De novo prediction of PTBP1 binding and splicing targets reveals unexpected features of its RNA recognition and function. [PDF]
PLoS Comput Biol 10:e1003683, 2014, 2014 The splicing regulator Polypyrimidine Tract Binding Protein (PTBP1) has four RNA binding domains that each binds a short pyrimidine element, allowing recognition of diverse pyrimidine-rich sequences.
Black, Douglas L +5 more
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Multiple binding sites for transcriptional repressors can produce regular bursting and enhance noise suppression [PDF]
Phys. Rev. E 95, 042412 (2017), 2017 Cells may control fluctuations in protein levels by means of negative autoregulation, where transcription factors bind DNA sites to repress their own production.
Lengyel, Iván M., Morelli, Luis G.
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The evolution of complex gene regulation by low specificity binding sites [PDF]
Proc. R. Soc. B 7 October 2013 vol. 280 no. 1768 20131313, 2012 Transcription factor binding sites vary in their specificity, both within and between species. Binding specificity has a strong impact on the evolution of gene expression, because it determines how easily regulatory interactions are gained and lost ...
Plotkin, Joshua B. +1 more
core +2 more sources
p53 binding sites in transposons [PDF]
Frontiers in Genetics, 2012 Repeated regions of the genome harbor more functional information than commonly assumed. Two decades ago, a highly influential paper describing the consensus binding site for the key transcription factor p53 was published in Nature Genetics by el-Deiry et al. (1992). Recently, it has been observed that many p53 binding sites are species-specific (Jegga
Tomasz eZemojtel, Martin eVingron
doaj +5 more sources
Adaptive evolution of transcription factor binding sites [PDF]
BMC Evolutionary Biology, 2004 Background The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks in ...
Berg Johannes +2 more
doaj +5 more sources
Identifying short motifs by means of extreme value analysis [PDF]
Europhysics Letters 84 18001 (2008), 2008 The problem of detecting a binding site -- a substring of DNA where transcription factors attach -- on a long DNA sequence requires the recognition of a small pattern in a large background.
+10 more
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Locating ligand binding sites in G-protein coupled receptors using combined information from docking and sequence conservation [PDF]
PeerJ, 2021 GPCRs (G-protein coupled receptors) are the largest family of drug targets and share a conserved structure. Binding sites are unknown for many important GPCR ligands due to the difficulties of GPCR recombinant expression, biochemistry, and ...
Ashley Ryan Vidad +2 more
doaj +2 more sources
Targeting determinants of dosage compensation in Drosophila [PDF]
, 2006 The dosage compensation complex (DCC) in Drosophila melanogaster is responsible for up-regulating transcription from the single male X chromosome to equal the transcription from the two X chromosomes in females.
Gregor D Gilfillan +5 more
core +12 more sources
Inferring binding energies from selected binding sites. [PDF]
PLoS Computational Biology, 2009 We employ a biophysical model that accounts for the non-linear relationship between binding energy and the statistics of selected binding sites. The model includes the chemical potential of the transcription factor, non-specific binding affinity of the ...
Yue Zhao, David Granas, Gary D Stormo
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Binding sites analyser (BiSA): software for genomic binding sites archiving and overlap analysis. [PDF]
PLoS ONE, 2014 Genome-wide mapping of transcription factor binding and histone modification reveals complex patterns of interactions. Identifying overlaps in binding patterns by different factors is a major objective of genomic studies, but existing methods to archive ...
Matloob Khushi +3 more
doaj +1 more source