Genomic strategies to identify mammalian regulatory sequences

By Len A. Pennacchio, Edward M. Rubin. Nature reviews genetics, 2001

414 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/dfaf4c5db7a0e3fdd010a23767b00fc2aca1a981

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Citations in the corpus

Computational prediction of transcription-factor binding site locations (2003, background): “It has been described as searching for “islands of conserved sequences in seas of less conserved noncoding sequence” [40].”
Sequencing and comparison of yeast species to identify genes and regulatory elements (2003, methodology): “This approach has long been used to study promoters of speciﬁc genes in many organisms 11,13,24,38,39 , and recently was applied across the entire human and mouse genomes 7 .”
Identification of conserved regulatory elements by comparative genome analysis (2003, background): “The utility of phylogenetic footprinting extends to a broad array of annotation challenges, but it is particularly suited to the identification of sequences with a functional role in the regulation of gene transcription [5,6].”
Long-range control of gene expression: emerging mechanisms and disruption in disease. (2005, background): “The conservation of these sequences is taken to imply functional significance, most likely in gene regulation (Hardison 2000; Pennacchio and Rubin 2001).”
Comparative Genomics (2007, neutral): “Many but not all of these regulatory regions are conserved among mammals (Hardison 2000; Pennacchio and Rubin 2001).”
LOGOS: a modular Bayesian model for de novo motif detection (2003, background): “, only 5% for mammalian genomes [Pennacchio and Rubin, 2001]), whereas the rest of the genome, besides playing purely structural roles such as forming the centromeres and telomeres of the chromosomes, contains a large number of short sequence motifs that make up an immensely rich”
High-resolution profiling of histone methylations in the human genome. (2007, methodology): “Comparative genomics has been used to predict a set of highly conserved noncoding sequences as enhancers (Loots et al., 2000; Miller et al., 2004; Pennacchio and Rubin, 2001).”
Distribution and intensity of constraint in mammalian genomic sequence. (2005, background): “2004), it is clear that comparative sequence analysis is a powerful paradigm for the discovery of those functional regions in the human genome whose experimental discovery is difficult (O’Brien et al. 1999; Hardison 2000; Pennacchio and Rubin 2001; Cooper and Sidow 2003).”