A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival

Authors: Samuel Abassah-Oppong, Matteo Zoia, Brandon J. Mannion, Raquel Rouco, Virginie Tissières, Cailyn H. Spurrell, Virginia Roland, Fabrice Darbellay, Anja Itum, Julie Gamart, Tabitha A. Festa-Daroux, Carly S. Sullivan, Michael Kosicki, Eddie Rodríguez-Carballo, Yoko Fukuda-Yuzawa, Riana D. Hunter, Catherine S. Novak, Ingrid Plajzer-Frick, Stella Tran, Jennifer A. Akiyama, Diane E. Dickel, Javier Lopez-Rios, Iros Barozzi, Guillaume Andrey, Axel Visel, Len A. Pennacchio, John Cobb, Marco Osterwalder

Source: Nature Communications, Vol 15, Iss 1, Pp 1-24 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/ea97ba56f1764b518e534e1063bf2e68

A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders

Authors: Arthur S. Lee, Lauren J. Ayers, Michael Kosicki, Wai-Man Chan, Lydia N. Fozo, Brandon M. Pratt, Thomas E. Collins, Boxun Zhao, Matthew F. Rose, Alba Sanchis-Juan, Jack M. Fu, Isaac Wong, Xuefang Zhao, Alan P. Tenney, Cassia Lee, Kristen M. Laricchia, Brenda J. Barry, Victoria R. Bradford, Julie A. Jurgens, Eleina M. England, Monkol Lek, Daniel G. MacArthur, Eunjung Alice Lee, Michael E. Talkowski, Harrison Brand, Len A. Pennacchio, Elizabeth C. Engle

Source: Nature Communications, Vol 15, Iss 1, Pp 1-26 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/1d31f2afe5204250bcedb785593a825f

Dynamic enhancer landscapes in human craniofacial development

Authors: Sudha Sunil Rajderkar, Kitt Paraiso, Maria Luisa Amaral, Michael Kosicki, Laura E. Cook, Fabrice Darbellay, Cailyn H. Spurrell, Marco Osterwalder, Yiwen Zhu, Han Wu, Sarah Yasmeen Afzal, Matthew J. Blow, Guy Kelman, Iros Barozzi, Yoko Fukuda-Yuzawa, Jennifer A. Akiyama, Veena Afzal, Stella Tran, Ingrid Plajzer-Frick, Catherine S. Novak, Momoe Kato, Riana D. Hunter, Kianna von Maydell, Allen Wang, Lin Lin, Sebastian Preissl, Steven Lisgo, Bing Ren, Diane E. Dickel, Len A. Pennacchio, Axel Visel

Source: Nature Communications, Vol 15, Iss 1, Pp 1-18 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/ad066eccb027472d812a541544ff79a2

Topologically associating domain boundaries are required for normal genome function

Authors: Sudha Rajderkar, Iros Barozzi, Yiwen Zhu, Rong Hu, Yanxiao Zhang, Bin Li, Ana Alcaina Caro, Yoko Fukuda-Yuzawa, Guy Kelman, Adyam Akeza, Matthew J. Blow, Quan Pham, Anne N. Harrington, Janeth Godoy, Eman M. Meky, Kianna von Maydell, Riana D. Hunter, Jennifer A. Akiyama, Catherine S. Novak, Ingrid Plajzer-Frick, Veena Afzal, Stella Tran, Javier Lopez-Rios, Michael E. Talkowski, K. C. Kent Lloyd, Bing Ren, Diane E. Dickel, Axel Visel, Len A. Pennacchio

Source: Communications Biology, Vol 6, Iss 1, Pp 1-10 (2023)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/2399-3642

Access URL: https://doaj.org/article/e14ddea1acbd44d0886ef92596b4bbe5

Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

Authors: Marc W. Van Goethem, Andrew R. Osborn, Benjamin P. Bowen, Peter F. Andeer, Tami L. Swenson, Alicia Clum, Robert Riley, Guifen He, Maxim Koriabine, Laura Sandor, Mi Yan, Chris G. Daum, Yuko Yoshinaga, Thulani P. Makhalanyane, Ferran Garcia-Pichel, Axel Visel, Len A. Pennacchio, Ronan C. O’Malley, Trent R. Northen

Source: Communications Biology, Vol 4, Iss 1, Pp 1-10 (2021)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/2399-3642

Access URL: https://doaj.org/article/eae224afa2b747cc9f684dcc3d7db239

Reactivation of a developmentally silenced embryonic globin gene

Authors: Andrew J. King, Duantida Songdej, Damien J. Downes, Robert A. Beagrie, Siyu Liu, Megan Buckley, Peng Hua, Maria C. Suciu, A. Marieke Oudelaar, Lars L. P. Hanssen, Danuta Jeziorska, Nigel Roberts, Stephanie J. Carpenter, Helena Francis, Jelena Telenius, Aude-Anais Olijnik, Jacqueline A. Sharpe, Jacqueline Sloane-Stanley, Jennifer Eglinton, Mira T. Kassouf, Stuart H. Orkin, Len A. Pennacchio, James O. J. Davies, Jim R. Hughes, Douglas R. Higgs, Christian Babbs

Source: Nature Communications, Vol 12, Iss 1, Pp 1-15 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/eb63b89aa9ae4973bb86a64000a9ce01

Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism

Authors: Evin M. Padhi, Tristan J. Hayeck, Zhang Cheng, Sumantra Chatterjee, Brandon J. Mannion, Marta Byrska-Bishop, Marjolaine Willems, Lucile Pinson, Sylvia Redon, Caroline Benech, Kevin Uguen, Séverine Audebert-Bellanger, Cédric Le Marechal, Claude Férec, Stephanie Efthymiou, Fatima Rahman, Shazia Maqbool, Reza Maroofian, Henry Houlden, Rajeeva Musunuri, Giuseppe Narzisi, Avinash Abhyankar, Riana D. Hunter, Jennifer Akiyama, Lauren E. Fries, Jeffrey K. Ng, Elvisa Mehinovic, Nick Stong, Andrew S. Allen, Diane E. Dickel, Raphael A. Bernier, David U. Gorkin, Len A. Pennacchio, Michael C. Zody, Tychele N. Turner

Source: Human Genomics, Vol 15, Iss 1, Pp 1-15 (2021)

Subject Terms: Autism, Neurodevelopmental disorder, Enhancer, Gene regulatory network, EBF3, hs737, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1479-7364

Access URL: https://doaj.org/article/a0957b4159c64ec8b85c8227ab117a02

Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice

Authors: Jessica L. Haigh, Anna Adhikari, Nycole A. Copping, Tyler Stradleigh, A. Ayanna Wade, Rinaldo Catta-Preta, Linda Su-Feher, Iva Zdilar, Sarah Morse, Timothy A. Fenton, Anh Nguyen, Diana Quintero, Samrawit Agezew, Michael Sramek, Ellie J. Kreun, Jasmine Carter, Andrea Gompers, Jason T. Lambert, Cesar P. Canales, Len A. Pennacchio, Axel Visel, Diane E. Dickel, Jill L. Silverman, Alex S. Nord

Source: Genome Medicine, Vol 13, Iss 1, Pp 1-22 (2021)

Subject Terms: Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/78fe0a2d5b104a109781adedaf6df4e5

Stable enhancers are active in development, and fragile enhancers are associated with evolutionary adaptation

Authors: Shan Li, Evgeny Z. Kvon, Axel Visel, Len A. Pennacchio, Ivan Ovcharenko

Source: Genome Biology, Vol 20, Iss 1, Pp 1-17 (2019)

Subject Terms: Enhancer, Evolution of gene regulation, Transcription factor interaction, Causal regulatory variants, Transgenic mouse reporter assay, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13059-019-1750-z; https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/bb5790f8891746f986ba64887aeec5e2

Genomic Resolution of DLX-Orchestrated Transcriptional Circuits Driving Development of Forebrain GABAergic Neurons

Authors: Susan Lindtner, Rinaldo Catta-Preta, Hua Tian, Linda Su-Feher, James D. Price, Diane E. Dickel, Vanille Greiner, Shanni N. Silberberg, Gabriel L. McKinsey, Michael T. McManus, Len A. Pennacchio, Axel Visel, Alex S. Nord, John L.R. Rubenstein

Source: Cell Reports, Vol 28, Iss 8, Pp 2048-2063.e8 (2019)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S221112471930912X; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/326f0e1b8fd34b5e82acec04b4ab2a64

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

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

Source: Nature Communications, Vol 7, Iss 1, Pp 1-13 (2016)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/b001d43a207246388e738ba39f9b2876

Single site-specific integration targeting coupled with embryonic stem cell differentiation provides a high-throughput alternative to in vivo enhancer analyses

Authors: Adam C. Wilkinson, Debbie K. Goode, Yi-Han Cheng, Diane E. Dickel, Sam Foster, Tim Sendall, Marloes R. Tijssen, Maria-Jose Sanchez, Len A. Pennacchio, Aileen M. Kirkpatrick, Berthold Göttgens

Source: Biology Open, Vol 2, Iss 11, Pp 1229-1238 (2013)

Subject Terms: ES cells, Enhancer, Haematopoiesis, Transcription, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://bio.biologists.org/content/2/11/1229; https://doaj.org/toc/2046-6390

Access URL: https://doaj.org/article/444509f52e364592a9c151c269f7490d

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Phylo-VISTA: interactive visualization of multiple DNA sequence alignments.

Authors: Nameeta Shah, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, E. Wes Bethel, Edward M. Rubin, Bernd Hamann, Inna Dubchak

Source: Bioinformatics; Mar2004, Vol. 20 Issue 5, p636-643, 8p

Cathepsin B but not cathepsins L or S contributes to the pathogenesis of Unverricht-Lundborg progressive myoclonus epilepsy (EPM1).

Authors: Megan K. Houseweart, Len A. Pennacchio, Alex Vilaythong, Christoph Peters, Jeffrey L. Noebels, Richard M. Myers

Source: Journal of Neurobiology; Sep2003, Vol. 56 Issue 4, p315-327, 13p

Subject Terms: MYOCLONUS, EPILEPSY, MICE, APOPTOSIS, ATAXIA

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

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

Source: PLoS Computational Biology, Vol 13, Iss 8, p e1005720 (2017)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/2df35e120b6d46c4941c2992b6a30bfe

A Cryptochrome 2 mutation yields advanced sleep phase in humans

Authors: Arisa Hirano, Guangsen Shi, Christopher R Jones, Anna Lipzen, Len A Pennacchio, Ying Xu, William C Hallows, Thomas McMahon, Maya Yamazaki, Louis J Ptáček, Ying-Hui Fu

Source: eLife, Vol 5 (2016)

Subject Terms: circadian clock, cryptochrome2, circadian rhythm, FBXL3, Familial Advanced Sleep Phase, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/16695; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/136bb08d5052403ab88a6847a7402a92

The Epigenomic Landscape of Prokaryotes.

Authors: Matthew J Blow, Tyson A Clark, Chris G Daum, Adam M Deutschbauer, Alexey Fomenkov, Roxanne Fries, Jeff Froula, Dongwan D Kang, Rex R Malmstrom, Richard D Morgan, Janos Posfai, Kanwar Singh, Axel Visel, Kelly Wetmore, Zhiying Zhao, Edward M Rubin, Jonas Korlach, Len A Pennacchio, Richard J Roberts

Source: PLoS Genetics, Vol 12, Iss 2, p e1005854 (2016)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC4752239?pdf=render; https://doaj.org/toc/1553-7390; https://doaj.org/toc/1553-7404

Access URL: https://doaj.org/article/611a8e3186b0460990c4d6a70850c22d