The evolution of gene regulation by transcription factors and microRNAs

By Kevin C. Chen, Nikolaus Rajewsky. Nature reviews genetics, 2007

1,576 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/431a18a4d9d8ada3bae1e8c4d3d89b23d735e9ab

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Citations in the corpus

Transfer String Kernel for Cross-Context DNA-Protein Binding Prediction (2016, background): “sequences have low conservation across species even though many TF proteins are conserved across large evolutionary distances [7].”
MicroRNA control of signal transduction (2010, background): “Just like transcription factor binding sites, 3′ UTR sequences are not constrained by coding needs and can potentially diverge rapidly to co-opt beneficial miRNA–target interactions and counter-select against deleterious pair”
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades (2011, background): “tion because they are too lowly abundant to have any real effect on protein output (51).”
An adaptive epigenetic memory in conifers with important implications for seed production (2012, background): “At the level of post-translational control sRNAs appear to be important (Chen and Rajewsky, 2007; Kaufmann et al., 2010).”
Evolution of microRNA diversity and regulation in animals (2011, background): “Because RNAs easily form non-perfect foldback structures, the evolution of a new miRNA gene appears to be more likely than the emergence of a novel protein-coding gen”
Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. (2011, background): “…expanded in the past 600–100 million years are the MADS box proteins, basic- region leucine-zipper proteins (bZIP), and the MYB and bHLH families (Figure 1), which are described extensively below (Becker et al., 2000; Riechmann et al., 2000; Shiu et al., 2005; Chen and Rajewsky, 2007).”
The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. (2007, neutral): “Since newly evolved miRNAs are thought to have fewer targets than highly conserved miRNAs (Chen and Rajewsky, 2007; J.G. Ruby, A. Stark, W. Johnston, M. Kellis, D. Bartel, and E.C.L., unpublished data), the regulatory networks involving mirtrons may be proportionally smaller than those mediated by…”
A human snoRNA with microRNA-like functions. (2008, background): “It is also known that highly conserved 7-mers in 3 0 UTRs are often complementary to seed sequences of known miRNAs (Chen and Rajewsky, 2007).”
Discovering microRNAs from deep sequencing data using miRDeep (2008, background): “In order to address an ongoing discussion about the importance of nonconserved miRNA”
Transposable elements and the evolution of regulatory networks (2008, background): “Thus, the logic of post-transcriptional regulation by smRNAs, whereby a single smRNA species can trans -regulate multiple genes through recognition of shared cis -elements, is similar to the logic of transcriptional regulation by transcription factor”
Altered expression of MicroRNA in synovial fibroblasts and synovial tissue in rheumatoid arthritis. (2008, background): “The miRNA are highly conserved among mammals ( 2 ).”
ScholarWorks @ UTRGV ScholarWorks @ UTRGV (background): “Over the last decade, research for mapping genotype to expression phenotype or disease phenotype such as expression quantitative trait loci (eQTL) study and genome wide association study have been actively performed [1].”
Transcription factors and evolution: An integral part of gene expression (Review) (2020, neutral): “with TFs, they play an important role in gene regulatory network evolution (47).”
MicroRNAs: the fine-tuners of Toll-like receptor signalling (2011, background): “Many studies have highlighted the fact that miRNA-mediated targeting of transcription factors is an important aspect of miRNA functio”
RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse (2015, background): “Gene regulatory events play crucial roles in a variety of physiological and developmental processes in a cell, in which macromolecules such as genes, RNAs and proteins are coordinated to orchestrate operative responses under different conditions (1).”
The QTN Program and the Alleles That Matter for Evolution: All That’s Gold Does Not Glitter (2011, neutral): “Transcription factor binding sites, miRNA binding sites, and miRNA genes arise spontaneously at quite considerable rates (Stone and Wray 2001; Dermitzakis and Clark 2002; MacArthur and Brookfield 2004; Chen and Rajewsky 2007; Lu et al. 2008).”
MicroRNA control in the immune system: basic principles. (2009, background): “Because of their simple structure and mode of target recognition, miRNAs as well as their targets can evolve rapidly (Chen and Rajewsky, 2007; Gardner and Vinther, 2008; Lu et al., 2008; Niwa and Slack, 2007).”