A
Amy Holt
Researcher at Lawrence Berkeley National Laboratory
Publications - 16
Citations - 5675
Amy Holt is an academic researcher from Lawrence Berkeley National Laboratory. The author has contributed to research in topics: Enhancer & Gene. The author has an hindex of 16, co-authored 16 publications receiving 5272 citations. Previous affiliations of Amy Holt include Joint Genome Institute.
Papers
More filters
Journal ArticleDOI
ChIP-seq accurately predicts tissue-specific activity of enhancers
Axel Visel,Matthew J. Blow,Matthew J. Blow,Zirong Li,Tao Zhang,Jennifer A. Akiyama,Amy Holt,Ingrid Plajzer-Frick,Malak Shoukry,Crystal Wright,Feng Chen,Veena Afzal,Bing Ren,Edward M. Rubin,Edward M. Rubin,Len A. Pennacchio,Len A. Pennacchio +16 more
TL;DR: In this paper, the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue.
Journal ArticleDOI
In vivo enhancer analysis of human conserved non-coding sequences
Len A. Pennacchio,Len A. Pennacchio,Nadav Ahituv,Alan M. Moses,Shyam Prabhakar,Marcelo A. Nobrega,Marcelo A. Nobrega,Malak Shoukry,Simon Minovitsky,Inna Dubchak,Inna Dubchak,Amy Holt,Keith D. Lewis,Ingrid Plajzer-Frick,Jennifer A. Akiyama,Sarah De Val,Veena Afzal,Brian L. Black,Olivier Couronne,Olivier Couronne,Michael B. Eisen,Michael B. Eisen,Axel Visel,Edward M. Rubin,Edward M. Rubin +24 more
TL;DR: This study characterized the in vivo enhancer activity of a large group of non-coding elements in the human genome that are conserved in human–pufferfish, Takifugu (Fugu) rubripes, or ultraconserved in human-mouse–rat.
Journal ArticleDOI
ChIP-Seq identification of weakly conserved heart enhancers
Matthew J. Blow,David J. McCulley,Zirong Li,Tao Zhang,Jennifer A. Akiyama,Amy Holt,Ingrid Plajzer-Frick,Malak Shoukry,Crystal Wright,Feng Chen,Veena Afzal,James Bristow,Bing Ren,Brian L. Black,Edward M. Rubin,Edward M. Rubin,Axel Visel,Axel Visel,Len A. Pennacchio,Len A. Pennacchio +19 more
TL;DR: Transgenic mouse assays of 130 candidate regions revealed that most function reproducibly as enhancers active in the heart, irrespective of their degree of evolutionary constraint, suggesting that the evolutionary conservation of embryonic enhancers can vary depending on tissue type.
Journal ArticleDOI
Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development
Alexander Nord,Matthew J. Blow,Matthew J. Blow,Catia Attanasio,Jennifer A. Akiyama,Amy Holt,Roya Hosseini,Sengthavy Phouanenavong,Ingrid Plajzer-Frick,Malak Shoukry,Veena Afzal,John L.R. Rubenstein,Edward M. Rubin,Edward M. Rubin,Len A. Pennacchio,Len A. Pennacchio,Axel Visel,Axel Visel,Axel Visel +18 more
TL;DR: The dynamic enhancer activities uncovered in this study illuminate rapid and pervasive temporal in vivo changes in enhancer usage that underlie processes central to development and disease.
Journal ArticleDOI
Human-specific gain of function in a developmental enhancer.
Shyam Prabhakar,Axel Visel,Jennifer A. Akiyama,Malak Shoukry,Keith D. Lewis,Amy Holt,Ingrid Plajzer-Frick,Harris Morrison,David R. FitzPatrick,Veena Afzal,Len A. Pennacchio,Len A. Pennacchio,Edward M. Rubin,Edward M. Rubin,James P. Noonan +14 more
TL;DR: In transgenic mice, a conserved noncoding sequence (HACNS1) that evolved extremely rapidly in humans acted as an enhancer of gene expression that has gained a strong limb expression domain relative to the orthologous elements from chimpanzee and rhesus macaque.