Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

By Alexander Stark, Michael F. Lin, Pouya Kheradpour, Jakob Skou Pedersen, Leopold Parts, Joseph W. Carlson, Madeline A. Crosby, Matthew D. Rasmussen, Sushmita Roy, Ameya N. Deoras and 34 more. Nature, 2007

657 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/05222402b5a48487fbde444d62fc631c96d6be13

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Citations in the corpus

Metazoan MicroRNAs (2018, background): “…nucleotide in either the 5′ or 3′ direction (Figure 5A), can sometimes also mediate detectable repression (Friedman et al., 2009; Jan et al., 2011; Kim et al., 2016a), as can 7–8-nt sites in ORFs or 5′ UTRs (Lewis et al., 2005; Stark et al., 2007b; Schnall-Levin et al., 2010; Agarwal et al., 2017).”
iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections (2014, methodology): “The library of motifs used in this manuscript is comprised of 6383 PWMs from several sources [73,74] and databases: TRANSFAC [5], Jaspar [21], FlyFactor-Survey [75], SelexConsensus [76], hPDI [77], YeTFaSCo [78] and Tiffin [76] (Table 1).”
Molecular Evolution and Functional Characterization of Drosophila Insulin-Like Peptides (2010, methodology): “Taking advantage of the 12 sequenced Drosophila genomes [26], we investigated the evolution of ILPs across the Drosophila genus.”
A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence (2008, background): “More recent reports have also shown that, contrary to other highly conserved coding region motifs, miRNA target sites are conserved in all three reading frames among Drosophila genomes (11), and that target sites introduced into the 5 UTR of transcripts can repress translation (12).”
Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. (2007, methodology): “…pseudoob-scura , Drosophila mojavensis , Drosophila virilis , and Drosophila grimshawi ) (Adams et al. 2000; Richards et al. 2005; Drosophila 12 Genomes Consortium 2007; Stark et al. 2007c), RNAfold (Hofacker et al. 1994) was used to identify candidate hairpins from across the entire genome.”
Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation (2014, background): “Comprehensive identification of smORFs has been challenging and has mainly relied on evolutionary conservation (Stark et al , 2007; Lin et al , 2011), known patterns of codon occurrence and mass spectrometry (Schwaid et al , 2013; Slavoff et al , 2013).”
PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions (2010, background): “…effective, performing competitively with a phylogenetic modeling approach with much less computational expense, and indeed we have applied it successfully in flies (Lin et al., 2007; Stark et al., 2007), fungi (Butler et al., 2009) and mammals (Clamp et al., 2007; Guttman et al., 2009, 2010).”
PlantRegMap: charting functional regulatory maps in plants (2019, background): “Conservation landscapes in humans and fruit flies have been widely used to illustrate their genome sequences (20,21); thus, our conservation landscapes of 63 plants provide the research community with a unique chance to decode plant genomes.”