VISTA Enhancer Browser—a database of tissue-specific human enhancers

Despite the known existence of distant-acting cis-regulatory elements in the human genome, only a small fraction of these elements has been identified and experimentally characterized in vivo. This paucity of enhancer collections with defined activities has thus hindered computational approaches for the genome-wide prediction of enhancers and their functions. To fill this void, we utilize comparative genome analysis to identify candidate enhancer elements in the human genome coupled with the experimental determination of their in vivo enhancer activity in transgenic mice [L. A. Pennacchio et al. (2006) Nature, in press]. These data are available through the VISTA Enhancer Browser (). This growing database currently contains over 250 experimentally tested DNA fragments, of which more than 100 have been validated as tissue-specific enhancers. For each positive enhancer, we provide digital images of whole-mount embryo staining at embryonic day 11.5 and an anatomical description of the reporter gene expression pattern. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to a particular tissue, or download entire collections of enhancers with a defined tissue specificity or conservation depth. These experimentally validated training sets are expected to provide a basis for a wide range of downstream computational and functional studies of enhancer function

ChIP-seq Mapping of Distant-Acting Enhancers and Their In Vivo Activities

The genomic location and function of most distant-acting transcriptional enhancers in the human genome remains unknown We performed ChIP-seq for various transcriptional coactivator proteins (such as p300) directly from different embryonic mouse tissues, identifying thousands of binding sitesTransgenic mouse experiments show that p300 and other co-activator peaks are highly predictive of genomic location AND tissue-specific activity patterns of distant-acting enhancersMost enhancers are active only in one or very few tissues Genomic location of tissue-specific p300 peaks correlates with tissue-specific expression of nearby genes Most binding sites are conserved, but the global degree of conservation varies between tissue

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

This is an Open Access article distributed under the terms of the Creative Commons Attribution License.-- et al.Comprehensive analysis of cis-regulatory elements is key to understanding the dynamic gene regulatory networks that control embryonic development. While transgenic animals represent the gold standard assay, their generation is costly, entails significant animal usage, and in utero development complicates time-course studies. As an alternative, embryonic stem (ES) cells can readily be differentiated in a process that correlates well with developing embryos. Here, we describe a highly effective platform for enhancer assays using an Hsp68/Venus reporter cassette that targets to the Hprt locus in mouse ES cells. This platform combines the flexibility of Gateway® cloning, live cell trackability of a fluorescent reporter, low background and the advantages of single copy insertion into a defined genomic locus. We demonstrate the successful recapitulation of tissue-specific enhancer activity for two cardiac and two haematopoietic enhancers. In addition, we used this assay to dissect the functionality of the highly conserved Ets/Ets/Gata motif in the Scl+19 enhancer, which revealed that the Gata motif is not required for initiation of enhancer activity. We further confirmed that Gata2 is not required for endothelial activity of the Scl+19 enhancer using Gata2−/− Scl+19 transgenic embryos. We have therefore established a valuable toolbox to study gene regulatory networks with broad applicability.Research in the authors' laboratory is supported by the National Centre for the Replacement, Refinement and Reduction of Animals in Research, Leukemia and Lymphoma Research, The Leukaemia and Lymphoma Society, Cancer Research UK, the Biotechnology and Biological Sciences Research Council, the Medical Research Council and core support grants from the Wellcome Trust to the Cambridge Institute for Medical Research and Wellcome Trust–MRC Cambridge Stem Cell Institute. D.E.D. was supported by the National Heart Lung and Blood Institute [grant number 5T32HL098057], and L.A.P. by the National Institute of Neurological Disorders and Stroke [grant number R01NS062859A] and by the National Human Genome Research Institute [grant numbers R01HG003988 and U54HG006997].Peer reviewe

Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease.

How stage-specific enhancer dynamics modulate gene expression patterns essential for organ development, homeostasis and disease is not well understood. Here, we addressed this question by mapping chromatin occupancy of GATA4--a master cardiac transcription factor--in heart development and disease. We find that GATA4 binds and participates in establishing active chromatin regions by stimulating H3K27ac deposition, which facilitates GATA4-driven gene expression. GATA4 chromatin occupancy changes markedly between fetal and adult heart, with a limited binding sites overlap. Cardiac stress restored GATA4 occupancy to a subset of fetal sites, but many stress-associated GATA4 binding sites localized to loci not occupied by GATA4 during normal heart development. Collectively, our data show that dynamic, context-specific transcription factors occupancy underlies stage-specific events in development, homeostasis and disease

SNP-VISTA: An interactive SNP visualization tool

BACKGROUND: Recent advances in sequencing technologies promise to provide a better understanding of the genetics of human disease as well as the evolution of microbial populations. Single Nucleotide Polymorphisms (SNPs) are established genetic markers that aid in the identification of loci affecting quantitative traits and/or disease in a wide variety of eukaryotic species. With today's technological capabilities, it has become possible to re-sequence a large set of appropriate candidate genes in individuals with a given disease in an attempt to identify causative mutations. In addition, SNPs have been used extensively in efforts to study the evolution of microbial populations, and the recent application of random shotgun sequencing to environmental samples enables more extensive SNP analysis of co-occurring and co-evolving microbial populations. The program is available at [1]. RESULTS: We have developed and present two modifications of an interactive visualization tool, SNP-VISTA, to aid in the analyses of the following types of data: A. Large-scale re-sequence data of disease-related genes for discovery of associated and/or causative alleles (GeneSNP-VISTA). B. Massive amounts of ecogenomics data for studying homologous recombination in microbial populations (EcoSNP-VISTA). The main features and capabilities of SNP-VISTA are: 1) mapping of SNPs to gene structure; 2) classification of SNPs, based on their location in the gene, frequency of occurrence in samples and allele composition; 3) clustering, based on user-defined subsets of SNPs, highlighting haplotypes as well as recombinant sequences; 4) integration of protein evolutionary conservation visualization; and 5) display of automatically calculated recombination points that are user-editable. CONCLUSION: The main strength of SNP-VISTA is its graphical interface and use of visual representations, which support interactive exploration and hence better understanding of large-scale SNP data by the user

Response to comment on "Human-specific gain of function in a developmental enhancer"

Duret and Galtier argue that human-specific sequence divergence and gain of function in the HACNS1 enhancer result from deleterious biased gene conversion (BGC) with no contribution from positive selection. We reinforce our previous conclusion by analyzing hypothesized BGC events genomewide and assessing the effect of recombination rates on human-accelerated conserved noncoding sequence ascertainment. We also provide evidence that AT → GC substitution bias can coexist with positive selection

Isolation, characterization, and genome sequence of the first representative of a novel class within the Chloroflexi that is abundant in some U.S. Great Basin hot springs and may play important roles in N and C cycling

A thermophilic, facultatively microaerophilic, heterotrophic bacterium, designated strain JAD2, was isolated from sediments of Great Boiling Spring (GBS), an ~80oC, circumneutral hot spring in the Great Basin GB). The strain grew anaerobically on yeast extract or peptone with an optimal growth temperature of 70-75oC. Growth was stimulated by addition of 0.01 atm O2 to the culture vessel headspace, but was inhibited by higher concentrations (0.2 atm). Cells of JAD2 formed non-motile filaments ranging from 10 to \u3e300 μm in length, which typically decreased in length during stationary phase. 16S rRNA gene-targeted pyrotag sequencing and clone library data suggest that close relatives of this isolate are prominent members of the sediment communities in GBS. Shotgun sequencing of the JAD2 genome produced an assembly consisting of ~3.2 Mbp with an average G+C content of 67.3%. Phylogenies inferred from the 16S rRNA gene and predicted amino acid sequences of various conserved proteins indicate that JAD2 is the first cultivated representative of the GAL35 group, a new class within the Chloroflexi. Predicted genes in the draft genome encoding a putative carbon monoxide dehydrogenase (coxMSL), nitrite reductase (nrfHA) and nitrous oxide reductase (nosZ) suggest that this isolate may play important roles in N and C cycling in GBS sediments