Wysocka Lab

Publications

2023

Precise modulation of transcription factor levels identifies features underlying dosage sensitivity.

Naqvi S, Kim S, Hoskens H, Matthews HS, Spritz RA, Klein OD, Hallgrímsson B, Swigut T, Claes P, Pritchard JK, Wysocka J. Nat Genet. 2023 May;55(5):841-851. doi: 10.1038/s41588-023-01366-2.

Co-transcriptional genome surveillance by HUSH is coupled to termination machinery.

Spencley AL, Bar S, Swigut T, Flynn RA, Lee CH, Chen LF, Bassik MC, Wysocka J. Mol Cell. 2023 May 18;83(10):1623-1639.e8. doi: 10.1016/j.molcel.2023.04.014

A genome-wide genetic screen uncovers determinants of human pigmentation.

Bajpai VK, Swigut T, Mohammed J, Naqvi S, Arreola M, Tycko J, Kim TC, Pritchard JK, Bassik MC, Wysocka J. Science. 2023 Aug 11;381(6658):eade6289. doi: 10.1126/science.ade6289.

Joint multi-ancestry and admixed GWAS reveals the complex genetics behind human cranial vault shape.

Goovaerts S, Hoskens H, Eller RJ, Herrick N, Musolf AM, Justice CM, Yuan M, Naqvi S, Lee MK, Vandermeulen D, Szabo-Rogers HL, Romitti PA, Boyadjiev SA, Marazita ML, Shaffer JR, Shriver MD, Wysocka J, Walsh S, Weinberg SM, Claes P. Nat Commun. 2023 Nov 16;14(1):7436. doi: 10.1038/s41467-023-43237-8.

2021

Enhancer-associated H3K4 methylation safeguards in vitro germline competence.

Bleckwehl T, Crispatzu G, Schaaf K, Respuela P, Bartusel M, Benson L, Clark SJ, Dorighi KM, Barral A, Laugsch M, van IJcken WFJ, Manzanares M, Wysocka J, Reik W, Rada-Iglesias Á. Nat Commun. 2021 Oct 1;12(1):5771. doi: 10.1038/s41467-021-26065-6.

Genome scans of facial features in East Africans and cross-population comparisons reveal novel associations.

Liu C, Lee MK, Naqvi S, Hoskens H, Liu D, White JD, Indencleef K, Matthews H, Eller RJ, Li J, Mohammed J, Swigut T, Richmond S, Manyama M, Hallgrímsson B, Spritz RA, Feingold E, Marazita ML, Wysocka J, Walsh S, Shriver MD, Claes P, Weinberg SM, Shaffer JR. PLoS Genet. 2021 Aug 19;17(8):e1009695. doi: 10.1371/journal.pgen.1009695.

3D facial phenotyping by biometric sibling matching used in contemporary genomic methodologies.

Hoskens H, Liu D, Naqvi S, Lee MK, Eller RJ, Indencleef K, White JD, Li J, Larmuseau MHD, Hens G, Wysocka J, Walsh S, Richmond S, Shriver MD, Shaffer JR, Peeters H, Weinberg SM, Claes P. PLoS Genet. 2021 May 13;17(5):e1009528. doi: 10.1371/journal.pgen.1009528.

Shared heritability of human face and brain shape.

Naqvi S, Sleyp Y, Hoskens H, Indencleef K, Spence JP, Bruffaerts R, Radwan A, Eller RJ, Richmond S, Shriver MD, Shaffer JR, Weinberg SM, Walsh S, Thompson J, Pritchard JK, Sunaert S, Peeters H, Wysocka J, Claes P. Nat Genet. 2021 Jun;53(6):830-839. doi: 10.1038/s41588-021-00827-w.

Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution.

Gokhman D, Agoglia RM, Kinnebrew M, Gordon W, Sun D, Bajpai VK, Naqvi S, Chen C, Chan A, Chen C, Petrov DA, Ahituv N, Zhang H, Mishina Y, Wysocka J, Rohatgi R, Fraser HB.Nat Genet. 2021 Apr;53(4):467-476. doi: 10.1038/s41588-021-00804-3.

The Intersection of the Genetic Architectures of Orofacial Clefts and Normal Facial Variation.

Indencleef K, Hoskens H, Lee MK, White JD, Liu C, Eller RJ, Naqvi S, Wehby GL, Moreno Uribe LM, Hecht JT, Long RE Jr, Christensen K, Deleyiannis FW, Walsh S, Shriver MD, Richmond S, Wysocka J, Peeters H, Shaffer JR, Marazita ML, Hens G, Weinberg SM, Claes P. Front Genet. 2021 Feb 22;12:626403. doi: 10.3389/fgene.2021.626403.

Reactivation of the pluripotency program precedes formation of the cranial neural crest.

Zalc A, Sinha R, Gulati GS, Wesche DJ, Daszczuk P, Swigut T, Weissman IL, Wysocka J. Science. 2021 Feb 5;371(6529):eabb4776. doi: 10.1126/science.abb4776.

Temporal dissection of an enhancer cluster reveals distinct temporal and functional contributions of individual elements.

Thomas HF, Kotova E, Jayaram S, Pilz A, Romeike M, Lackner A, Penz T, Bock C, Leeb M, Halbritter F, Wysocka J, Buecker C. Mol Cell. 2021 Mar 4;81(5):969-982.e13. doi: 10.1016/j.molcel.2020.12.047.

2020

Insights into the genetic architecture of the human face.

White JD, Indencleef K, Naqvi S, Eller RJ, Hoskens H, Roosenboom J, Lee MK, Li J, Mohammed J, Richmond S, Quillen EE, Norton HL, Feingold E, Swigut T, Marazita ML, Peeters H, Hens G, Shaffer JR, Wysocka J, Walsh S, Weinberg SM, Shriver MD, Claes P. Nat Genet. 2021 Jan;53(1):45-53. doi: 10.1038/s41588-020-00741-7.

Opposing Effects of Cohesin and Transcription on CTCF Organization Revealed by Super-resolution Imaging.

Gu B, Comerci CJ, McCarthy DG, Saurabh S, Moerner WE, Wysocka J. Mol Cell. 2020 Nov 19;80(4):699-711.e7. doi: 10.1016/j.molcel.2020.10.001.

Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder.

Long HK, Osterwalder M, Welsh IC, Hansen K, Davies JOJ, Liu YE, Koska M, Adams AT, Aho R, Arora N, Ikeda K, Williams RM, Sauka-Spengler T, Porteus MH, Mohun T, Dickel DE, Swigut T, Hughes JR, Higgs DR, Visel A, Selleri L, Wysocka J. Cell Stem Cell. 2020 Nov 5;27(5):765-783.e14. doi: 10.1016/j.stem.2020.09.001.

FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research. Development.

Samuels BD, Aho R, Brinkley JF, Bugacov A, Feingold E, Fisher S, Gonzalez-Reiche AS, Hacia JG, Hallgrimsson B, Hansen K, Harris MP, Ho TV, Holmes G, Hooper JE, Jabs EW, Jones KL, Kesselman C, Klein OD, Leslie EJ, Li H, Liao EC, Long H, Lu N, Maas RL, Marazita ML, Mohammed J, Prescott S, Schuler R, Selleri L, Spritz RA, Swigut T, van Bakel H, Visel A, Welsh I, Williams C, Williams TJ, Wysocka J, Yuan Y, Chai Y. 2020 Sep 21;147(18):dev191213. doi: 10.1242/dev.191213.

Epigenomic and Transcriptomic Changes During Human RPE EMT in a Stem Cell Model of Epiretinal Membrane Pathogenesis and Prevention by Nicotinamide.

Boles NC, Fernandes M, Swigut T, Srinivasan R, Schiff L, Rada-Iglesias A, Wang Q, Saini JS, Kiehl T, Stern JH, Wysocka J, Blenkinsop TA, Temple S. Stem Cell Reports. 2020 Apr 14;14(4):631-647. doi: 10.1016/j.stemcr.2020.03.009.

Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage.

Srinivasan R, Nady N, Arora N, Hsieh LJ, Swigut T, Narlikar GJ, Wossidlo M, Wysocka J. Sci Adv. 2020 Mar 20;6(12):eaaz9115. doi: 10.1126/sciadv.aaz9115.

Transposable elements as a potent source of diverse cis-regulatory sequences in mammalian genomes.

Sundaram V, Wysocka J. Philos Trans R Soc Lond B Biol Sci. 2020 Mar 30;375(1795):20190347. doi: 10.1098/rstb.2019.0347.

2019

Heterogeneity in old fibroblasts is linked to variability in reprogramming and wound healing.

Mahmoudi S, Mancini E, Xu L, Moore A, Jahanbani F, Hebestreit K, Srinivasan R, Li X, Devarajan K, Prélot L, Ang CE, Shibuya Y, Benayoun BA, Chang ALS, Wernig M, Wysocka J, Longaker MT, Snyder MP, Brunet A.
Nature. 2019 Oct;574(7779):553-558. doi: 10.1038/s41586-019-1658-5.

Single Amino Acid Change Underlies Distinct Roles of H2A.Z Subtypes in Human Syndrome.

Greenberg RS, Long HK, Swigut T, Wysocka J. Cell. 2019 178(6):1421-1436.

2018 ISSCR Strategic Planning: Looking to the Future.

Wysocka J, Rossant J. Stem Cell Reports. 2019 Jun 11;12(6):1183-1185. doi:
10.1016/j.stemcr.2019.05.015.

The Spatiotemporal Pattern and Intensity of p53 Activation Dictates Phenotypic Diversity in p53-Driven Developmental Syndromes.

Bowen ME, McClendon J, Long HK, Sorayya A, Van Nostrand JL, Wysocka J, Attardi LD.
Dev Cell. 2019. 50(2):212-228.e6. doi: 10.1016/j.devcel.2019.05.015.

Hunting for genes that shape human faces: Initial successes and challenges for the
future.

Weinberg SM, Roosenboom J, Shaffer JR, Shriver MD, Wysocka J, Claes P. Orthod Craniofac Res. 2019 May;22 Suppl 1:207-212. doi:
10.1111/ocr.12268.

2018

Systematic perturbation of retroviral LTRs
reveals widespread long-range effects on human gene regulation.

Fuentes DR, Swigut T, Wysocka J. (2018) Elife. 2018 Aug 2;7. pii: e35989. doi: 10.7554/eLife.35989.

Single cell expression analysis of primate-specific
retroviruses-derived HPAT lincRNAs in viable human blastocysts identifies
embryonic cells co-expressing genetic markers of multiple lineages.

Glinsky G, Durruthy-Durruthy J, Wossidlo M, Grow EJ, Weirather JL, Au KF,
Wysocka J, Sebastiano V Heliyon. (2018)
Jun 28;4(6):e00667. doi: 10.1016/j.heliyon.2018.e00667

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. Cell Res. (2018)
Mar;28(3):387. doi: 10.1038/cr.2018.18.

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