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Bioinformatics of Gene Regulations and Structure - 2022

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 20792

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Special Issue Editors

Prof. Dr. Yuriy L. Orlov

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The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119991 Moscow, Russia
Interests: computer genomics; bioinformatics; digital medicine (e-Health); gene expression regulation; ChIP-seq
Special Issues, Collections and Topics in MDPI journals

Dr. Anastasia A. Anashkina

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Guest Editor

1. Engelhardt Institute of Molecular Biology RAS, 119991 Moscow, Russia
2. The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119991 Moscow, Russia
Interests: structural bioinformatics; biophysics; bioinformatics
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Nikolay A. Kolchanov

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Guest Editor

Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
Interests: bioinformatics; systems biology; genetics; genomics; gene networks
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special issue, which shall collect papers on genomics in biomedicine and biotechnology, is based on the materials presented at “Bioinformatics of Genome Regulation and Structure/Systems Biology” (BGRS\SB-2022) on 04–08 of July 2022 in Novosibirsk, Russia (https://bgrssb.icgbio.ru/2022/). BGRS is a traditional biannual conference series in Novosibirsk which started in 1998 and which gathers scientists, bioinformaticians, medical doctors, and geneticists. Gene expression regulation at transcriptional level is key topic of this journal issue. This IJMS Special Issue shall continue the earlier IJMS Special Issue and the thematic collection of recent advances in computer genomics and bioinformatics following the recent bioinformatics conferences in Russia:

https://0-www-mdpi-com.brum.beds.ac.uk/journal/ijms/special_issues/Bioinformatics_Genomics (Molecular Mechanisms of Gene Expression: “Bioinformatics of Gene Regulations and Structure”)

https://0-www-mdpi-com.brum.beds.ac.uk/journal/ijms/special_issues/Medical_Genetics_Bioinformatics

https://0-www-mdpi-com.brum.beds.ac.uk/journal/ijms/special_issues/Medical_Genetics_Bioinformatics_2

https://0-www-mdpi-com.brum.beds.ac.uk/journal/ijms/special_issues/Medical_Genetics_2021

and

https://0-www-mdpi-com.brum.beds.ac.uk/journal/ijms/special_issues/Plant_Biotechnology

Here, we focus on bioinformatics and systems biology approaches to genomics and biotechnology problems. The central problem is that analysis of gene expression regulations, bioinformatics of regulatory molecular mechanisms and network interaction underlying gene function manifestation.

Topics of the Special Issue include:

Genomics and omics technology applications;
Analysis of gene expression regulation;
Gene networks and associative networks analysis;
Protein structure analysis and biophysical models;
Interdisciplinary research in genomics of model organisms;
Computer genomics and systems biology.

We welcome novel materials beyond the conference discussion.

Prof. Dr. Yuriy L. Orlov
Dr. Anastasia A. Anashkina
Prof. Dr. Nikolay Kolchanov
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

bioinformatics
systems biology
human genomics
computational plant genomics
genomics of model organisms
gene expression regulation
fundamental biomedicine
gene networks

Published Papers (11 papers)

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Editorial

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5 pages, 223 KiB

Open AccessEditorial

Research Topics of the Bioinformatics of Gene Regulation

by Yuriy L. Orlov, Anastasia A. Anashkina, Vadim V. Kumeiko, Ming Chen and Nikolay A. Kolchanov

Int. J. Mol. Sci. 2023, 24(10), 8774; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24108774 - 15 May 2023

Cited by 3 | Viewed by 1144

Abstract

The study of gene expression regulation raises the challenge of developing bioinformatics tools and algorithms, demanding data integration [...] Full article

(This article belongs to the Special Issue Bioinformatics of Gene Regulations and Structure - 2022)

Research

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16 pages, 1205 KiB

Open AccessArticle

BioGraph: Data Model for Linking and Querying Diverse Biological Metadata

by Aleksandar N. Veljković, Yuriy L. Orlov and Nenad S. Mitić

Int. J. Mol. Sci. 2023, 24(8), 6954; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24086954 - 09 Apr 2023

Cited by 3 | Viewed by 1452

Abstract

Studying the association of gene function, diseases, and regulatory gene network reconstruction demands data compatibility. Data from different databases follow distinct schemas and are accessible in heterogenic ways. Although the experiments differ, data may still be related to the same biological entities. Some entities may not be strictly biological, such as geolocations of habitats or paper references, but they provide a broader context for other entities. The same entities from different datasets can share similar properties, which may or may not be found within other datasets. Joint, simultaneous data fetching from multiple data sources is complicated for the end-user or, in many cases, unsupported and inefficient due to differences in data structures and ways of accessing the data. We propose BioGraph—a new model that enables connecting and retrieving information from the linked biological data that originated from diverse datasets. We have tested the model on metadata collected from five diverse public datasets and successfully constructed a knowledge graph containing more than 17 million model objects, of which 2.5 million are individual biological entity objects. The model enables the selection of complex patterns and retrieval of matched results that can be discovered only by joining the data from multiple sources. Full article

(This article belongs to the Special Issue Bioinformatics of Gene Regulations and Structure - 2022)

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10 pages, 2035 KiB

Open AccessArticle

Epi-Impute: Single-Cell RNA-seq Imputation via Integration with Single-Cell ATAC-seq

by Mikhail Raevskiy, Vladislav Yanvarev, Sascha Jung, Antonio Del Sol and Yulia A. Medvedeva

Int. J. Mol. Sci. 2023, 24(7), 6229; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24076229 - 25 Mar 2023

Cited by 4 | Viewed by 2263

Abstract

Single-cell RNA-seq data contains a lot of dropouts hampering downstream analyses due to the low number and inefficient capture of mRNAs in individual cells. Here, we present Epi-Impute, a computational method for dropout imputation by reconciling expression and epigenomic data. Epi-Impute leverages single-cell ATAC-seq data as an additional source of information about gene activity to reduce the number of dropouts. We demonstrate that Epi-Impute outperforms existing methods, especially for very sparse single-cell RNA-seq data sets, significantly reducing imputation error. At the same time, Epi-Impute accurately captures the primary distribution of gene expression across cells while preserving the gene-gene and cell-cell relationship in the data. Moreover, Epi-Impute allows for the discovery of functionally relevant cell clusters as a result of the increased resolution of scRNA-seq data due to imputation. Full article

(This article belongs to the Special Issue Bioinformatics of Gene Regulations and Structure - 2022)

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36 pages, 3697 KiB

Open AccessArticle

Genetic Structure Analysis of 155 Transboundary and Local Populations of Cattle (Bos taurus, Bos indicus and Bos grunniens) Based on STR Markers

by Evgenia Solodneva, Gulnara Svishcheva, Rodion Smolnikov, Sergey Bazhenov, Evgenii Konorov, Vera Mukhina and Yurii Stolpovsky

Int. J. Mol. Sci. 2023, 24(5), 5061; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24055061 - 06 Mar 2023

Cited by 1 | Viewed by 2085

Abstract

Every week, 1–2 breeds of farm animals, including local cattle, disappear in the world. As the keepers of rare allelic variants, native breeds potentially expand the range of genetic solutions to possible problems of the future, which means that the study of the genetic structure of these breeds is an urgent task. Providing nomadic herders with valuable resources necessary for life, domestic yaks have also become an important object of study. In order to determine the population genetic characteristics, and clarify the phylogenetic relationships of modern representatives of 155 cattle populations from different regions of the world, we collected a large set of STR data (10,250 individuals), including unique native cattle, 12 yak populations from Russia, Mongolia and Kyrgyzstan, as well as zebu breeds. Estimation of main population genetic parameters, phylogenetic analysis, principal component analysis and Bayesian cluster analysis allowed us to refine genetic structure and provided insights in relationships of native populations, transboundary breeds and populations of domestic yak. Our results can find practical application in conservation programs of endangered breeds, as well as become the basis for future fundamental research. Full article

(This article belongs to the Special Issue Bioinformatics of Gene Regulations and Structure - 2022)

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16 pages, 5176 KiB

Open AccessArticle

Genome-Wide Mining of the Tandem Duplicated Type III Polyketide Synthases and Their Expression, Structure Analysis of Senna tora

by Zeping Cai, Xingkun Zhao, Chaoye Zhou, Ting Fang, Guodao Liu and Jiajia Luo

Int. J. Mol. Sci. 2023, 24(5), 4837; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24054837 - 02 Mar 2023

Cited by 2 | Viewed by 1616

Abstract

Senna tora is one of the homologous crops used as a medicinal food containing an abundance of anthraquinones. Type III polyketide synthases (PKSs) are key enzymes that catalyze polyketide formation; in particular, the chalcone synthase-like (CHS-L) genes are involved in anthraquinone production. Tandem duplication is a fundamental mechanism for gene family expansion. However, the analysis of the tandem duplicated genes (TDGs) and the identification and characterization of PKSs have not been reported for S. tora. Herein, we identified 3087 TDGs in the S. tora genome; the synonymous substitution rates (Ks) analysis indicated that the TDGs had recently undergone duplication. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the type III PKSs were the most enriched TDGs involved in the biosynthesis of the secondary metabolite pathways, as evidenced by 14 tandem duplicated CHS-L genes. Subsequently, we identified 30 type III PKSs with complete sequences in the S. tora genome. Based on the phylogenetic analysis, the type III PKSs were classified into three groups. The protein conserved motifs and key active residues showed similar patterns in the same group. The transcriptome analysis showed that the chalcone synthase (CHS) genes were more highly expressed in the leaves than in the seeds in S. tora. The transcriptome and qRT-PCR analysis showed that the CHS-L genes had a higher expression in the seeds than in other tissues, particularly seven tandem duplicated CHS-L2/3/5/6/9/10/13 genes. The key active-site residues and three-dimensional models of the CHS-L2/3/5/6/9/10/13 proteins showed slight variation. These results indicated that the rich anthraquinones in S. tora seeds might be ascribed to the PKSs’ expansion from tandem duplication, and the seven key CHS-L2/3/5/6/9/10/13 genes provide candidate genes for further research. Our study provides an important basis for further research on the regulation of anthraquinones’ biosynthesis in S. tora. Full article

(This article belongs to the Special Issue Bioinformatics of Gene Regulations and Structure - 2022)

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17 pages, 3456 KiB

Open AccessArticle

The New Version of the ANDDigest Tool with Improved AI-Based Short Names Recognition

by Timofey V. Ivanisenko, Pavel S. Demenkov, Nikolay A. Kolchanov and Vladimir A. Ivanisenko

Int. J. Mol. Sci. 2022, 23(23), 14934; https://doi.org/10.3390/ijms232314934 - 29 Nov 2022

Cited by 11 | Viewed by 1271

Abstract

The body of scientific literature continues to grow annually. Over 1.5 million abstracts of biomedical publications were added to the PubMed database in 2021. Therefore, developing cognitive systems that provide a specialized search for information in scientific publications based on subject area ontology and modern artificial intelligence methods is urgently needed. We previously developed a web-based information retrieval system, ANDDigest, designed to search and analyze information in the PubMed database using a customized domain ontology. This paper presents an improved ANDDigest version that uses fine-tuned PubMedBERT classifiers to enhance the quality of short name recognition for molecular-genetics entities in PubMed abstracts on eight biological object types: cell components, diseases, side effects, genes, proteins, pathways, drugs, and metabolites. This approach increased average short name recognition accuracy by 13%. Full article

(This article belongs to the Special Issue Bioinformatics of Gene Regulations and Structure - 2022)

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11 pages, 1799 KiB

Open AccessArticle

Single-Cell DNA Methylation Analysis of Chicken Lampbrush Chromosomes

by Artem Nurislamov, Timofey Lagunov, Maria Gridina, Alla Krasikova and Veniamin Fishman

Int. J. Mol. Sci. 2022, 23(20), 12601; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232012601 - 20 Oct 2022

Cited by 3 | Viewed by 1734

Abstract

DNA methylation is an essential epigenetic regulation mechanism implicated in transcription and replication control, developmental reprogramming, retroelements silencing and other genomic processes. During mammalian development, a specific DNA methylation pattern should be established in germ cells to allow embryonic development. Less is known about germ cell DNA methylation in other species. To close this gap, we performed a single-cell methylome analysis of chicken diplotene oocytes. We comprehensively characterized methylation patterns in these cells, obtained methylation-based chicken genome segmentation and identified oocyte-specific methylated gene promoters. Our data show that despite the formation of specific transcriptionally hyperactive genome architecture in chicken diplotene oocytes, methylation patterns in these cells closely resemble genomic distribution observed in somatic tissues. Full article

(This article belongs to the Special Issue Bioinformatics of Gene Regulations and Structure - 2022)

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23 pages, 2334 KiB

Open AccessArticle

Bioinformatic Assessment of Factors Affecting the Correlation between Protein Abundance and Elongation Efficiency in Prokaryotes

by Aleksandra E. Korenskaia, Yury G. Matushkin, Sergey A. Lashin and Alexandra I. Klimenko

Int. J. Mol. Sci. 2022, 23(19), 11996; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231911996 - 09 Oct 2022

Cited by 3 | Viewed by 1688

Abstract

Protein abundance is crucial for the majority of genetically regulated cell functions to act properly in prokaryotic organisms. Therefore, developing bioinformatic methods for assessing the efficiency of different stages of gene expression is of great importance for predicting the actual protein abundance. One of these steps is the evaluation of translation elongation efficiency based on mRNA sequence features, such as codon usage bias and mRNA secondary structure properties. In this study, we have evaluated correlation coefficients between experimentally measured protein abundance and predicted elongation efficiency characteristics for 26 prokaryotes, including non-model organisms, belonging to diverse taxonomic groups The algorithm for assessing elongation efficiency takes into account not only codon bias, but also number and energy of secondary structures in mRNA if those demonstrate an impact on predicted elongation efficiency of the ribosomal protein genes. The results show that, for a number of organisms, secondary structures are a better predictor of protein abundance than codon usage bias. The bioinformatic analysis has revealed several factors associated with the value of the correlation coefficient. The first factor is the elongation efficiency optimization type—the organisms whose genomes are optimized for codon usage only have significantly higher correlation coefficients. The second factor is taxonomical identity—bacteria that belong to the class Bacilli tend to have higher correlation coefficients among the analyzed set. The third is growth rate, which is shown to be higher for the organisms with higher correlation coefficients between protein abundance and predicted translation elongation efficiency. The obtained results can be useful for further improvement of methods for protein abundance prediction. Full article

(This article belongs to the Special Issue Bioinformatics of Gene Regulations and Structure - 2022)

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29 pages, 8473 KiB

Open AccessArticle

Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core Promoters

by Anastasia V. Melikhova, Anastasia A. Anashkina and Irina A. Il’icheva

Int. J. Mol. Sci. 2022, 23(18), 10873; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231810873 - 17 Sep 2022

Cited by 3 | Viewed by 1099

Abstract

Eukaryotic and archaeal RNA polymerase II (POL II) machinery is highly conserved, regardless of the extreme changes in promoter sequences in different organisms. The goal of our work is to find the cause of this conservatism. The representative sets of aligned promoter sequences of fifteen organisms belonging to different evolutional stages were studied. Their textual profiles, as well as profiles of the indexes that characterize the secondary structure and the mechanical and physicochemical properties, were analyzed. The evolutionarily stable, extremely heterogeneous special secondary structure of POL II core promoters was revealed, which includes two singular regions—hexanucleotide “INR” around TSS and octanucleotide “TATA element” of about −28 bp upstream. Such structures may have developed at some stage of evolution. It turned out to be so well matched for the pre-initiation complex formation and the subsequent initiation of transcription for POL II machinery that in the course of evolution there were selected only those nucleotide sequences that were able to reproduce these structural properties. The individual features of specific sequences representing the singular region of the promoter of each gene can affect the kinetics of DNA-protein complex formation and facilitate strand separation in double-stranded DNA at the TSS position. Full article

(This article belongs to the Special Issue Bioinformatics of Gene Regulations and Structure - 2022)

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10 pages, 2223 KiB

Open AccessArticle

Web-MCOT Server for Motif Co-Occurrence Search in ChIP-Seq Data

by Victor G. Levitsky, Alexey M. Mukhin, Dmitry Yu. Oshchepkov, Elena V. Zemlyanskaya and Sergey A. Lashin

Int. J. Mol. Sci. 2022, 23(16), 8981; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23168981 - 11 Aug 2022

Cited by 2 | Viewed by 1629

Abstract

(1) Background: The widespread application of ChIP-seq technology requires annotation of cis-regulatory modules through the search of co-occurred motifs. (2) Methods: We present the web server Motifs Co-Occurrence Tool (Web-MCOT) that for a single ChIP-seq dataset detects the composite elements (CEs) or overrepresented homo- and heterotypic pairs of motifs with spacers and overlaps, with any mutual orientations, uncovering various similarities to recognition models within pairs of motifs. The first (Anchor) motif in CEs respects the target transcription factor of the ChIP-seq experiment, while the second one (Partner) can be defined either by a user or a public library of Partner motifs being processed. (3) Results: Web-MCOT computes the significances of CEs without reference to motif conservation and those with more conserved Partner and Anchor motifs. Graphic results show histograms of CE abundance depending on orientations of motifs, overlap and spacer lengths; logos of the most common CE structural types with an overlap of motifs, and heatmaps depicting the abundance of CEs with one motif possessing higher conservation than another. (4) Conclusions: Novel capacities of Web-MCOT allow retrieving from a single ChIP-seq dataset with maximal information on the co-occurrence of motifs and potentiates planning of next ChIP-seq experiments. Full article

(This article belongs to the Special Issue Bioinformatics of Gene Regulations and Structure - 2022)

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Review

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21 pages, 2065 KiB

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Function and Evolution of the Loop Extrusion Machinery in Animals

by Evelyn Kabirova, Artem Nurislamov, Artem Shadskiy, Alexander Smirnov, Andrey Popov, Pavel Salnikov, Nariman Battulin and Veniamin Fishman

Int. J. Mol. Sci. 2023, 24(5), 5017; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24055017 - 06 Mar 2023

Cited by 5 | Viewed by 2785

Abstract

Structural maintenance of chromosomes (SMC) complexes are essential proteins found in genomes of all cellular organisms. Essential functions of these proteins, such as mitotic chromosome formation and sister chromatid cohesion, were discovered a long time ago. Recent advances in chromatin biology showed that SMC proteins are involved in many other genomic processes, acting as active motors extruding DNA, which leads to the formation of chromatin loops. Some loops formed by SMC proteins are highly cell type and developmental stage specific, such as SMC-mediated DNA loops required for VDJ recombination in B-cell progenitors, or dosage compensation in Caenorhabditis elegans and X-chromosome inactivation in mice. In this review, we focus on the extrusion-based mechanisms that are common for multiple cell types and species. We will first describe an anatomy of SMC complexes and their accessory proteins. Next, we provide biochemical details of the extrusion process. We follow this by the sections describing the role of SMC complexes in gene regulation, DNA repair, and chromatin topology. Full article

(This article belongs to the Special Issue Bioinformatics of Gene Regulations and Structure - 2022)

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