Wysocka Lab

Publications

2018

Genome-Wide Mapping Of Global-To-Local Genetic Effects On Human Facial Shape.

Claes P, Roosenboom J, White JD, Swigut T, Sero D, Li J, Lee MK, Zaidi A, Mattern BC, Liebowitz C, Pearson L, González T, Leslie EJ, Carlson JC, Orlova E, Suetens P, Vandermeulen D, Feingold E, Marazita ML, Shaffer JR, Wysocka J, Shriver MD, Weinberg SM. (2018) Nat Genet. 2018 Feb 19. doi: 10.1038/s41588-018-0057-4.

Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements.

Gu B, Swigut T, Spencley A, Bauer MR, Chung M, Meyer T, Wysocka J. (2018) Science. 2018 Jan 25. pii: eaao3136. doi: 10.1126/science.aao3136.

Tissue-Selective Effects Of Nucleolar Stress And rDNA Damage In Developmental Disorders.

Calo E, Gu B, Bowen ME, Aryan F, Zalc A, Liang J, Flynn RA, Swigut T, Chang HY, Attardi LD, Wysocka J. (2018) Nature. 2018 Jan 24. doi: 10.1038/nature25449.

Histone H3 Lysine 4 Monomethylation Modulates Long-Range Chromatin Interactions At Enhancers.

Yan J, Chen SA, Local A, Liu T, Qiu Y, Dorighi KM, Preissl S, Rivera CM, Wang C, Ye Z, Ge K, Hu M, Wysocka J, Ren B. (2018) Cell Res. 2018 Jan 9. doi: 10.1038/cr.2018.1.

2017

Selective Silencing Of Euchromatic L1s Revealed By Genome-Wide Screens For L1 Regulators.

Liu N, Lee CH, Swigut T, Grow E, Gu B, Bassik M, Wysocka J. (2017) Nature. 2017 Dec 6. doi: 10.1038/nature25179. 29211708.

CHARGE syndrome modeling using patient-iPSCs reveals defective migration of neural crest cells harboring CHD7 mutations.

Okuno H, Renault Mihara F, Ohta S, Fukuda K, Kurosawa K, Akamatsu W, Sanosaka T, Kohyama J, Hayashi K, Nakajima K, Takahashi T, Wysocka J, Kosaki K, Okano H. (2017) Elife. 2017 Nov 28;6. pii: e21114. doi: 10.7554/eLife.21114.

CSNK1a1 Regulates PRMT1 to Maintain the Progenitor State in Self-Renewing Somatic Tissue.

Bao X, Siprashvili Z, Zarnegar BJ, Shenoy RM, Rios EJ, Nady N, Qu K, Mah A, Webster DE, Rubin AJ, Wozniak GG, Tao S, Wysocka J, Khavari PA. (2017) Dev Cell. 2017 Sep 18. pii: S1534-5807(17)30681-0. doi: 10.1016/j.devcel.2017.08.021.

MLL3 and MLL4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation.

Dorighi KM, Swigut T, Henriques T, Bhanu NV, Scruggs BS, Nady N, Still CD 2nd, Garcia BA, Adelman K, Wysocka J. (2017) Mol Cell. 2017 May 18. doi: 10.1016/j.molcel.2017.04.018.

Transcriptional Dependencies in Diffuse Intrinsic Pontine Glioma.

Nagaraja S, Vitanza NA, Woo PJ, Taylor KR, Liu F, Zhang L, Li M, Meng W, Ponnuswami A, Sun W, Ma J, Hulleman E, Swigut T, Wysocka J, Tang Y, Monje M. (2017) Cancer Cell. 2017 Apr 11. doi: 10.1016/j.ccell.2017.03.011.

2016

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution.

Long HK, Prescott SL, Wysocka J.(2016) Cell. 2016 Nov 17;167(5):1170-1187.doi: 10.1016/j.cell.2016.09.018.

Zika Virus Infection Induces Cranial Neural Crest Cells to Produce Cytokines at Levels Detrimental for Neurogenesis.

Bayless NL, Greenberg RS, Swigut T, Wysocka J, Blish CA. (2016) Cell Host Microbe. 2016 Sep 28. pii: S1931-3128(16)30383-3. doi: 10.1016/j.chom.2016.09.006.

Hipstr and Thousands of Lncrnas Are Heterogeneously Expressed in Human Embryos, Primordial Germ Cells and Stable Cell Lines.

Yunusov D, Anderson L, DaSilva LF, Wysocka J, Ezashi T, Roberts RM, Verjovski-Almeida S. (2016) Sci Rep. 2016 Sep 8;6:32753. doi: 10.1038/srep32753.

The Facebase Consortium: a Comprehensive Resource for Craniofacial Researchers.

Brinkley JF, Fisher S, Harris MP, Holmes G, Hooper JE, Jabs EW, Jones KL, Kesselman C, Klein OD, Maas RL, Marazita ML, Selleri L, Spritz RA, van Bakel H, Visel A, Williams TJ, Wysocka J; FaceBase Consortium, Chai Y. (2016) Development. 2016 Jun 10. pii: dev.135434.

7SK-Baf Axis Controls Pervasive Transcription at Enhancers.

Flynn RA, Do BT, Rubin AJ, Calo E, Lee B, Kuchelmeister H, Rale M, Chu C, Kool ET, Wysocka J, Khavari PA, Chang HY (2016) Nat Struct Mol Biol. 2016 Feb 15.

Foxd3 Promotes Exit from Naive Pluripotency Through Enhancer Decommissioning and Inhibits Germline Specification.

Respuela P, Nikolić M, Tan M, Frommolt P, Zhao Y, Wysocka J, Rada–Iglesias A. (2016) Cell Stem Cell. 2016 Jan 7;18(1):118-33. doi: 10.1016/j.stem.2015.09.010.

The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming.

Durruthy-Durruthy J, Sebastiano V, Wossidlo M, Cepeda D, Cui J, Grow EJ, Davila J, Mall M, Wong WH, Wysocka J, Au KF, Reijo Pera RA. Nat Genet. 2016 Jan;48(1):44-52. doi: 10.1038/ng.3449. Epub 2015 Nov 23.

2015

ETO Family Protein MTGR1 Mediates PRDM14 Functions in Stem Cell Maintenance and Primordial Germ Cell Formation.

Nady N, Gupta A, Ma Z, Swigut T, Koide A, Koide S, Wysocka J. (2015) Elife. 2015 Nov 2;4. pii: e10150.

Enhancer Divergence and Cis-Regulatory Evolution in the Human and Chimp Neural Crest.

Prescott SL, Srinivasan R, Marchetto MC, Grishina I, Narvaiza I, Selleri L, Gage FH, Swigut T, Wysocka J. (2015) Cell. Sep 24;163(1):68-83.

Intrinsic Retroviral Reactivation in Human Preimplantation Embryos and Pluripotent Cells.

Grow EJ, Flynn RA, Chavez SL, Bayless NL, Wossidlo M, Wesche DJ, Martin L, Ware CB, Blish CA, Chang HY, Reijo Pera RA, Wysocka J. (2015) Nature. 2015 Jun 11;522(7555):221-5.

RNA helicase DDX21 coordinates transcription and ribosomal RNA processing.

Calo E, Flynn RA, Martin L, Spitale RC, Chang HY, Wysocka J. (2015) Nature. 2015 Feb 12;518(7538):249-53.

2014

Inappropriate p53 activation during development induces features of CHARGE syndrome.

Van Nostrand JL, Brady CA, Jung H, Fuentes DR, Kozak MM, Johnson TM, Lin CY, Lin CJ, Swiderski DL, Vogel H, Bernstein JA, Attié-Bitach T, Chang CP, Wysocka J, Martin DM, Attardi LD. (2014) Nature. 2014 Oct 9;514(7521):228-32.

Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency.

Buecker C, Srinivasan R, Wu Z, Calo E, Acampora D, Faial T, Simeone A, Tan M, Swigut T, Wysocka J. (2014) Cell Stem Cell. 2014 Jun 5;14(6):838-53.

2011

Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.

Rada-Iglesias A, Wysocka J. Genome Med. 2011 Jun 7;3(6):36. doi: 10.1186/gm252.

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression.

Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA, Chang HY. Nature. 2011 Apr 7;472(7341):120-4. doi: 10.1038/nature09819. Epub 2011 Mar 20.

Sequence-specific regulator Prdm14 safeguards mouse ESCs from entering extraembryonic endoderm fates.

Ma Z, Swigut T, Valouev A, Rada-Iglesias A, Wysocka J. (2011) Nat. Struct. Mol. Biol. 18(2):120-7

A unique chromatin signature uncovers early developmental enhancers in humans.

Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J. (2011) Nature 470(7333):279-83