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Special Issue "Molecular Mechanisms of Gene Expression: “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 Informatics".

Deadline for manuscript submissions: closed (30 September 2020).

Special Issue Editors

Prof. Dr. Yuriy L Orlov
Website1 Website2 Website3
Guest Editor
1. Novosibirsk State University, Novosibirsk, Russia
2. Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
3. Agrarian and Technological Institute, People's Friendship University of Russia, Moscow, Russia
Interests: bioinformatics; medical genomics; e-health
Special Issues and Collections in MDPI journals
Prof. Dr. Tatiana V. Tatarinova
Website
Guest Editor
University of La Verne, La Verne, CA, USA
Interests: medical genomics; population genetics; plant genetics; bioinformatics
Special Issues and Collections in MDPI journals
Dr. Anastasia A. Anashkina
Website1 Website2
Guest Editor
Affiliation 1: Engelhardt Institute of Molecular Biology RAS, Moscow, Russia
Affiliation 2: I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
Interests: structural bioinformatics; biophysics; bioinformatics

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-2020) Multi-Conference 6–10 July, in Novosibirsk, Russia (https://bgrssb.icgbio.ru/2020/). BGRS is a traditional biannual conference series in Novosibirsk which started in 1998 and which gathers scientists, bioinformaticians, medical doctors, and geneticists. This IJMS Special Issue shall continue the thematic collection of recent advances in medical genetics and bioinformatics following the recent human population genetics conference in Moscow
https://www.mdpi.com/journal/ijms/special_issues/Medical_Genetics_Bioinformatics

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;
  • Medical genetics;
  • Gene networks in diseases;
  • Interdisciplinary research in genomics of model organisms;
  • Genomics and systems biology.

We welcome novel materials beyond the conference discussion.

Prof. Dr. Yuriy L Orlov
Prof. Dr. Tatiana V. Tatarinova
Dr. Anastasia A. Anashkina
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 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. 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 (2 papers)

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Research

Open AccessArticle
Predicting FOXM1-Mediated Gene Regulation through the Analysis of Genome-Wide FOXM1 Binding Sites in MCF-7, K562, SK-N-SH, GM12878 and ECC-1 Cell Lines
Int. J. Mol. Sci. 2020, 21(17), 6141; https://doi.org/10.3390/ijms21176141 - 26 Aug 2020
Abstract
Forkhead box protein M1 (FOXM1) is a key transcription factor (TF) that regulates a common set of genes related to the cell cycle in various cell types. However, the mechanism by which FOXM1 controls the common gene set in different cellular contexts is [...] Read more.
Forkhead box protein M1 (FOXM1) is a key transcription factor (TF) that regulates a common set of genes related to the cell cycle in various cell types. However, the mechanism by which FOXM1 controls the common gene set in different cellular contexts is unclear. In this study, a comprehensive meta-analysis of genome-wide FOXM1 binding sites in ECC-1, GM12878, K562, MCF-7, and SK-N-SH cell lines was conducted to predict FOXM1-driven gene regulation. Consistent with previous studies, different TF binding motifs were identified at FOXM1 binding sites, while the NFY binding motif was found at 81% of common FOXM1 binding sites in promoters of cell cycle-related genes. The results indicated that FOXM1 might control the gene set through interaction with the NFY proteins, while cell type-specific genes were predicted to be regulated by enhancers with FOXM1 and cell type-specific TFs. We also found that the high expression level of FOXM1 was significantly associated with poor prognosis in nine types of cancer. Overall, these results suggest that FOXM1 is predicted to function as a master regulator of the cell cycle through the interaction of NFY-family proteins, and therefore the inhibition of FOXM1 could be an attractive strategy for cancer therapy. Full article
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Open AccessArticle
Asymmetric Conservation within Pairs of Co-Occurred Motifs Mediates Weak Direct Binding of Transcription Factors in ChIP-Seq Data
Int. J. Mol. Sci. 2020, 21(17), 6023; https://doi.org/10.3390/ijms21176023 - 21 Aug 2020
Abstract
(1) Background: Transcription factors (TFs) are main regulators of eukaryotic gene expression. The cooperative binding to genomic DNA of at least two TFs is the widespread mechanism of transcription regulation. Cooperating TFs can be revealed through the analysis of co-occurrence of their motifs. [...] Read more.
(1) Background: Transcription factors (TFs) are main regulators of eukaryotic gene expression. The cooperative binding to genomic DNA of at least two TFs is the widespread mechanism of transcription regulation. Cooperating TFs can be revealed through the analysis of co-occurrence of their motifs. (2) Methods: We applied the motifs co-occurrence tool (MCOT) that predicted pairs of spaced or overlapped motifs (composite elements, CEs) for a single ChIP-seq dataset. We improved MCOT capability for the prediction of asymmetric CEs with one of the participating motifs possessing higher conservation than another does. (3) Results: Analysis of 119 ChIP-seq datasets for 45 human TFs revealed that almost for all families of TFs the co-occurrence with an overlap between motifs of target TFs and more conserved partner motifs was significantly higher than that for less conserved partner motifs. The asymmetry toward partner TFs was the most clear for partner motifs of TFs from the ETS (E26 Transformation Specific) family. (4) Conclusion: Co-occurrence with an overlap of less conserved motif of a target TF and more conserved motifs of partner TFs explained a substantial portion of ChIP-seq data lacking conserved motifs of target TFs. Among other TF families, conservative motifs of TFs from ETS family were the most prone to mediate interaction of target TFs with its weak motifs in ChIP-seq. Full article
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