From Cis-Regulatory Elements to Complex RNPs and Back
نویسندگان
چکیده
منابع مشابه
Investigating transcriptional regulation: from analysis of complex networks to discovery of cis-regulatory elements.
Regulation of gene expression at the transcriptional level is a fundamental mechanism that is well conserved in all cellular systems. Due to advances in large-scale experimental analyses, we now have a wealth of information on gene regulation such as mRNA expression level across multiple conditions, genome-wide location data of transcription factors and data on transcription factor binding site...
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Modification of gene regulation has long been considered an important force in human evolution, particularly through changes to cis-regulatory elements (CREs) that function in transcriptional regulation. For decades, however, the study of cis-regulatory evolution was severely limited by the available data. New data sets describing the locations of CREs and genetic variation within and between s...
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Accurate and efficient splicing of eukaryotic pre-mRNAs requires recognition by trans-acting factors of a complex array of cis-acting RNA elements. Here, we developed a generalized Bayesian network to model the coevolution of splicing cis elements in diverse eukaryotic taxa. Cross-exon but not cross-intron compensatory interactions between the 5' splice site (5'ss) and 3' splice site (3'ss) wer...
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Variable order Markov models and variable order Bayesian trees have been proposed for the recognition of cis-regulatory elements, and it has been demonstrated that they outperform traditional models such as position weight matrices, Markov models, and Bayesian trees for the recognition of binding sites in prokaryotes. Here, we study to which degree variable order models can improve the recognit...
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Gene regulatory pathways converge at the level of transcription, where interactions among regulatory genes and between regulators and target genes result in the establishment of spatiotemporal patterns of gene expression. The growing identification of direct target genes for key transcription factors (TFs) through traditional and high-throughput experimental approaches has facilitated the eluci...
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ژورنال
عنوان ژورنال: Cold Spring Harbor Perspectives in Biology
سال: 2012
ISSN: 1943-0264
DOI: 10.1101/cshperspect.a012245