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
Shin SW, John Vogt E, Jimenez-Movilla M, Baibakov B, Dean J. Cytoplasmic cleavage of DPPA3 is required for intracellular trafficking and cleavage-stage development in mice. Nat Commun. 2017 Nov 21; 8 (2017 Nov 21; 8; 1):1643. [Full Text/Abstract]
Chen D, Dale RK, Lei EP. Shep regulates Drosophila neuronal remodeling by controlling transcription of its chromatin targets. Development. 2017 Nov 20; (2017 Nov 20). [Full Text/Abstract]
Krivega I, Dean A. A tetrad of chromatin interactions for chromosome pairing in X inactivation. Nat Struct Mol Biol. 2017 Aug 3; 24 (8; 2017 Aug 3; 24):607-608. [Full Text/Abstract]
Krivega I, Dean A. CTCF fences make good neighbours. Nat Cell Biol. 2017 Jul 28; 19 (2017 Jul 28; 8; 19):883-885. [Full Text/Abstract]
Lee J, Krivega I, Dale RK, Dean A. The LDB1 Complex Co-opts CTCF for Erythroid Lineage-Specific Long-Range Enhancer Interactions. Cell Rep. 2017 Jun 20; 19 (19; 2017 Jun 20; 12):2490-2502. [Full Text/Abstract]
Krivega I, Dean A. LDB1-mediated enhancer looping can be established independent of mediator and cohesin. Nucleic Acids Res. 2017 May 18; 45 (2017 May 18; 14; 45):8255-8268. [Full Text/Abstract]
Yang H, Basquin D, Pauli D, Oliver B. Drosophila melanogaster positive transcriptional elongation factors regulate metabolic and sex-biased expression in adults. BMC Genomics. 2017 May 18; 18 (2017 May 18; 1; 18):384. [Full Text/Abstract]
Zhou L, Canagarajah B, Zhao Y, Baibakov B, Tokuhiro K, Maric D, Dean J. BTBD18 Regulates a Subset of piRNA-Generating Loci through Transcription Elongation in Mice. Dev Cell. 2017 Mar 13; 40 (40; 5; 2017 Mar 13):453-466.e5. [Full Text/Abstract]
McJunkin K, Ambros V. A microRNA family exerts maternal control on sex determination in C. elegans. Genes Dev. 2017 Feb 15; 31 (2017 Feb 15; 4; 31):422-437. [Full Text/Abstract]
Xiong B, Zhao Y, Beall S, Sadusky AB, Dean J. A Unique Egg Cortical Granule Localization Motif Is Required for Ovastacin Sequestration to Prevent Premature ZP2 Cleavage and Ensure Female Fertility in Mice. PLoS Genet. 2017 Jan 23; 13 (2017 Jan 23; 13; 1):e1006580. [Full Text/Abstract]
Sherrard R, Luehr S, Holzkamp H, McJunkin K, Memar N, Conradt B. miRNAs cooperate in apoptosis regulation during C. elegans development. Genes Dev. 2017 Jan 15; 31 (2; 2017 Jan 15; 31):209-222. [Full Text/Abstract]
Chinen M, Lei EP. Drosophila Argonaute2 turnover is regulated by the ubiquitin proteasome pathway. Biochem Biophys Res Commun. 2017 Jan 10; 483 (2017 Jan 10; 483; 3):951-957. [Full Text/Abstract]
Zhou L, Baibakov B, Canagarajah B, Xiong B, Dean J. Genetic mosaics and time-lapse imaging identify functions of histone H3.3 residues in mouse oocytes and embryos. Development. 2016 Dec 19; 144 (2016 Dec 19; 144; 3):519-528. [Full Text/Abstract]
Jannot G, Michaud P, Quévillon Huberdeau M, Morel-Berryman L, Brackbill JA, Piquet S, McJunkin K, Nakanishi K, Simard MJ. GW182-Free microRNA Silencing Complex Controls Post-transcriptional Gene Expression during Caenorhabditis elegans Embryogenesis. PLoS Genet. 2016 Dec; 12 (12; 2016 Dec):e1006484. [Full Text/Abstract]
Cubeñas-Potts C, Rowley MJ, Lyu X, Li G, Lei EP, Corces VG. Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture. Nucleic Acids Res. 2016 Nov 28; 45 (2016 Nov 28; 4; 45):1714-1730. [Full Text/Abstract]
Lin Y, Chen ZX, Oliver B, Harbison ST. Microenvironmental Gene Expression Plasticity Among Individual Drosophila melanogaster. G3 (Bethesda). 2016 Oct 21; 6 (2016 Oct 21; 6; 12):4197-4210. [Full Text/Abstract]
Lee H, Cho DY, Whitworth C, Eisman R, Phelps M, Roote J, Kaufman T, Cook K, Russell S, Przytycka T, Oliver B. Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster. PLoS Genet. 2016 Sep; 12 (12; 9; 2016 Sep):e1006295. [Full Text/Abstract]
Wu D, Dean J. BTG4, a maternal mRNA cleaner. J Mol Cell Biol. 2016 Jun 23; 8 (8; 2016 Jun 23; 4):369-70. [Full Text/Abstract]
Tschapalda K, Zhang YQ, Liu L, Golovnina K, Schlemper T, Eichmann TO, Lal-Nag M, Sreenivasan U, McLenithan J, Ziegler S, Sztalryd C, Lass A, Auld D, Oliver B, Waldmann H, Li Z, Shen M, Boxer MB, Beller M. A Class of Diacylglycerol Acyltransferase 1 Inhibitors Identified by a Combination of Phenotypic High-throughput Screening, Genomics, and Genetics. EBioMedicine. 2016 Jun; 8 (8; 2016 Jun):49-59. [Full Text/Abstract]
Avella MA, Baibakov BA, Jimenez-Movilla M, Sadusky AB, Dean J. ZP2 peptide beads select human sperm in vitro, decoy mouse sperm in vivo, and provide reversible contraception. Sci Transl Med. 2016 Apr 27; 8 (8; 2016 Apr 27; 336):336ra60. [Full Text/Abstract]
Caravaca JM, Lei EP. Maintenance of a Drosophila melanogaster Population Cage. J Vis Exp. 2016 Mar 15; (2016 Mar 15; 109). [Full Text/Abstract]
Krivega I, Dean A. Chromatin looping as a target for altering erythroid gene expression. Ann N Y Acad Sci. 2016 Feb 25; 1368 (1368; 2016 Feb 25; 1):31-9. [Full Text/Abstract]
Dean J. Exacting Requirements for Development of the Egg. N Engl J Med. 2016 Jan 21; 374 (374; 2016 Jan 21; 3):279-80. [Full Text/Abstract]
Lin Y, Golovnina K, Chen ZX, Lee HN, Negron YL, Sultana H, Oliver B, Harbison ST. Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster. BMC Genomics. 2016 Jan 5; 17 (2016 Jan 5; 17):28. [Full Text/Abstract]
Krivega I, Byrnes C, de Vasconcellos JF, Lee YT, Kaushal M, Dean A, Miller JL. Inhibition of G9a methyltransferase stimulates fetal hemoglobin production by facilitating LCR/γ-globin looping. Blood. 2015 May 15; 126 (126; 2015 May 15; 5):665-72. [Full Text/Abstract]
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. Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing. Mol Cell. 2015 Mar 25; 58 (2015 Mar 25; 2; 58):216-231. [Full Text/Abstract]
Krivega I, Dean A. Chromosome togetherness at the onset of ESC differentiation. Cell Stem Cell. 2015 Mar 5; 16 (16; 2015 Mar 5; 3):213-4. [Full Text/Abstract]
Clough E, Jimenez E, Kim YA, Whitworth C, Neville MC, Hempel LU, Pavlou HJ, Chen ZX, Sturgill D, Dale RK, Smith HE, Przytycka TM, Goodwin SF, Van Doren M, Oliver B. Sex- and tissue-specific functions of Drosophila doublesex transcription factor target genes. Dev Cell. 2014 Dec 22; 31 (2014 Dec 22; 6; 31):761-73. [Full Text/Abstract]
Zhou LQ, Dean J. Reprogramming the genome to totipotency in mouse embryos. Trends Cell Biol. 2014 Oct 21; 25 (25; 2; 2014 Oct 21):82-91. [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]
Rudalska R, Dauch D, Longerich T, McJunkin K, Wuestefeld T, Kang TW, Hohmeyer A, Pesic M, Leibold J, von Thun A, Schirmacher P, Zuber J, Weiss KH, Powers S, Malek NP, Eilers M, Sipos B, Lowe SW, Geffers R, Laufer S, Zender L. In vivo RNAi screening identifies a mechanism of sorafenib resistance in liver cancer. Nat Med. 2014 Oct; 20 (20; 2014 Oct; 10):1138-46. [Full Text/Abstract]
Yu XJ, Yi Z, Gao Z, Qin D, Zhai Y, Chen X, Ou-Yang Y, Wang ZB, Zheng P, Zhu MS, Wang H, Sun QY, Dean J, Li L. The subcortical maternal complex controls symmetric division of mouse zygotes by regulating F-actin dynamics. Nat Commun. 2014 Sep 11; 5 (2014 Sep 11; 5):4887. [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]
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]
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):849-860. [Full Text/Abstract]
McJunkin K, Ambros V. The embryonic mir-35 family of microRNAs promotes multiple aspects of fecundity in Caenorhabditis elegans. G3 (Bethesda). 2014 Jul 21; 4 (2014 Jul 21; 4; 9):1747-54. [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]
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]