Genome-wide compendium and functional assessment of in vivo heart enhancers

Autor: Marco Osterwalder, Catherine S. Pickle, Yiwen Zhu, Elizabeth Lee, David U. Gorkin, Ah Young Lee, Momoe Kato, Jennifer A. Akiyama, Ingrid Plajzer-Frick, Brandon J. Mannion, Axel Visel, Dalit May, Edward M. Rubin, Diane E. Dickel, Bing Ren, Cailyn H. Spurrell, Tyler H. Garvin, Iros Barozzi, Len A. Pennacchio, Yoko Fukuda-Yuzawa, Veena Afzal

Publikováno v: Nature Communications, Vol 7, Iss 1, Pp 1-13 (2016)
Dickel, DE; Barozzi, I; Zhu, Y; Fukuda-Yuzawa, Y; Osterwalder, M; Mannion, BJ; et al.(2016). Genome-wide compendium and functional assessment of in vivo heart enhancers. Nature Communications, 7. doi: 10.1038/ncomms12923. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/750894b2
Nature Communications
Nature communications, vol 7, iss 1

Whole-genome sequencing is identifying growing numbers of non-coding variants in human disease studies, but the lack of accurate functional annotations prevents their interpretation. We describe the genome-wide landscape of distant-acting enhancers a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::eb3f44f1fbee816dac2c4fc48be990d5
https://doaj.org/article/b001d43a207246388e738ba39f9b2876

Ultraconserved Enhancers Are Required for Normal Development

Autor: Yiwen Zhu, Yupar S. Khin, Veena Afzal, Elizabeth Lee, Jennifer A. Akiyama, Momoe Kato, Axel Visel, Len A. Pennacchio, Diane E. Dickel, Tyler H. Garvin, Ingrid Plajzer-Frick, Ramón Pla, Yoko Fukuda-Yuzawa, Brandon J. Mannion, Catherine S. Pickle, Quan T. Pham, Anne N. Harrington, John L.R. Rubenstein, Iros Barozzi, Athena R. Ypsilanti, Marco Osterwalder

Publikováno v: Cell, vol 172, iss 3
499.e15
Dickel, DE; Ypsilanti, AR; Pla, R; Zhu, Y; Barozzi, I; Mannion, BJ; et al.(2018). Ultraconserved Enhancers Are Required for Normal Development. Cell, 172(3), 491-499.e15. doi: 10.1016/j.cell.2017.12.017. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/9nr7s9m3

© 2017 Elsevier Inc. Non-coding “ultraconserved” regions containing hundreds of consecutive bases of perfect sequence conservation across mammalian genomes can function as distant-acting enhancers. However, initial deletion studies in mice revea

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c7646f4ad1dffbcfaad2d6def8c5e41f
https://escholarship.org/uc/item/9nr7s9m3

Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb

Autor: Marco Osterwalder, Tyler H. Garvin, Elizabeth Lee, Catherine S. Pickle, Momoe Kato, Iros Barozzi, Axel Visel, Ingrid Plajzer-Frick, Jennifer A. Akiyama, Remo Monti, Niko Beerenwinkel, Len A. Pennacchio, Veena Afzal, Diane E. Dickel

Publikováno v: PLoS Computational Biology, Vol 13, Iss 8, p e1005720 (2017)
Monti, R; Barozzi, I; Osterwalder, M; Lee, E; Kato, M; Garvin, TH; et al.(2017). Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb. PLoS computational biology, 13(8), e1005720. doi: 10.1371/journal.pcbi.1005720. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/5f99f1p8
PLoS Computational Biology
PLoS Computational Biology, 13 (8)
PLoS computational biology, vol 13, iss 8

Epigenomic mapping of enhancer-associated chromatin modifications facilitates the genome-wide discovery of tissue-specific enhancers in vivo. However, reliance on single chromatin marks leads to high rates of false-positive predictions. More sophisti

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3169b250da43ba2efdbfbe58cd0a49bd
https://doaj.org/article/2df35e120b6d46c4941c2992b6a30bfe

Precise and Heritable Genome Editing in Evolutionarily Diverse Nematodes Using TALENs and CRISPR/Cas9 to Engineer Insertions and Deletions

Autor: Edward J. Ralston, Qian Bian, Caitlin M. Schartner, Catherine S. Pickle, Mark Gurling, Jennifer A. Doudna, Te Wen Lo, Barbara J Meyer, Steven Lin

Publikováno v: Lo, TW; Pickle, CS; Lin, S; Ralston, EJ; Gurling, M; Schartner, CM; et al.(2013). Precise and heritable genome editing in evolutionarily diverse nematodes using TALENs and CRISPR/Cas9 to engineer insertions and deletions. Genetics, 195(2), 331-348. doi: 10.1534/genetics.113.155382. UC Berkeley: Retrieved from: http://www.escholarship.org/uc/item/268787zz

Exploitation of custom-designed nucleases to induce DNA double-strand breaks (DSBs) at genomic locations of choice has transformed our ability to edit genomes, regardless of their complexity. DSBs can trigger either error-prone repair pathways that i

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::dde63efb1a69deb51bc28eb8c1e664f1
https://doi.org/10.1534/genetics.113.155382

Targeted genome editing across species using ZFNs and TALENs

Autor: Lei Zhang, Te-Wen Lo, Bryan Zeitler, Edward J. Ralston, Andrew H. Lee, Barbara J Meyer, Catherine S. Pickle, Andrew J. Wood, Elo Leung, Edward J. Rebar, Rainier Amora, Philip D. Gregory, Fyodor D. Urnov, Xiangdong Meng, Jeffrey C. Miller

Publikováno v: Wood, A, Lo, T-W, Zeitler, B, Pickle, C S, Ralston, E J, Lee, A H, Amora, R, Miller, J C, Leung, E, Meng, X, Zhang, L, Rebar, E J, Gregory, P D, Urnov, F D & Meyer, B J 2011, ' Targeted genome editing across species using ZFNs and TALENs ', Science, vol. 333, no. 6040, pp. 307 . https://doi.org/10.1126/science.1207773
Wood, AJ; Lo, TW; Zeitler, B; Pickle, CS; Ralston, EJ; Lee, AH; et al.(2011). Targeted genome editing across species using ZFNs and TALENs. Science, 333(6040), 307. doi: 10.1126/science.1207773. UC Berkeley: Retrieved from: http://www.escholarship.org/uc/item/4nn2f895

Evolutionary studies necessary to dissect diverse biological processes have been limited by the lack of reverse genetic approaches in most organisms with sequenced genomes. We established a broadly applicable strategy using zinc finger nucleases (ZFN

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::68707b82e2dc8f6a21bbe05e257b9c74
https://pubmed.ncbi.nlm.nih.gov/21985000