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Protein-DNA Interactions
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Protein-DNA Interactions

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (31 May 2017) | Viewed by 50527

Special Issue Editors

Prof. Dr. Linda Bloom

E-Mail Website
Guest Editor
Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
Interests: dynamic protein-DNA interactions; DNA replication; DNA repair
Prof. Dr. Jörg Bungert

E-Mail Website
Guest Editor
Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
Interests: Protein-DNA interactions; synthetic DNA-binding proteins; transcription

Special Issue Information

Dear Colleagues,

The binding of proteins to DNA is critical for maintaining and expressing genetic information. Protein-DNA interactions are involved in condensing chromosomes to fit into cells, regulating the expression of genetic information, duplicating the genome to pass copies to daughter cells, and preserving the structure and integrity of genomic DNA. Our understanding of protein-DNA interactions required for these critical functions has advanced on many levels. Structural approaches have elucidated mechanisms by which proteins physically interact with DNA to perform their functions. Biochemical studies have defined dynamic and transient protein-DNA interactions essential for enzyme transactions on DNA. Recently, exciting progress has been made in two areas: single molecule and in vivo studies of protein-DNA interactions. Single molecule approaches reveal the complex dynamics of molecular interactions between single protein molecules and DNA that are hidden by the ensemble averaging inherent in bulk methods. Observation of the behavior of individual molecules allows us to answer questions that are impossible to address by examining a large population of molecules where the dynamics are unsynchronized, and thus “blur” the picture that we get. Exciting progress has also been made in investigating protein-DNA interactions inside cells in the crowded and complex molecular environment where they naturally function. Researchers have been able to query unique loci to identify protein-DNA interactions that are required for a specific cellular process, and recent advances in DNA sequencing have permitted the development of approaches to map protein-DNA interactions across the genome and in a cell-type specific manner. These studies revealed that DNA shape and DNA motif environment contribute to efficient protein-DNA interactions. Articles in this special issue should provide insight into mechanisms of protein-DNA interactions, and papers using single-molecule approaches or investigating interactions in vivo would be of special interest.

Prof. Dr. Linda Bloom
Prof. Dr. Jörg Bungert
Guest Editors

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 submissions that pass pre-check are 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. Genes 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 2600 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.

Keywords

  • protein-DNA interactions
  • chromatin structure
  • transcription
  • DNA replication
  • DNA repair
  • DNA recombination

Published Papers (6 papers)

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Research

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14 pages, 1241 KiB  
Article
Transcription Factor and lncRNA Regulatory Networks Identify Key Elements in Lung Adenocarcinoma
by Dan Li, William Yang, Jialing Zhang, Jack Y. Yang, Renchu Guan and Mary Qu Yang
Genes 2018, 9(1), 12; https://doi.org/10.3390/genes9010012 - 05 Jan 2018
Cited by 12 | Viewed by 5883
Abstract
Lung cancer is the second most commonly diagnosed carcinoma and is the leading cause of cancer death. Although significant progress has been made towards its understanding and treatment, unraveling the complexities of lung cancer is still hampered by a lack of comprehensive knowledge [...] Read more.
Lung cancer is the second most commonly diagnosed carcinoma and is the leading cause of cancer death. Although significant progress has been made towards its understanding and treatment, unraveling the complexities of lung cancer is still hampered by a lack of comprehensive knowledge on the mechanisms underlying the disease. High-throughput and multidimensional genomic data have shed new light on cancer biology. In this study, we developed a network-based approach integrating somatic mutations, the transcriptome, DNA methylation, and protein-DNA interactions to reveal the key regulators in lung adenocarcinoma (LUAD). By combining Bayesian network analysis with tissue-specific transcription factor (TF) and targeted gene interactions, we inferred 15 disease-related core regulatory networks in co-expression gene modules associated with LUAD. Through target gene set enrichment analysis, we identified a set of key TFs, including known cancer genes that potentially regulate the disease networks. These TFs were significantly enriched in multiple cancer-related pathways. Specifically, our results suggest that hepatitis viruses may contribute to lung carcinogenesis, highlighting the need for further investigations into the roles that viruses play in treating lung cancer. Additionally, 13 putative regulatory long non-coding RNAs (lncRNAs), including three that are known to be associated with lung cancer, and nine novel lncRNAs were revealed by our study. These lncRNAs and their target genes exhibited high interaction potentials and demonstrated significant expression correlations between normal lung and LUAD tissues. We further extended our study to include 16 solid-tissue tumor types and determined that the majority of these lncRNAs have putative regulatory roles in multiple cancers, with a few showing lung-cancer specific regulations. Our study provides a comprehensive investigation of transcription factor and lncRNA regulation in the context of LUAD regulatory networks and yields new insights into the regulatory mechanisms underlying LUAD. The novel key regulatory elements discovered by our research offer new targets for rational drug design and accompanying therapeutic strategies. Full article
(This article belongs to the Special Issue Protein-DNA Interactions)
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2252 KiB  
Article
A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle
by Bohdan Schneider, Paulína Božíková, Petr Čech, Daniel Svozil and Jiří Černý
Genes 2017, 8(10), 278; https://doi.org/10.3390/genes8100278 - 18 Oct 2017
Cited by 9 | Viewed by 5239
Abstract
We analyzed the structural behavior of DNA complexed with regulatory proteins and the nucleosome core particle (NCP). The three-dimensional structures of almost 25 thousand dinucleotide steps from more than 500 sequentially non-redundant crystal structures were classified by using DNA structural alphabet CANA (Conformational [...] Read more.
We analyzed the structural behavior of DNA complexed with regulatory proteins and the nucleosome core particle (NCP). The three-dimensional structures of almost 25 thousand dinucleotide steps from more than 500 sequentially non-redundant crystal structures were classified by using DNA structural alphabet CANA (Conformational Alphabet of Nucleic Acids) and associations between ten CANA letters and sixteen dinucleotide sequences were investigated. The associations showed features discriminating between specific and non-specific binding of DNA to proteins. Important is the specific role of two DNA structural forms, A-DNA, and BII-DNA, represented by the CANA letters AAA and BB2: AAA structures are avoided in non-specific NCP complexes, where the wrapping of the DNA duplex is explained by the periodic occurrence of BB2 every 10.3 steps. In both regulatory and NCP complexes, the extent of bending of the DNA local helical axis does not influence proportional representation of the CANA alphabet letters, namely the relative incidences of AAA and BB2 remain constant in bent and straight duplexes. Full article
(This article belongs to the Special Issue Protein-DNA Interactions)
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4750 KiB  
Article
Mutational and Kinetic Analysis of Lesion Recognition by Escherichia coli Endonuclease VIII
by Olga A. Kladova, Alexandra A. Kuznetsova, Olga S. Fedorova and Nikita A. Kuznetsov
Genes 2017, 8(5), 140; https://doi.org/10.3390/genes8050140 - 13 May 2017
Cited by 21 | Viewed by 3819
Abstract
Escherichia coli endonuclease VIII (Endo VIII) is a DNA glycosylase with substrate specificity for a wide range of oxidatively damaged pyrimidine bases. Endo VIII catalyzes hydrolysis of the N-glycosidic bond and β, δ-elimination of 3′- and 5′-phosphate groups of an apurinic/apyrimidinic site. Single [...] Read more.
Escherichia coli endonuclease VIII (Endo VIII) is a DNA glycosylase with substrate specificity for a wide range of oxidatively damaged pyrimidine bases. Endo VIII catalyzes hydrolysis of the N-glycosidic bond and β, δ-elimination of 3′- and 5′-phosphate groups of an apurinic/apyrimidinic site. Single mutants of Endo VIII L70S, L70W, Y71W, F121W, F230W, and P253W were analyzed here with the aim to elucidate the kinetic mechanism of protein conformational adjustment during damaged-nucleotide recognition and catalytic-complex formation. F121W substitution leads to a slight reduction of DNA binding and catalytic activity. F230W substitution slows the rate of the δ-elimination reaction indicating that interaction of Phe230 with a 5′-phosphate group proceeds in the latest catalytic step. P253W Endo VIII has the same activity as the wild type (WT) enzyme. Y71W substitution slightly reduces the catalytic activity due to the effect on the later steps of catalytic-complex formation. Both L70S and L70W substitutions significantly decrease the catalytic activity, indicating that Leu70 plays an important role in the course of enzyme-DNA catalytic complex formation. Our data suggest that Leu70 forms contacts with DNA earlier than Tyr71 does. Therefore, most likely, Leu70 plays the role of a DNA lesion “sensor”, which is used by Endo VIII for recognition of a DNA damage site. Full article
(This article belongs to the Special Issue Protein-DNA Interactions)
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Review

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2817 KiB  
Review
Acetylation- and Methylation-Related Epigenetic Proteins in the Context of Their Targets
by Nasir Javaid and Sangdun Choi
Genes 2017, 8(8), 196; https://doi.org/10.3390/genes8080196 - 07 Aug 2017
Cited by 68 | Viewed by 10220
Abstract
The nucleosome surface is covered with multiple modifications that are perpetuated by eight different classes of enzymes. These enzymes modify specific target sites both on DNA and histone proteins, and these modifications have been well identified and termed “epigenetics”. These modifications play critical [...] Read more.
The nucleosome surface is covered with multiple modifications that are perpetuated by eight different classes of enzymes. These enzymes modify specific target sites both on DNA and histone proteins, and these modifications have been well identified and termed “epigenetics”. These modifications play critical roles, either by affecting non-histone protein recruitment to chromatin or by disturbing chromatin contacts. Their presence dictates the condensed packaging of DNA and can coordinate the orderly recruitment of various enzyme complexes for DNA manipulation. This genetic modification machinery involves various writers, readers, and erasers that have unique structures, functions, and modes of action. Regarding human disease, studies have mainly focused on the genetic mechanisms; however, alteration in the balance of epigenetic networks can result in major pathologies including mental retardation, chromosome instability syndromes, and various types of cancers. Owing to its critical influence, great potential lies in developing epigenetic therapies. In this regard, this review has highlighted mechanistic and structural interactions of the main epigenetic families with their targets, which will help to identify more efficient and safe drugs against several diseases. Full article
(This article belongs to the Special Issue Protein-DNA Interactions)
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3870 KiB  
Review
Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors
by Dhanusha Yesudhas, Maria Batool, Muhammad Ayaz Anwar, Suresh Panneerselvam and Sangdun Choi
Genes 2017, 8(8), 192; https://doi.org/10.3390/genes8080192 - 01 Aug 2017
Cited by 21 | Viewed by 15428
Abstract
Proteins in the form of transcription factors (TFs) bind to specific DNA sites that regulate cell growth, differentiation, and cell development. The interactions between proteins and DNA are important toward maintaining and expressing genetic information. Without knowing TFs structures and DNA-binding properties, it [...] Read more.
Proteins in the form of transcription factors (TFs) bind to specific DNA sites that regulate cell growth, differentiation, and cell development. The interactions between proteins and DNA are important toward maintaining and expressing genetic information. Without knowing TFs structures and DNA-binding properties, it is difficult to completely understand the mechanisms by which genetic information is transferred between DNA and proteins. The increasing availability of structural data on protein-DNA complexes and recognition mechanisms provides deeper insights into the nature of protein-DNA interactions and therefore, allows their manipulation. TFs utilize different mechanisms to recognize their cognate DNA (direct and indirect readouts). In this review, we focus on these recognition mechanisms as well as on the analysis of the DNA-binding domains of stem cell TFs, discussing the relative role of various amino acids toward facilitating such interactions. Unveiling such mechanisms will improve our understanding of the molecular pathways through which TFs are involved in repressing and activating gene expression. Full article
(This article belongs to the Special Issue Protein-DNA Interactions)
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2961 KiB  
Review
Eukaryotic Replicative Helicase Subunit Interaction with DNA and Its Role in DNA Replication
by Matthew P. Martinez, Amanda L. Wacker, Irina Bruck and Daniel L. Kaplan
Genes 2017, 8(4), 117; https://doi.org/10.3390/genes8040117 - 06 Apr 2017
Cited by 9 | Viewed by 8972
Abstract
The replicative helicase unwinds parental double-stranded DNA at a replication fork to provide single-stranded DNA templates for the replicative polymerases. In eukaryotes, the replicative helicase is composed of the Cdc45 protein, the heterohexameric ring-shaped Mcm2-7 complex, and the tetrameric GINS complex (CMG). The [...] Read more.
The replicative helicase unwinds parental double-stranded DNA at a replication fork to provide single-stranded DNA templates for the replicative polymerases. In eukaryotes, the replicative helicase is composed of the Cdc45 protein, the heterohexameric ring-shaped Mcm2-7 complex, and the tetrameric GINS complex (CMG). The CMG proteins bind directly to DNA, as demonstrated by experiments with purified proteins. The mechanism and function of these DNA-protein interactions are presently being investigated, and a number of important discoveries relating to how the helicase proteins interact with DNA have been reported recently. While some of the protein-DNA interactions directly relate to the unwinding function of the enzyme complex, other protein-DNA interactions may be important for minichromosome maintenance (MCM) loading, origin melting or replication stress. This review describes our current understanding of how the eukaryotic replicative helicase subunits interact with DNA structures in vitro, and proposed models for the in vivo functions of replicative helicase-DNA interactions are also described. Full article
(This article belongs to the Special Issue Protein-DNA Interactions)
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