Scanning Human Gene Deserts for Long-Range Enhancers

By Marcelo Araujo da Nóbrega, Ivan Ovcharenko, Veena Afzal, Edward M. Rubin. Science, 2003

658 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/80b7b7b3f266740de04ba313b51e67dfbe46229d

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Citations in the corpus

VISTA Enhancer Browser—a database of tissue-specific human enhancers (2006, methodology): “For instance, a systematic search for such conserved non-coding elements was successfully used to identify enhancers in a gene-sparse region of the human genome (6).”
A bivalent chromatin structure marks key developmental genes in embryonic stem cells. (2006, background): “Recent studies have revealed that the most highly conserved noncoding elements (HCNEs) in mammalian genomes cluster within 200 HCNE-rich genomic loci, which include all four Hox clusters (Nobrega et al., 2003; Bejerano et al., 2004; Lindblad-Toh et al., 2005; Woolfe et al., 2005).”
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes (2004, methodology): “A similar prioritization strategy, using comparisons between human sequence and that of a single distantly related species, the puffer fish, was recently used to identify evolutionarily conserved regions (ECRs) corresponding to critical regulatory elements in large (>1 Mb), highly conserved gene des”
Long-range control of gene expression: emerging mechanisms and disruption in disease. (2005, background): “Some developmental regulator genes with a network of multiple elements to control their intricate spatiotemporal expression pattern have a relatively simple genomic organization: they reside in regions that have been termed “gene deserts” (Nobrega et al. 2003).”
Comparative Genomics (2007, positive): “The Dc2 region was shown to be an enhancer by Nobrega et al. (2003); the image is from the Enhancer Browser (Table Q.3).”
Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development (2004, positive): “Although non-coding sequences generally lack sequence conservation between highly divergent species [22], there are a number of striking examples where comparison between human and pufferfish (Fugu rubripes) gene regions has readily identified highly conserved non-coding sequences that have been sho”
Genome sequence, comparative analysis and haplotype structure of the domestic dog (2005, background): “Although the function of conserved non-coding elements is unknown, on the basis of recent studies 59,63–66 it seems likely that many regulate gene expression.”
PEDLA: predicting enhancers with a deep learning-based algorithmic framework (2016, background): “The first genome-scale efforts to identify enhancers were based on evolutionary sequence conservation (19-22) because regulatory sequences are likely to evolve under negative evolutionary selection (23-25).”
Genomic Views of Distant-Acting Enhancers (2009, background): “These approaches are based on the assumption that the sequences of gene regulatory elements, like those of protein-coding genes, are under negative evolutionary selection, because most changes in functional sequences have deleterious consequence”
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. (2005, background): “For example, Dermitzakis et al. (2002) and Nobrega et al. (2003) have defined conserved elements as intervals of at least 100 bp with >70% identity.”