandari R, Kimmel AR. TOR complex 2 (TORC2) in Dictyostelium suppresses phagocytic nutrient capture independently of TORC1-mediated nutrient sensing. J Cell Sci. 2012 Jan 1; 125 (Pt 1; 125; 2012 Jan 1):37-48. [Full Text/Abstract]
Matzat LH, Dale RK, Moshkovich N, Lei EP. Tissue-specific regulation of chromatin insulator function. PLoS Genet. 2012; 8 (2012; 8; 11):e1003069. [Full Text/Abstract]
Avella MA, Dean J. Fertilization with acrosome-reacted mouse sperm: implications for the site of exocytosis. Proc Natl Acad Sci U S A. 2011 Dec 13; 108 (108; 50; 2011 Dec 13):19843-4. [Full Text/Abstract]
Kiefer CM, Lee J, Hou C, Dale RK, Lee YT, Meier ER, Miller JL, Dean A. Distinct Ldb1/NLI complexes orchestrate γ-globin repression and reactivation through ETO2 in human adult erythroid cells. Blood. 2011 Dec 1; 118 (118; 23; 2011 Dec 1):6200-8. [Full Text/Abstract]
Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR, Shendure J, Waterston RH, Oliver B, Lieb JD, Disteche CM. Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nat Genet. 2011 Oct 23; 43 (2011 Oct 23; 43; 12):1179-85. [Full Text/Abstract]
Krivega M, Dean A. Insulators organize chromatin: emerging rules of the game. Mol Cell. 2011 Oct 7; 44 (2011 Oct 7; 44; 1):1-2. [Full Text/Abstract]
Lienert F, Wirbelauer C, Som I, Dean A, Mohn F, Schübeler D. Identification of genetic elements that autonomously determine DNA methylation states. Nat Genet. 2011 Oct 2; 43 (2011 Oct 2; 43; 11):1091-7. [Full Text/Abstract]
Moshkovich N, Nisha P, Boyle PJ, Thompson BA, Dale RK, Lei EP. RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function. Genes Dev. 2011 Aug 15; 25 (25; 2011 Aug 15; 16):1686-701. [Full Text/Abstract]
Malone JH, Oliver B. Microarrays, deep sequencing and the true measure of the transcriptome. BMC Biol. 2011 May 31; 9 (9; 2011 May 31):34. [Full Text/Abstract]
Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE. The developmental transcriptome of Drosophila melanogaster. Nature. 2011 Mar 24; 471 (7339; 471; 2011 Mar 24):473-9. [Full Text/Abstract]
Jimenez-Movilla M, Dean J. ZP2 and ZP3 cytoplasmic tails prevent premature interactions and ensure incorporation into the zona pellucida. J Cell Sci. 2011 Mar 15; 124 (124; Pt 6; 2011 Mar 15):940-50. [Full Text/Abstract]