Results 11 to 20 of about 8,121,841 (424)

Multiple binding sites for transcriptional repressors can produce regular bursting and enhance noise suppression [PDF]

Phys. Rev. E 95, 042412 (2017), 2016
Cells may control fluctuations in protein levels by means of negative autoregulation, where transcription factors bind DNA sites to repress their own production. Theoretical studies have assumed a single binding site for the repressor, while in most species it is found that multiple binding sites are arranged in clusters.
Lengyel, Iván M., Morelli, Luis G.
arxiv   +5 more sources

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., Stewart, Alexander J.   +1 more
arxiv   +3 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

Biophysical Fitness Landscapes for Transcription Factor Binding Sites [PDF]

PLoS Comput Biol 10:e1003683, 2014, 2013
Evolutionary trajectories and phenotypic states available to cell populations are ultimately dictated by intermolecular interactions between DNA, RNA, proteins, and other molecular species. Here we study how evolution of gene regulation in a single-cell eukaryote S.
Haldane, Allan, Manhart, Michael, Morozov, Alexandre V.   +2 more
arxiv   +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, Willmann Stana, Lässig Michael   +2 more
doaj   +5 more sources

Formation of regulatory modules by local sequence duplication [PDF]

, 2011
Turnover of regulatory sequence and function is an important part of molecular evolution. But what are the modes of sequence evolution leading to rapid formation and loss of regulatory sites? Here, we show that a large fraction of neighboring transcription factor binding sites in the fly genome have formed from a common sequence origin by local ...
A Stark, A Tanay, AL Halpern, AM Moses, AM Moses, AM Moses, Amos Tanay, Armita Nourmohammad, B Ondek, BP Berman, CM Bergman, CM Bergman, CT Harbison, D Gruen, D Stanojevic, DN Arnosti, DS Fields, E Segal, EE Hare, EH Davidson, EH Davidson, G Badis, G Benson, G Leung, GD Stormo, I Abnizova, J Berg, J Berg, J Monod, JM Hancock, K Thornton, L Li, M Kimura, M Kimura, M Levine, M Lynch, M Lynch, M Lässig, M Markstein, M Pachkov, M Ptashne, MC King, MD Vinces, Michael Lässig, MM Kulkarni, MS Halfon, MS Halfon, MV Katti, MZ Ludwig, MZ Ludwig, MZ Ludwig, MZ Ludwig, N Rajewsky, NE Buchler, O Berg, PW Messer, R Durbin, RJ Britten, RW Lusk, S Kullback, S Mukherjee, S Sinha, S Sinha, S Sinha, S Small, SJ Maerkl, SM Gallo, SW Doniger, V Boeva, V Mustonen, V Mustonen, V Mustonen, Z Wunderlich   +72 more
arxiv   +6 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. For short binding sites, the matching probability can display large fluctuations from one putative binding site to another.
, , , B. Tirozzi, Bianchi D. Tirozzi B., Bourdeau V., Coles S. G., Cordero F., D. Bianchi, Embrechts P., Wood J.   +10 more
arxiv   +3 more sources

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, Stephen Macaspac, Ho Leung Ng   +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, Ina K Dahlsveen, Peter B Becker, R. Scott Hawley, Rosemarie Lamm, Vladimir I Shelest   +5 more
core   +13 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
doaj   +1 more source