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New Sights into Bioinformatics of Gene Regulations and Structure
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New Sights into Bioinformatics of Gene Regulations and Structure

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

Deadline for manuscript submissions: closed (15 July 2024) | Viewed by 11973

Special Issue Editors

Prof. Dr. Yuriy L. Orlov

E-Mail Website
Guest Editor
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

E-Mail Website1 Website2
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

E-Mail Website
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 collects papers on bioinformatics of gene expression regulation discussed at the “Bioinformatics of Genome Regulation and Structure/Systems Biology” (BGRS/SB) conference series in Novosibirsk, Russia. Begun in 1998, BGRS is the longest-running biannual conference series gathering scientists, bioinformaticians, medical doctors, and geneticists in Novosibirsk (https://bgrssb.icgbio.ru/2022/).

The key topic of this Special Issue is the regulation of gene expression at the transcriptional level. This IJMS Special Issue shall continue the trends set by earlier IJMS Special Issues and other collections of advances in computer genomics and bioinformatics following recent bioinformatics events and young scientists’ schools in Russia.

MDPI has already published several successful Special Issues on the bioinformatics of gene expression, including:

Here, we focus on bioinformatics and systems biology approaches to genomics and biotechnology problems. The central problem includes the analysis of molecular mechanisms of gene expression regulations, analysis of transcription regulation, and network interactions.

The topics of the Special Issue include the following:

  • Analysis of the regulation of gene expression;
  • Applications of genomics and other -omics technology;
  • Gene networks and associative networks analysis;
  • Protein structure analysis and biophysical models;
  • Interdisciplinary research in computational genomics of model organisms—plants, animals, bacteria;
  • Systems approaches for gene expression analysis, including Machine Learning and AI.

The BGRS conference series has a history of initiating successful Special Issues on bioinformatics with IJMS, dating back to 2019. Some examples include:

Recent issues have presented research on the computer analysis of genome structure and gene expression in plants:

The MDPI journals Genes and Life have published Special Issues on the applications of gene transcription regulation and computational genomics:

Previously we have organized a similar Special Issue on the bioinformatics of gene expression regulation at Frontiers in Genetics

and another series with BioMedCentral:

Research on this topic is in high demand at IJMS.

We welcome novel research on these topics that extends the discussion beyond the frames of the BGRS conference series.

Prof. Dr. Yuriy L. Orlov
Dr. Anastasia A. Anashkina
Prof. Dr. Nikolay A. 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
  • genomics of model organisms
  • gene expression regulation
  • transcriptomics
  • fundamental biomedicine
  • gene networks
  • Machine Learning in bioinformatics

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  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue polices can be found here.

Published Papers (8 papers)

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15 pages, 5116 KiB  
Article
DeepPGD: A Deep Learning Model for DNA Methylation Prediction Using Temporal Convolution, BiLSTM, and Attention Mechanism
by Shoryu Teragawa, Lei Wang and Yi Liu
Int. J. Mol. Sci. 2024, 25(15), 8146; https://doi.org/10.3390/ijms25158146 - 26 Jul 2024
Viewed by 1034
Abstract
As part of the field of DNA methylation identification, this study tackles the challenge of enhancing recognition performance by introducing a specialized deep learning framework called DeepPGD. DNA methylation, a crucial biological modification, plays a vital role in gene expression analyses, cellular differentiation, [...] Read more.
As part of the field of DNA methylation identification, this study tackles the challenge of enhancing recognition performance by introducing a specialized deep learning framework called DeepPGD. DNA methylation, a crucial biological modification, plays a vital role in gene expression analyses, cellular differentiation, and the study of disease progression. However, accurately and efficiently identifying DNA methylation sites remains a pivotal concern in the field of bioinformatics. The issue addressed in this paper is the presence of methylation in DNA, which is a binary classification problem. To address this, our research aimed to develop a deep learning algorithm capable of more precisely identifying these sites. The DeepPGD framework combined a dual residual structure involving Temporal convolutional networks (TCNs) and bidirectional long short-term memory (BiLSTM) networks to effectively extract intricate DNA structural and sequence features. Additionally, to meet the practical requirements of DNA methylation identification, extensive experiments were conducted across a variety of biological species. The experimental results highlighted DeepPGD’s exceptional performance across multiple evaluation metrics, including accuracy, Matthews’ correlation coefficient (MCC), and the area under the curve (AUC). In comparison to other algorithms in the same domain, DeepPGD demonstrated superior classification and predictive capabilities across various biological species datasets. This significant advancement in algorithmic prowess not only offers substantial technical support, but also holds potential for research and practical implementation within the DNA methylation identification domain. Moreover, the DeepPGD framework shows potential for application in genomics research, biomedicine, and disease diagnostics, among other fields. Full article
(This article belongs to the Special Issue New Sights into Bioinformatics of Gene Regulations and Structure)
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18 pages, 2735 KiB  
Article
Stable Production of a Recombinant Single-Chain Eel Follicle-Stimulating Hormone Analog in CHO DG44 Cells
by Munkhzaya Byambaragchaa, Sei Hyen Park, Sang-Gwon Kim, Min Gyu Shin, Shin-Kwon Kim, Myung-Hum Park, Myung-Hwa Kang and Kwan-Sik Min
Int. J. Mol. Sci. 2024, 25(13), 7282; https://doi.org/10.3390/ijms25137282 - 2 Jul 2024
Viewed by 980
Abstract
This study aimed to produce single-chain recombinant Anguillid eel follicle-stimulating hormone (rec-eel FSH) analogs with high activity in Cricetulus griseus ovary DG44 (CHO DG44) cells. We recently reported that an O-linked glycosylated carboxyl-terminal peptide (CTP) of the equine chorionic gonadotropin (eCG) β-subunit contributes [...] Read more.
This study aimed to produce single-chain recombinant Anguillid eel follicle-stimulating hormone (rec-eel FSH) analogs with high activity in Cricetulus griseus ovary DG44 (CHO DG44) cells. We recently reported that an O-linked glycosylated carboxyl-terminal peptide (CTP) of the equine chorionic gonadotropin (eCG) β-subunit contributes to high activity and time-dependent secretion in mammalian cells. We constructed a mutant (FSH-M), in which a linker including the eCG β-subunit CTP region (amino acids 115–149) was inserted between the β-subunit and α-subunit of wild-type single-chain eel FSH (FSH-wt). Plasmids containing eel FSH-wt and eel FSH-M were transfected into CHO DG44 cells, and single cells expressing each protein were isolated from 10 and 7 clones. Secretion increased gradually during the cultivation period and peaked at 4000–5000 ng/mL on day 9. The molecular weight of eel FSH-wt was 34–40 kDa, whereas that of eel FSH-M increased substantially, with two bands at 39–46 kDa. Treatment with PNGase F to remove the N glycosylation sites decreased the molecular weight remarkably to approximately 8 kDa. The EC50 value and maximal responsiveness of eel FSH-M were approximately 1.23- and 1.06-fold higher than those of eel FSH-wt, indicating that the mutant showed slightly higher biological activity. Phosphorylated extracellular-regulated kinase (pERK1/2) activation exhibited a sharp peak at 5 min, followed by a rapid decline. These findings indicate that the new rec-eel FSH molecule with the eCG β-subunit CTP linker shows potent activity and could be produced in massive quantities using the stable CHO DG44 cell system. Full article
(This article belongs to the Special Issue New Sights into Bioinformatics of Gene Regulations and Structure)
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18 pages, 7798 KiB  
Article
Unlocking the Transcriptional Control of NCAPG in Bovine Myoblasts: CREB1 and MYOD1 as Key Players
by Zongchang Chen, Jingsheng Li, Yanbin Bai, Zhanxin Liu, Yali Wei, Dashan Guo, Xue Jia, Bingang Shi, Xiaolan Zhang, Zhidong Zhao, Jiang Hu, Xiangmin Han, Jiqing Wang, Xiu Liu, Shaobin Li and Fangfang Zhao
Int. J. Mol. Sci. 2024, 25(5), 2506; https://doi.org/10.3390/ijms25052506 - 21 Feb 2024
Viewed by 1469
Abstract
Muscle formation directly determines meat production and quality. The non-SMC condensin I complex subunit G (NCAPG) is strongly linked to the growth features of domestic animals because it is essential in controlling muscle growth and development. This study aims to elucidate the tissue [...] Read more.
Muscle formation directly determines meat production and quality. The non-SMC condensin I complex subunit G (NCAPG) is strongly linked to the growth features of domestic animals because it is essential in controlling muscle growth and development. This study aims to elucidate the tissue expression level of the bovine NCAPG gene, and determine the key transcription factors for regulating the bovine NCAPG gene. In this study, we observed that the bovine NCAPG gene exhibited high expression levels in longissimus dorsi and spleen tissues. Subsequently, we cloned and characterized the promoter region of the bovine NCAPG gene, consisting of a 2039 bp sequence, through constructing the deletion fragment double-luciferase reporter vector and site-directed mutation-identifying core promoter region with its key transcription factor binding site. In addition, the key transcription factors of the core promoter sequence of the bovine NCAPG gene were analyzed and predicted using online software. Furthermore, by integrating overexpression experiments and the electrophoretic mobility shift assay (EMSA), we have shown that cAMP response element binding protein 1 (CREB1) and myogenic differentiation 1 (MYOD1) bind to the core promoter region (−598/+87), activating transcription activity in the bovine NCAPG gene. In conclusion, these findings shed important light on the regulatory network mechanism that underlies the expression of the NCAPG gene throughout the development of the muscles in beef cattle. Full article
(This article belongs to the Special Issue New Sights into Bioinformatics of Gene Regulations and Structure)
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19 pages, 28984 KiB  
Article
Physical Peculiarity of Two Sites in Human Promoters: Universality and Diverse Usage in Gene Function
by Kohei Uemura and Takashi Ohyama
Int. J. Mol. Sci. 2024, 25(3), 1487; https://doi.org/10.3390/ijms25031487 - 25 Jan 2024
Viewed by 1192
Abstract
Since the discovery of physical peculiarities around transcription start sites (TSSs) and a site corresponding to the TATA box, research has revealed only the average features of these sites. Unsettled enigmas include the individual genes with these features and whether they relate to [...] Read more.
Since the discovery of physical peculiarities around transcription start sites (TSSs) and a site corresponding to the TATA box, research has revealed only the average features of these sites. Unsettled enigmas include the individual genes with these features and whether they relate to gene function. Herein, using 10 physical properties of DNA, including duplex DNA free energy, base stacking energy, protein-induced deformability, and stabilizing energy of Z-DNA, we clarified for the first time that approximately 97% of the promoters of 21,056 human protein-coding genes have distinctive physical properties around the TSS and/or position −27; of these, nearly 65% exhibited such properties at both sites. Furthermore, about 55% of the 21,056 genes had a minimum value of regional duplex DNA free energy within TSS-centered ±300 bp regions. Notably, distinctive physical properties within the promoters and free energies of the surrounding regions separated human protein-coding genes into five groups; each contained specific gene ontology (GO) terms. The group represented by immune response genes differed distinctly from the other four regarding the parameter of the free energies of the surrounding regions. A vital suggestion from this study is that physical-feature-based analyses of genomes may reveal new aspects of the organization and regulation of genes. Full article
(This article belongs to the Special Issue New Sights into Bioinformatics of Gene Regulations and Structure)
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14 pages, 2778 KiB  
Article
Comprehensive Analysis of CircRNA Expression Profiles in Multiple Tissues of Pigs
by Qingpeng Shen, Wentao Gong, Xiangchun Pan, Jiali Cai, Yao Jiang, Mingran He, Shanghui Zhao, Yipeng Li, Xiaolong Yuan and Jiaqi Li
Int. J. Mol. Sci. 2023, 24(22), 16205; https://doi.org/10.3390/ijms242216205 - 11 Nov 2023
Cited by 2 | Viewed by 1559
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs with diverse functions, and previous studies have reported that circRNAs are involved in the growth and development of pigs. However, studies about porcine circRNAs over the past few years have focused on a limited [...] Read more.
Circular RNAs (circRNAs) are a class of non-coding RNAs with diverse functions, and previous studies have reported that circRNAs are involved in the growth and development of pigs. However, studies about porcine circRNAs over the past few years have focused on a limited number of tissues. Based on 215 publicly available RNA sequencing (RNA-seq) samples, we conducted a comprehensive analysis of circRNAs in nine pig tissues, namely, the gallbladder, heart, liver, longissimus dorsi, lung, ovary, pituitary, skeletal muscle, and spleen. Here, we identified a total of 82,528 circRNAs and discovered 3818 novel circRNAs that were not reported in the CircAtlas database. Moreover, we obtained 492 housekeeping circRNAs and 3489 tissue-specific circRNAs. The housekeeping circRNAs were enriched in signaling pathways regulating basic biological tissue activities, such as chromatin remodeling, nuclear-transcribed mRNA catabolic process, and protein methylation. The tissue-specific circRNAs were enriched in signaling pathways related to tissue-specific functions, such as muscle system process in skeletal muscle, cilium organization in pituitary, and cortical cytoskeleton in ovary. Through weighted gene co-expression network analysis, we identified 14 modules comprising 1377 hub circRNAs. Additionally, we explored circRNA–miRNA–mRNA networks to elucidate the interaction relationships between tissue-specific circRNAs and tissue-specific genes. Furthermore, our conservation analysis revealed that 19.29% of circRNAs in pigs shared homologous positions with their counterparts in humans. In summary, this extensive profiling of housekeeping, tissue-specific, and co-expressed circRNAs provides valuable insights into understanding the molecular mechanisms of pig transcriptional expression, ultimately deepening our understanding of genetic and biological processes. Full article
(This article belongs to the Special Issue New Sights into Bioinformatics of Gene Regulations and Structure)
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15 pages, 3680 KiB  
Article
Readthrough Approach Using NV Translational Readthrough-Inducing Drugs (TRIDs): A Study of the Possible Off-Target Effects on Natural Termination Codons (NTCs) on TP53 and Housekeeping Gene Expression
by Riccardo Perriera, Emanuele Vitale, Ivana Pibiri, Pietro Salvatore Carollo, Davide Ricci, Federica Corrao, Ignazio Fiduccia, Raffaella Melfi, Maria Grazia Zizzo, Marco Tutone, Andrea Pace and Laura Lentini
Int. J. Mol. Sci. 2023, 24(20), 15084; https://doi.org/10.3390/ijms242015084 - 11 Oct 2023
Viewed by 1502
Abstract
Nonsense mutations cause several genetic diseases such as cystic fibrosis, Duchenne muscular dystrophy, β-thalassemia, and Shwachman–Diamond syndrome. These mutations induce the formation of a premature termination codon (PTC) inside the mRNA sequence, resulting in the synthesis of truncated polypeptides. Nonsense suppression therapy mediated [...] Read more.
Nonsense mutations cause several genetic diseases such as cystic fibrosis, Duchenne muscular dystrophy, β-thalassemia, and Shwachman–Diamond syndrome. These mutations induce the formation of a premature termination codon (PTC) inside the mRNA sequence, resulting in the synthesis of truncated polypeptides. Nonsense suppression therapy mediated by translational readthrough-inducing drugs (TRIDs) is a promising approach to correct these genetic defects. TRIDs generate a ribosome miscoding of the PTC named “translational readthrough” and restore the synthesis of full-length and potentially functional proteins. The new oxadiazole-core TRIDs NV848, NV914, and NV930 (NV) showed translational readthrough activity in nonsense-related in vitro systems. In this work, the possible off-target effect of NV molecules on natural termination codons (NTCs) was investigated. Two different in vitro approaches were used to assess if the NV molecule treatment induces NTC readthrough: (1) a study of the translational-induced p53 molecular weight and functionality; (2) the evaluation of two housekeeping proteins’ (Cys-C and β2M) molecular weights. Our results showed that the treatment with NV848, NV914, or NV930 did not induce any translation alterations in both experimental systems. The data suggested that NV molecules have a specific action for the PTCs and an undetectable effect on the NTCs. Full article
(This article belongs to the Special Issue New Sights into Bioinformatics of Gene Regulations and Structure)
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13 pages, 1731 KiB  
Article
Short Interrupted Repeat Cassette (SIRC)—Novel Type of Repetitive DNA Element Found in Arabidopsis thaliana
by Igor V. Gorbenko, Ivan S. Petrushin, Andrey B. Shcherban, Yuriy L. Orlov and Yuri M. Konstantinov
Int. J. Mol. Sci. 2023, 24(13), 11116; https://doi.org/10.3390/ijms241311116 - 5 Jul 2023
Cited by 2 | Viewed by 1825
Abstract
Short interrupted repeat cassette (SIRC)—a novel DNA element found throughout the A. thaliana nuclear genome. SIRCs are represented by short direct repeats interrupted by diverse DNA sequences. The maxima of SIRC’s distribution are located within pericentromeric regions. We suggest that originally SIRC was [...] Read more.
Short interrupted repeat cassette (SIRC)—a novel DNA element found throughout the A. thaliana nuclear genome. SIRCs are represented by short direct repeats interrupted by diverse DNA sequences. The maxima of SIRC’s distribution are located within pericentromeric regions. We suggest that originally SIRC was a special case of the complex internal structure of the miniature inverted repeat transposable element (MITE), and further MITE amplification, transposition, and loss of terminal inverted repeats gave rise to SIRC as an independent DNA element. SIRC sites were significantly enriched with several histone modifications associated with constitutive heterochromatin and mobile genetic elements. The majority of DNA-binding proteins, strongly associated with SIRC, are related to histone modifications for transcription repression. A part of SIRC was found to overlap highly inducible protein-coding genes, suggesting a possible regulatory role for these elements, yet their definitive functions need further investigation. Full article
(This article belongs to the Special Issue New Sights into Bioinformatics of Gene Regulations and Structure)
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14 pages, 4062 KiB  
Brief Report
Identification of Laccase Family of Auricularia auricula-judae and Structural Prediction Using Alphafold
by Jeong-Heon Kim, Youn-Jin Park and Myoung-Jun Jang
Int. J. Mol. Sci. 2024, 25(21), 11784; https://doi.org/10.3390/ijms252111784 - 2 Nov 2024
Viewed by 597
Abstract
Laccase is an enzyme that plays an important role in fungi, including lignin degradation, stress defense, and formation of fruiting bodies. Auricularia auricula-judae is a white-rot fungus in the Basidiomycota phylum, capable of delignifying wood. In this study, seven genes belonging to the [...] Read more.
Laccase is an enzyme that plays an important role in fungi, including lignin degradation, stress defense, and formation of fruiting bodies. Auricularia auricula-judae is a white-rot fungus in the Basidiomycota phylum, capable of delignifying wood. In this study, seven genes belonging to the laccase family were identified through de novo sequencing, containing Cu-Oxidase, Cu-Oxidase_2, and Cu-Oxidase_3 domains. Subsequently, the physical characteristics, phylogenetic relationships, protein secondary structure, and tertiary structure of the laccase family (AaLac1–AaLac7) were analyzed. Prediction of N-glycosylation sites identified 2 to 10 sites in the laccase family, with AaLac7 having the highest number of sites at 10. Sequence alignment and analysis of the laccase family showed high consistency in signature sequences. Phylogenetic analysis confirmed the relationship among laccases within the family, with AaLac3–AaLac4 and AaLac5–AaLac6 being closely positioned on the tree, exhibiting high similarity in tertiary structure predictions. This study identified and analyzed laccase family genes in Auricularia auricula-judae using de novo sequencing, offering a simple method for identifying and analyzing the laccase family in organisms with unknown genetic information. Full article
(This article belongs to the Special Issue New Sights into Bioinformatics of Gene Regulations and Structure)
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