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https://www.readbyqxmd.com/read/29040720/genome-wide-prediction-of-minor-groove-electrostatic-potential-enables-biophysical-modeling-of-protein-dna-binding
#1
Tsu-Pei Chiu, Satyanarayan Rao, Richard S Mann, Barry Honig, Remo Rohs
Protein-DNA binding is a fundamental component of gene regulatory processes, but it is still not completely understood how proteins recognize their target sites in the genome. Besides hydrogen bonding in the major groove (base readout), proteins recognize minor-groove geometry using positively charged amino acids (shape readout). The underlying mechanism of DNA shape readout involves the correlation between minor-groove width and electrostatic potential (EP). To probe this biophysical effect directly, rather than using minor-groove width as an indirect measure for shape readout, we developed a methodology, DNAphi, for predicting EP in the minor groove and confirmed the direct role of EP in protein-DNA binding using massive sequencing data...
October 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28927002/predicting-variation-of-dna-shape-preferences-in-protein-dna-interaction-in-cancer-cells-with-a-new-biophysical-model
#2
Kirill Batmanov, Junbai Wang
DNA shape readout is an important mechanism of transcription factor target site recognition, in addition to the sequence readout. Several machine learning-based models of transcription factor-DNA interactions, considering DNA shape features, have been developed in recent years. Here, we present a new biophysical model of protein-DNA interactions by integrating the DNA shape properties. It is based on the neighbor dinucleotide dependency model BayesPI2, where new parameters are restricted to a subspace spanned by the dinucleotide form of DNA shape features...
September 18, 2017: Genes
https://www.readbyqxmd.com/read/28676789/importance-of-the-sequence-directed-dna-shape-for-specific-binding-site-recognition-by-the-estrogen-related-receptor
#3
Kareem Mohideen-Abdul, Karima Tazibt, Maxime Bourguet, Isabelle Hazemann, Isabelle Lebars, Maria Takacs, Sarah Cianférani, Bruno P Klaholz, Dino Moras, Isabelle M L Billas
Most nuclear receptors (NRs) bind DNA as dimers, either as hetero- or as homodimers on DNA sequences organized as two half-sites with specific orientation and spacing. The dimerization of NRs on their cognate response elements (REs) involves specific protein-DNA and protein-protein interactions. The estrogen-related receptor (ERR) belongs to the steroid hormone nuclear receptor (SHR) family and shares strong similarity in its DNA-binding domain (DBD) with that of the estrogen receptor (ER). In vitro, ERR binds with high affinity inverted repeat REs with a 3-bps spacing (IR3), but in vivo, it preferentially binds to single half-site REs extended at the 5'-end by 3 bp [estrogen-related response element (ERREs)], thus explaining why ERR was often inferred as a purely monomeric receptor...
2017: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/28642456/predicting-conformational-ensembles-and-genome-wide-transcription-factor-binding-sites-from-dna-sequences
#4
Munazah Andrabi, Andrew Paul Hutchins, Diego Miranda-Saavedra, Hidetoshi Kono, Ruth Nussinov, Kenji Mizuguchi, Shandar Ahmad
DNA shape is emerging as an important determinant of transcription factor binding beyond just the DNA sequence. The only tool for large scale DNA shape estimates, DNAshape was derived from Monte-Carlo simulations and predicts four broad and static DNA shape features, Propeller twist, Helical twist, Minor groove width and Roll. The contributions of other shape features e.g. Shift, Slide and Opening cannot be evaluated using DNAshape. Here, we report a novel method DynaSeq, which predicts molecular dynamics-derived ensembles of a more exhaustive set of DNA shape features...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28631437/control-of-virulence-gene-transcription-by-indirect-readout-in-vibrio-cholerae-and-salmonella-enterica-serovar-typhimurium
#5
Charles J Dorman, Matthew J Dorman
Indirect readout mechanisms of transcription control rely on the recognition of DNA shape by transcription factors (TFs). TFs may also employ a direct readout mechanism that involves the reading of the base sequence in the DNA major groove at the binding site. TFs with winged helix-turn-helix (wHTH) motifs use an alpha helix to read the base sequence in the major groove while inserting a beta sheet 'wing' into the adjacent minor groove. Such wHTH proteins are important regulators of virulence gene transcription in many pathogens; they also control housekeeping genes...
June 19, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28580956/correspondence-dna-shape-is-insufficient-to-explain-binding
#6
Matthew J Rossi, William K M Lai, B Franklin Pugh
No abstract text is available yet for this article.
June 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/28580953/correspondence-reply-to-dna-shape-is-insufficient-to-explain-binding
#7
Sivakanthan Kasinathan, Gabriel E Zentner, Beibei Xin, Remo Rohs, Steven Henikoff
No abstract text is available yet for this article.
June 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/28541376/dna-sequence-shape-kernel-enables-alignment-free-modeling-of-transcription-factor-binding
#8
Wenxiu Ma, Lin Yang, Remo Rohs, William Stafford Noble
Motivation: Transcription factors (TFs) bind to specific DNA sequence motifs. Several lines of evidence suggest that TF-DNA binding is mediated in part by properties of the local DNA shape: the width of the minor groove, the relative orientations of adjacent base pairs, etc. Several methods have been developed to jointly account for DNA sequence and shape properties in predicting TF binding affinity. However, a limitation of these methods is that they typically require a training set of aligned TF binding sites...
October 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28355537/ephemeral-protein-binding-to-dna-shapes-stable-nuclear-bodies-and-chromatin-domains
#9
Chris A Brackley, Benno Liebchen, Davide Michieletto, Francois Mouvet, Peter R Cook, Davide Marenduzzo
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear bodies exchange rapidly with the soluble pool while the underlying structure persists; such observations await a satisfactory biophysical explanation. To shed light on this, we perform large-scale Brownian dynamics simulations of a chromatin fiber interacting with an ensemble of (multivalent) DNA-binding proteins able to switch between an "on" (binding) and an "off" (nonbinding) state. This system provides a model for any DNA-binding protein that can be posttranslationally modified to change its affinity for DNA (e...
March 28, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28167566/transcription-factor-family-specific-dna-shape-readout-revealed-by-quantitative-specificity-models
#10
Lin Yang, Yaron Orenstein, Arttu Jolma, Yimeng Yin, Jussi Taipale, Ron Shamir, Remo Rohs
Transcription factors (TFs) achieve DNA-binding specificity through contacts with functional groups of bases (base readout) and readout of structural properties of the double helix (shape readout). Currently, it remains unclear whether DNA shape readout is utilized by only a few selected TF families, or whether this mechanism is used extensively by most TF families. We resequenced data from previously published HT-SELEX experiments, the most extensive mammalian TF-DNA binding data available to date. Using these data, we demonstrated the contributions of DNA shape readout across diverse TF families and its importance in core motif-flanking regions...
February 6, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/27830804/evolution-cat-dna-shaped-by-diet
#11
(no author information available yet)
No abstract text is available yet for this article.
November 10, 2016: Nature
https://www.readbyqxmd.com/read/27768937/homeodomain-proteins-in-action-similar-dna-binding-preferences-highly-variable-connectivity
#12
REVIEW
Nicoletta Bobola, Samir Merabet
Homeodomain proteins are evolutionary conserved proteins present in the entire eukaryote kingdom. They execute functions that are essential for life, both in developing and adult organisms. Most homeodomain proteins act as transcription factors and bind DNA to control the activity of other genes. In contrast to their similar DNA binding specificity, homeodomain proteins execute highly diverse and context-dependent functions. Several factors, including genome accessibility, DNA shape, combinatorial binding and the ability to interact with many transcriptional partners, diversify the activity of homeodomain proteins and culminate in the activation of highly dynamic, context-specific transcriptional programs...
October 18, 2016: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/27745836/comprehensive-genetic-landscape-of-uveal-melanoma-by-whole-genome-sequencing
#13
Beryl Royer-Bertrand, Matteo Torsello, Donata Rimoldi, Ikram El Zaoui, Katarina Cisarova, Rosanna Pescini-Gobert, Franck Raynaud, Leonidas Zografos, Ann Schalenbourg, Daniel Speiser, Michael Nicolas, Laureen Vallat, Robert Klein, Serge Leyvraz, Giovanni Ciriello, Nicolò Riggi, Alexandre P Moulin, Carlo Rivolta
Uveal melanoma (UM) is a rare intraocular tumor that, similar to cutaneous melanoma, originates from melanocytes. To gain insights into its genetics, we performed whole-genome sequencing at very deep coverage of tumor-control pairs in 33 samples (24 primary and 9 metastases). Genome-wide, the number of coding mutations was rather low (only 17 variants per tumor on average; range 7-28), thus radically different from cutaneous melanoma, where hundreds of exonic DNA insults are usually detected. Furthermore, no UV light-induced mutational signature was identified...
November 3, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27569553/self-assembly-programming-of-dna-polyominoes
#14
Hui San Ong, Mohd Syafiq-Rahim, Noor Hayaty Abu Kasim, Mohd Firdaus-Raih, Effirul Ikhwan Ramlan
Fabrication of functional DNA nanostructures operating at a cellular level has been accomplished through molecular programming techniques such as DNA origami and single-stranded tiles (SST). During implementation, restrictive and constraint dependent designs are enforced to ensure conformity is attainable. We propose a concept of DNA polyominoes that promotes flexibility in molecular programming. The fabrication of complex structures is achieved through self-assembly of distinct heterogeneous shapes (i.e., self-organised optimisation among competing DNA basic shapes) with total flexibility during the design and assembly phases...
October 20, 2016: Journal of Biotechnology
https://www.readbyqxmd.com/read/27546793/dna-shape-features-improve-transcription-factor-binding-site-predictions-in%C3%A2-vivo
#15
Anthony Mathelier, Beibei Xin, Tsu-Pei Chiu, Lin Yang, Remo Rohs, Wyeth W Wasserman
Interactions of transcription factors (TFs) with DNA comprise a complex interplay between base-specific amino acid contacts and readout of DNA structure. Recent studies have highlighted the complementarity of DNA sequence and shape in modeling TF binding in vitro. Here, we have provided a comprehensive evaluation of in vivo datasets to assess the predictive power obtained by augmenting various DNA sequence-based models of TF binding sites (TFBSs) with DNA shape features (helix twist, minor groove width, propeller twist, and roll)...
September 28, 2016: Cell Systems
https://www.readbyqxmd.com/read/27257066/quantitative-modeling-of-gene-expression-using-dna-shape-features-of-binding-sites
#16
Pei-Chen Peng, Saurabh Sinha
Prediction of gene expression levels driven by regulatory sequences is pivotal in genomic biology. A major focus in transcriptional regulation is sequence-to-expression modeling, which interprets the enhancer sequence based on transcription factor concentrations and DNA binding specificities and predicts precise gene expression levels in varying cellular contexts. Such models largely rely on the position weight matrix (PWM) model for DNA binding, and the effect of alternative models based on DNA shape remains unexplored...
July 27, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27147539/statistical-analysis-of-structural-determinants-for-protein-dna-binding-specificity
#17
Rosario I Corona, Jun-Tao Guo
DNA-binding proteins play critical roles in biological processes including gene expression, DNA packaging and DNA repair. They bind to DNA target sequences with different degrees of binding specificity, ranging from highly specific (HS) to nonspecific (NS). Alterations of DNA-binding specificity, due to either genetic variation or somatic mutations, can lead to various diseases. In this study, a comparative analysis of protein-DNA complex structures was carried out to investigate the structural features that contribute to binding specificity...
August 2016: Proteins
https://www.readbyqxmd.com/read/27066866/to-be-specific-or-not-the-critical-relationship-between-hox-and-tale-proteins
#18
REVIEW
Samir Merabet, Richard S Mann
Hox proteins are key regulatory transcription factors that act in different tissues of the embryo to provide specific spatial and temporal coordinates to each cell. These patterning functions often depend on the presence of the TALE-homeodomain class cofactors, which form cooperative DNA-binding complexes with all Hox proteins. How this family of cofactors contributes to the highly diverse and specific functions of Hox proteins in vivo remains an important unsolved question. We review here the most recent advances in understanding the molecular mechanisms underlying Hox-TALE function...
June 2016: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/26840719/dna-shape-versus-sequence-variations-in-the-protein-binding-process
#19
Chuanying Chen, B Montgomery Pettitt
The binding process of a protein with a DNA involves three stages: approach, encounter, and association. It has been known that the complexation of protein and DNA involves mutual conformational changes, especially for a specific sequence association. However, it is still unclear how the conformation and the information in the DNA sequences affects the binding process. What is the extent to which the DNA structure adopted in the complex is induced by protein binding, or is instead intrinsic to the DNA sequence? In this study, we used the multiscale simulation method to explore the binding process of a protein with DNA in terms of DNA sequence, conformation, and interactions...
February 2, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/26681693/binding-of-transcription-factor-gabr-to-dna-requires-recognition-of-dna-shape-at-a-location-distinct-from-its-cognate-binding-site
#20
Walid A Al-Zyoud, Robert M G Hynson, Lorraine A Ganuelas, Adelle C F Coster, Anthony P Duff, Matthew A B Baker, Alastair G Stewart, Eleni Giannoulatou, Joshua W K Ho, Katharina Gaus, Dali Liu, Lawrence K Lee, Till Böcking
Mechanisms for transcription factor recognition of specific DNA base sequences are well characterized and recent studies demonstrate that the shape of these cognate binding sites is also important. Here, we uncover a new mechanism where the transcription factor GabR simultaneously recognizes two cognate binding sites and the shape of a 29 bp DNA sequence that bridges these sites. Small-angle X-ray scattering and multi-angle laser light scattering are consistent with a model where the DNA undergoes a conformational change to bend around GabR during binding...
February 18, 2016: Nucleic Acids Research
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