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]
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 (7515):445-8. [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]
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]
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]
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]
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]
Kimmel AR, Sztalryd C. Perilipin 5, a lipid droplet protein adapted to mitochondrial energy utilization. Curr Opin Lipidol. 2014 Apr; 25 (2):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 (Pt 7):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):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]
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]
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]
Sztalryd C, Kimmel AR. Perilipins: Lipid droplet coat proteins adapted for tissue-specific energy storage and utilization, and lipid cytoprotection. Biochimie. 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 (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 :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 (Pt 20):4614-26. [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]
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]
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]
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):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 (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]
Platt JL, Kent NA, Harwood AJ, Kimmel AR. Analysis of chromatin organization by deep sequencing technologies. Methods Mol Biol. 2013; 983 :173-83. [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 :249-67. [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]