Axel ViselScientist, Genomics Division
Lawrence Berkeley National Laboratory
Phone: 1-510-495-2301
e-mail: avisel at lbl dot gov |
|
|---|---|
Research Interests | |
The sequence of the human genome has been known for nearly a decade, but well-defined functional annotations exist mainly for the small portion of the genome that encodes proteins. In sharp contrast, the 98% non-coding regions of the genome remain poorly annotated. Individual examples from gene-centric studies have provided strong evidence that the non-coding portion of the genome harbors distant-acting transcriptional enhancers and have shown that these regulatory sequences are critical for normal embryonic development. Human genetic studies also identified examples of human disease caused by perturbed enhancer sequences. However, systematic identification and functional characterization of distant-acting enhancers in the human genome proved to present a formidable challenge for several reasons:
|
Publications | |
| Visel A*, Blow MJ*, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 2009, 457:854-858. PubMed Data Sets |
|---|---|
| Visel A, Akiyama JA, Shoukry M, Afzal V, Rubin EM, Pennacchio LA. Functional autonomy of distant-acting human enhancers. Genomics 2009, Epub ahead of print. PubMed |
| 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, 40:158-60. PubMed Data Sets |
| Prabhakar S, Visel A, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Morrison H, Fitzpatrick DR, Afzal V, Pennacchio LA, Rubin EM, Noonan JP. Human-specific gain of function in a developmental enhancer. Science 2008, 312:1346-50. PubMed |
| Rahimov F, Marazita ML, Visel A, ..., Murray JC (23 authors). Disruption of an AP-2alpha binding site in an IRF6 enhancer is associated with cleft lip. Nature Genet 2008, 40:1341-7. PubMed |
| De Val S, Chi NC, Meadows SM, Minovitsky S, Anderson JP, Harris IS, Ehlers ML, Agarwal P, Visel A, Xu SM, Pennacchio LA, Dubchak I, Krieg PA, Stainier DY, Black BL. Combinatorial regulation of endothelial gene expression by ets and forkhead transcription factors. Cell 2008, 135:1053-64. PubMed |
| 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 |
|---|---|
| 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 2009