Axel Visel
Lawrence Berkeley National Laboratory
MS84-171
Phone: 1-510-495-2301
e-mail: avisel at lbl dot gov |
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Research Interests | |
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My research revolves around the fundamental question how the considerable complexity of the body and its organ systems can arise from a static genome whose sequence is identical in all cells. A plethora of gene-centric studies, mainly in the domain of developmental biology, have highlighted the differential regulation of transcription as a most important mechanism that confers functional identity to cells. Precise control of gene regulation is a prerequisite for essentially all known pathways of organismal development. However, the identity of the regulatory regions that control gene expression in time and space has to date remained unknown for the vast majority of genes. Comparative Vertebrate GenomicsThe comparison of vertebrate genome sequences is a powerful tool to study the evolution of genomes at an unprecedented level of detail. In particular, comparative methods enable the identification of genome regions that are highly conserved between species, but do not encode proteins. Such non-coding sequence conservation may be due to a regulatory function of such elements. In fact, some types of conserved elements have been found to be highly enriched in developmental cis-regulatory activity. One focus of my current work in the laboratories of Eddy Rubin and Len Pennacchio at LBNL is the development and application of comparative genomic methods for identification of distant-acting enhancers in the human genome.
Mouse TransgenesisComparative genomics enables the identification of conserved non-coding genome elements that are likely to be developmental enhancers. In order to validate such enhancers and define the tissues to which they target gene expression during embryonic development, we use transgenic mouse methods. Experimental details, as well as transgenic results for several hundred human genome regions are available through the VISTA Enhancer Browser. |
Publications | |
| Visel A, Prabhakar S, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Afzal V, Rubin EM, Pennacchio LA. Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nature Genet 2008, 40(2):158-60. PubMed |
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| Moldrich RX, Laine J, Visel A, Beart PM, Laffaire J, Rossier J, Potier MC. Tmem50b (C21orf4), a candidate for Down syndrome neurophenotypes, encodes an intracellular membrane protein expressed in the rodent brain. Neuroscience 2008, 154(4):1255-1266. PubMed |
| Visel A, Carson J, Oldekamp J, Warnecke M, Jakubcakova V, Zhou X, Shaw CA, Alvarez-Bolado G, Eichele G. Regulatory Pathway Analysis by High-Throughput In Situ Hybridization. PLoS Genet 2007, 3(10):e234. PubMed Full Text Small PDF Large PDF |
| Ahituv N, Zhu Y, Visel A, Holt A, Afzal V, Pennacchio LA, Rubin EM. Deletion of ultraconserved elements yields viable mice. PLoS Biol 2007, 5(9):e234. PubMed Full Text Small PDF Large PDF |
| Visel A, Bristow J, Pennacchio LA. Enhancer identification through comparative genomics. Semin Cell Dev Biol 2007, 18(1):140-52. PubMed | |
| Lein ES, Hawrylycz MJ, ..., Visel A, ..., Jones AR (108 authors). Genome-wide atlas of gene expression in the adult mouse brain. Nature 2007, 445(7124):168-76. PubMed |
| Visel A, Minovitsky S, Dubchak I, Pennacchio LA. VISTA Enhancer Browser--a database of tissue-specific human enhancers. Nucleic Acids Res 2007, 35:D88-92. PubMed Full Text Small PDF Large PDF |
| Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, Couronne O, Eisen MB, Visel A, Rubin EM. In vivo enhancer analysis of human conserved non-coding sequences. Nature 2006, 444(7118):499-502. PubMed |
| Visel A, Alvarez-Bolado G, Thaller C, Eichele G. Comprehensive analysis of the expression patterns of the adenylate cyclase gene family in the developing and adult mouse brain. J Comp Neurol 2006, 496(5):684-97. PubMed |
| Yaylaoglu MB, Titmus A, Visel A, Alvarez-Bolado G, Thaller C, Eichele G. Comprehensive expression atlas of fibroblast growth factors and their receptors generated by a novel robotic in situ hybridization platform. Dev Dyn 2005, 234(2):371-86. PubMed Full Text PDF |
| Schumacher S, Laass K, Kant S, Shi Y, Visel A, Gruber AD, Kotlyarov A, Gaestel M. Scaffolding by ERK3 regulates MK5 in development. EMBO J 2004, 23(24):4770-9. PubMed Full Text PDF |
| Plas DT, Visel A, Gonzalez E, She WC, Crair MC. Adenylate Cyclase 1 dependent refinement of retinotopic maps in the mouse. Vision Res 2004, 44(28):3357-64. PubMed | |
| Danilova N, Visel A, Willett CE, Steiner LA. Expression of the winged helix/forkhead gene, foxn4, during zebrafish development. Dev Brain Res 2004, 153(1):115-9. PubMed |
| Visel A, Thaller C, Eichele G. GenePaint.org: an atlas of gene expression patterns in the mouse embryo. Nucleic Acids Res 2004, 32:D552-6. PubMed Full Text PDF |
| Herzig U, Cadenas C, Sieckmann F, Sierralta W, Thaller C, Visel A, Eichele G. Development of high-throughput tools to unravel the complexity of gene expression patterns in the mammalian brain. Novartis Found Symp 2001, 239:129-46. PubMed |
Links | |
Databases | |
| VISTA Enhancer Browser - activity of conserved developmental enhancers in transgenic mouse embryos at e11.5 |
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| Genepaint.org - ISH-based expression atlas of the e14.5 mouse embryo |
| Allen Brain Atlas - Genome-wide ISH-based high-resolution expression atlas of the adult mouse brain |
last edited Feb 2008