Special Issue "Protein-DNA Interactions: From Biophysics to Genomics"
Deadline for manuscript submissions: 31 December 2018
Prof. Junji Iwahara
Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophyiscs, University of Texas Medical Branch, Galveston, Texas, United States
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Interests: protein-DNA interactions; transcription factors; dynamics; kinetics; biophysical chemistry; spectroscopy
Protein-DNA interactions are vital for gene regulation, replication, and repair. These essential cellular processes result from a complex action of systems involving various proteins such as transcription factors and DNA repair/modifying enzymes. Many mechanistic aspects of these proteins should be delineated to understand how genes are regulated and maintained. Such knowledge is important, particularly because many human diseases are related to abnormalities in protein-DNA interactions. Adverse effects may be caused by mutations in the genes and cis-regulatory elements, by alteration in post-translational modifications of transcription factors and DNA repair/modifying enzymes, and by epigenetic modifications of DNA and histones. In many cases, these are related to each other in complex networks of molecular interplays. This special issue is intended for providing a forum to discuss protein-DNA interactions from broader perspectives, ranging from an atomic/molecular level to a cellular/organismic level. Review articles by experts in the field are particularly welcomed.Prof. Junji Iwahara
Manuscript Submission Information
Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.
Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access monthly journal published by MDPI.
Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.
- Biochemistry/biophysics of protein-DNA interactions
- Chromatin biology
- DNA repair
- Gene regulation
- Genetic regulatory network/circuit
- Molecular genetics/genomics
- Protein-DNA dynamics
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
Title: Regulation by bacterial transcription factors: relationship between binding energy and binding site functionality
Author: Marko Djordjevic
Affiliation: Faculty of Biology, University of Belgrade, Studentski Trg 16, 11000 Belgrade, Serbia
Abstract: TF binding sites are relatively short and degenerate motifs, which appear frequently by random in longer stretches of DNA sequence. Such randomly occurring sites with high estimated TF binding energies are often called non-sites, and are considered a major contributor to high number of false positives in bioinformatic (and possibly also experimental) searches of regulatory elements. We recently observed an absence of overrepresentation for sigma70 (bacterial transcription regulator responsible for transcription initiation) binding sites, in genomic regions where transcription initiation signals are abundant. This suggests significant negative selection on non-sites, which might notably reduce their number in genome sequence. We here investigate in detail the extent of such negative selection in different genomic regions, for three pleiotropic bacterial regulators. We find that more accurate energy matrices (describing TF binding specificity) and sequence alignments, lead to a larger extent of underrepresentation, which we interpret in terms of more accurate models being able to better separate between sites and non-sites. We however consistently obtain that while the negative selection is statistically significant, its extent is relatively small, leading to up to 30% reduction in the number of non-sites. We here propose that additional mechanisms may contribute to reduction of TF binding to regions where functional regulation is not expected (e.g., to coding and convergent intergenic regions). In particular our results, based on comparison with genome-wide binding data (ChIP-chip, ChIP-seq), indicate that such regions may be less accessible to TF binding.