Publications

Selected publications. For complete list, see PubMed records of L. Pennacchio and A. Visel

Osterwalder M, Tran S, Hunter RD, Meky EM, von Maydell K, Harrington AN, Godoy J, Novak CS, Plajzer-Frick I, Zhu Y, Akiyama JA, Afzal V, Kvon EZ, Pennacchio LA, Dickel DE, Visel A. Characterization of Mammalian In Vivo Enhancers Using Mouse Transgenesis and CRISPR Genome Editing. Methods Molecular Biology. 2022;2403:147-186. PubMed
Snetkova V, Pennacchio LA, Visel A, Dickel DE. Perfect and imperfect views of ultraconserved sequences. Nature Reviews Genetics. 2021 Nov 11; online ahead of print. PubMed
Snetkova V, Ypsilanti AR, Akiyama JA, Mannion BJ, Plajzer-Frick I, Novak CS, Harrington AN, Pham QT, Kato M, Zhu Y, Godoy J, Meky E, Hunter RD, Shi M, Kvon EZ, Afzal V, Tran S, Rubenstein JLR, Visel A, Pennacchio LA, Dickel DE. Ultraconserved enhancer function does not require perfect sequence conservation. Nature Genetics. 2021 Apr;53(4):521-528. PubMed
ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 Jul;583(7818):699-710. doi: 10.1038/s41586-020-2493-4. Epub 2020 Jul 29. PubMed
He P, Williams BA, Trout D, Marinov GK, Amrhein H, Berghella L, Goh ST, Plajzer-Frick I, Afzal V, Pennacchio LA, Dickel DE, Visel A, Ren B, Hardison RC, Zhang Y, Wold BJ. The changing mouse embryo transcriptome at whole tissue and single-cell resolution. Nature. 2020 Jul;583(7818):760-767. PubMed
He Y, Hariharan M, Gorkin DU, Dickel DE, Luo C, Castanon RG, Nery JR, Lee AY, Zhao Y, Huang H, Williams BA, Trout D, Amrhein H, Fang R, Chen H, Li B, Visel A, Pennacchio LA, Ren B, Ecker JR. Spatiotemporal DNA methylome dynamics of the developing mouse fetus. Nature. 2020 Jul;583(7818):752-759. PubMed
Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, Afzal V, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Garvin TH, Pham QT, Harrington AN, Mannion BJ, Lee EA, Fukuda-Yuzawa Y, He Y, Preissl S, Chee S, Han JY, Williams BA, Trout D, Amrhein H, Yang H, Cherry JM, Wang W, Gaulton K, Ecker JR, Shen Y, Dickel DE, Visel A, Pennacchio LA, Ren B. An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. 2020 Jul;583(7818):744-751. PubMed
Kvon EZ, Zhu Y, Kelman G, Novak CS, Plajzer-Frick I, Kato M, Garvin TH, Pham Q, Harrington AN, Hunter RD, Godoy J, Meky EM, Akiyama JA, Afzal V, Tran S, Escande F, Gilbert-Dussardier B, Jean-Marçais N, Hudaiberdiev S, Ovcharenko I, Dobbs MB, Gurnett CA, Manouvrier-Hanu S, Petit F, Visel A, Dickel DE, Pennacchio LA. Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants. Cell. 2020 Mar 19;180(6):1262-1271.e15. PubMed
Oz-Levi D, Olender T, Bar-Joseph I, Zhu Y, Marek-Yagel D, Barozzi I, Osterwalder M, Alkelai A, Ruzzo EK, Han Y, Vos ESM, Reznik-Wolf H, Hartman C, Shamir R, Weiss B, Shapiro R, Pode-Shakked B, Tatarskyy P, Milgrom R, Schvimer M, Barshack I, Imai DM, Coleman-Derr D, Dickel DE, Nord AS, Afzal V, van Bueren KL, Barnes RM, Black BL, Mayhew CN, Kuhar MF, Pitstick A, Tekman M, Stanescu HC, Wells JM, Kleta R, de Laat W, Goldstein DB, Pras E, Visel A, Lancet D, Anikster Y, Pennacchio LA. Noncoding deletions reveal a gene that is critical for intestinal function. Nature. 2019 Jul;571(7763);107-111. PubMed
Preissl S, Fang R, Huang H, Zhao Y, Raviram R, Gorkin DU, Zhang Y, Sos BC, Afzal V, Dickel DE, Kuan S, Visel A, Pennacchio LA, Zhang K, Ren B. Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nature Neuroscience. 2018 Mar;21(3):432-439. PubMed
Osterwalder M, Barozzi I, Tissières V, Fukuda-Yuzawa Y, Mannion BJ, Afzal SY, Lee EA, Zhu Y, Plajzer-Frick I, Pickle CS, Kato M, Garvin TH, Pham QT, Harrington AN, Akiyama JA, Afzal V, Lopez-Rios J, Dickel DE, Visel A, Pennacchio LA. Enhancer redundancy provides phenotypic robustness in mammalian development. Nature. 2018 Feb 8;554(7691):239-243. PubMed
Dickel DE, Ypsilanti AR, Pla R, Zhu Y, Barozzi I, Mannion BJ, Khin YS, Fukuda-Yuzawa Y, Plajzer-Frick I, Pickle CS, Lee EA, Harrington AN, Pham QT, Garvin TH, Kato M, Osterwalder M, Akiyama JA, Afzal V, Rubenstein JLR, Pennacchio LA, Visel A. Ultraconserved Enhancers Are Required for Normal Development. Cell. 2018 Jan 25;172(3):491-499.e15. PubMed
Monti R, Barozzi I, Osterwalder M, Lee E, Kato M, Garvin TH, Plajzer-Frick I, Pickle CS, Akiyama JA, Afzal V, Beerenwinkel N, Dickel DE, Visel A, Pennacchio LA. Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb. PLoS Computational Biology. 2017 Aug 21;13(8):e1005720. PubMed
Gompers AL, Su-Feher L, Ellegood J, Copping NA, Riyadh MA, Stradleigh TW, Pride MC, Schaffler MD, Wade AA, Catta-Preta R, Zdilar I, Louis S, Kaushik G, Mannion BJ, Plajzer-Frick I, Afzal V, Visel A, Pennacchio LA, Dickel DE, Lerch JP, Crawley JN, Zarbalis KS, Silverman JL, Nord AS. Germline Chd8 haploinsufficiency alters brain development in mouse. Nature Neuroscience. 2017 Aug;20(8):1062-1073. PubMed
He Y, Gorkin D, Dickel DE, Nery JR, Castanon RG, Lee AY, Shen Y, Visel A, Pennacchio LA, Ren B, Ecker JR. Improved regulatory element prediction based on tissue-specific local epigenomic signatures. Proc Natl Acad Sci 2017 Feb 28; 114(9):E1633-E1640. PubMed
Spurrell CH, Dickel DE, Visel A. The Ties That Bind: Mapping the Dynamic Enhancer-Promoter Interactome. Cell 2016 Nov 17;167(5):1163-1166. PubMed
Kvon EZ, Kamneva OK, Melo US, Barozzi I, Osterwalder M, Mannion BJ, Tissières V, Pickle CS, Plajzer-Frick I, Lee EA, Kato M, Garvin TH, Akiyama JA, Afzal V, Lopez-Rios J, Rubin EM, Dickel DE, Pennacchio LA, Visel A. Progressive Loss of Function in a Limb Enhancer during Snake Evolution. Cell 2016 Oct 20;167(3):633-642. PubMed
Dickel DE, Barozzi I, Zhu Y, Fukuda-Yuzawa Y, Osterwalder M, Mannion BJ, May D, Spurrell CH, Plajzer-Frick I, Pickle CS, Lee E, Garvin TH, Kato M, Akiyama JA, Afzal V, Lee AY, Gorkin DU, Ren B, Rubin EM, Visel A, Pennacchio LA. Genome-wide compendium and functional assessment of in vivo heart enhancers. Nature Communications 2016 Oct 5;7:12923. PubMed
Lupiáñez DG, Kraft K, Heinrich V, Krawitz P, Brancati F, Klopocki E, Horn D, Kayserili H, Opitz JM, Laxova R, Santos-Simarro F, Gilbert-Dussardier B, Wittler L, Borschiwer M, Haas SA, Osterwalder M, Franke M, Timmermann B, Hecht J, Spielmann M, Visel A, Mundlos S. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell 2015 May 21;161(5):1012-25. PubMed
Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B; Mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP. Principles of regulatory information conservation between mouse and human. Nature 2014 Nov 20;515(7527):371-5. PubMed
Wu H, Nord AS, Akiyama JA, Shoukry M, Afzal V, Rubin EM, Pennacchio LA, Visel A. Tissue-specific RNA expression marks distant-acting developmental enhancers. PLoS Genetics 2014 Sep 4; 10(9):e1004610. PubMed
Pattabiraman K, Golonzhka O, Lindtner S, Nord AS, Taher L, Hoch R, Silberberg SN, Zhang D, Chen B, Zeng H, Pennacchio LA, Puelles L, Visel A, Rubenstein JL. Transcriptional regulation of enhancers active in protodomains of the developing cerebral cortex. Neuron 2014 Jun 4; 82(5):989-1003. PubMed
Ivanova NN, Schwientek P, Tripp HJ, Rinke C, Pati A, Huntemann M, Visel A, Woyke T, Kyrpides NC, Rubin EM. Stop codon reassignments in the wild. Science 2014 May 23; 344(6186):909-13. PubMed
Attanasio C, Nord AS, Zhu Y, Blow MJ, Biddie SC, Mendenhall EM, Dixon J, Wright C, Hosseini R, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Afzal V, Ren B, Bernstein BE, Rubin EM, Visel A, Pennacchio LA. Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. Genome Research 2014 Jun; 24(6):920-9. PubMed
Dickel DE, Zhu Y, Nord AS, Wylie JN, Akiyama JA, Afzal V, Plajzer-Frick I, Kirkpatrick A, Gottgens B, Bruneau BG, Visel A, Pennacchio LA. Function-based identification of mammalian enhancers using site-specific integration. Nature Methods 2014, 11:566-571. PubMed
Nord AS, …, Rubenstein JL, Rubin EM, Pennacchio LA*, Visel A*. (14 authors). Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development. Cell 2013, 155:1521-1531. PubMed Data Sets
Attanasio C, Nord AS, Zhu Y, …, Rubin EM, FitzPatrick DR, Ren B, Hallgrímsson B, Pennacchio LA, Visel A. (20 authors). Fine tuning of craniofacial morphology by distant-acting enhancers. Science 2013, 342:1241006. PubMed Free Full Text Free PDF
Visel A*, …, Ovcharenko I, Pennacchio LA, Rubenstein JL. (25 authors). A High-Resolution Enhancer Atlas of the Developing Telencephalon. Cell 2013, 152:895-908 PubMed PMC Full Text PMC Free PDF
ENCODE Project Consortium. (400+ authors incl. Visel A and Pennacchio LA). An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74. PubMed Open Access Full Text Open Access PDF
May D, …, Simpson PC, Rubin EM, Black BL, Bristow J, Pennacchio LA*, Visel A*. (17 authors). Large-scale discovery of enhancers from human heart tissue. Nature Genetics 2011, PubMed PMC Full Text PMC Free PDF
Blow MJ, …, Ren B, Black BL, Rubin EM, Visel A*, Pennacchio LA* (17 authors). ChIP-seq Identification of Weakly Conserved Heart Enhancers.Nature Genetics 2010, 42:806-10. PubMed News and Views PMC Full Text PMC Free PDF
Visel A, …, Cohen JC, Rubin EM, Pennacchio LA (10 authors). Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice. Nature 2010, 464:409-412. PubMed PMC Full Text PMC Free PDF
Visel A, Rubin EM, Pennacchio LA. Genomic views of distant-acting enhancers (Review). Nature 2009, 461:199-205. PubMed PMC Full Text PMC Free PDF
Visel A*, Blow MJ*, …, Ren B, Rubin EM, Pennacchio LA (14 authors). ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 2009, 457:854-858. PubMed PMC Full Text PMC Free PDF Data Sets
Prabhakar S, Visel A, …, Pennacchio LA, Rubin EM, Noonan JP (13 authors). Human-specific gain of function in a developmental enhancer. Science 2008, 312:1346-50. PubMed PMC Full Text PMC Free PDF
Visel A, …, Rubin EM, Pennacchio LA (10 authors). Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nature Genetics 2008, 40:158-60. PubMed PMC Full Text PMC Free PDF Data Sets
Pennacchio LA, …, Visel A, Rubin EM (19 authors). In vivo enhancer analysis of human conserved non-coding sequences. Nature 2006, 444(7118):499-502. PubMed