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Animal Genomes and Epigenomes 2.0
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Animal Genomes and Epigenomes 2.0

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 (29 February 2024) | Viewed by 3244

Special Issue Editors

Prof. Dr. Elena Giulotto

E-Mail Website
Guest Editor
Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy
Interests: mammalian centromeres; neo-centromeres; centromere evolution; telomeres; telomere transcription; interstitial telomeres; genomics of horse and other equids; comparative genomics; gene amplification; molecular cytogenetics; ChIP-seq; production of recombinant proteins in mammalian cells
Special Issues, Collections and Topics in MDPI journals
Dr. Francesca M. Piras

E-Mail Website
Co-Guest Editor
Unit of Anatomic Pathology, IRCCS San Matteo Hospital Foundation, 27100 Pavia, Italy
Interests: genome stability; centromere and karyotype evolution; comparative genomics; centromere biology; telomeres and interstitial telomeres
Dr. Eleonora Cappelletti

E-Mail Website
Co-Guest Editor
Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
Interests: centromere biology; telomeres and interstitial telomeres; molecular evolution; comparative genomics and epigenomics; genome annotation

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue “Animal Genomes and Epigenomes”.

The growing number of sequenced animal genomes is paving the way to the study of chromatin organization, genomics, comparative genomics and molecular evolution. Although the basic molecular processes are largely conserved in animals, several differences can be observed among species. For example, while telomere maintenance is usually accomplished by telomerase-based mechanisms, in some species, such as Drosophila, retrotransposons are involved in preserving chromosome ends. Another example comes from the centromeric function that is typically associated with defined chromosomal regions but, in some nematodes and arthropods, covers the entire length of chromosomes.

After almost two decades of the ENCODE initiative, the approach that has been used to understand the biology of the human genome and epigenome is now being applied to a number of domestic and wild animal species. In this context, an international collaboration, named Functional Annotation of Animal Genomes (FAANG), is carrying out a coordinated effort to systematically annotate farmed animal genomes and investigate the genotype-to-phenotype connection.

In the present Special Issue, reviews and research articles related to analyses of animal genomes and epigenomes are welcomed, with the goal of improving the knowledge of basic molecular processes and unraveling their evolution.

Prof. Dr. Elena Giulotto
Dr. Francesca M. Piras
Dr. Eleonora Cappelletti
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

  • animals
  • chromatin organization
  • genomics
  • comparative genomics
  • genome annotation
  • molecular evolution
  • NGS methodologies

Related Special Issue

Published Papers (3 papers)

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Research

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16 pages, 4254 KiB  
Article
Maternal Hypermethylated Genes Contribute to Intrauterine Growth Retardation of Piglets in Rongchang Pigs
by Pingxian Wu, Junge Wang, Xiang Ji, Jie Chai, Li Chen, Tinghuan Zhang, Xi Long, Zhi Tu, Siqing Chen, Lijuan Zhang, Ketian Wang, Liang Zhang, Zongyi Guo and Jinyong Wang
Int. J. Mol. Sci. 2024, 25(12), 6462; https://doi.org/10.3390/ijms25126462 - 12 Jun 2024
Viewed by 184
Abstract
The placenta is a crucial determinant of fetal survival, growth, and development. Deficiency in placental development directly causes intrauterine growth retardation (IUGR). IUGR can lead to fetal growth restriction and an increase in the mortality rate. The genetic mechanisms underlying IUGR development, however, [...] Read more.
The placenta is a crucial determinant of fetal survival, growth, and development. Deficiency in placental development directly causes intrauterine growth retardation (IUGR). IUGR can lead to fetal growth restriction and an increase in the mortality rate. The genetic mechanisms underlying IUGR development, however, remain unclear. In the present study, we integrated whole-genome DNA methylation and transcriptomic analyses to determine distinct gene expression patterns in various placental tissues to identify pivotal genes that are implicated with IUGR development. By performing RNA-sequencing analysis, 1487 differentially expressed genes (DEGs), with 737 upregulated and 750 downregulated genes, were identified in IUGR pigs (H_IUGR) compared with that in normal birth weight pigs (N_IUGR) (p < 0.05); furthermore, 77 miRNAs, 1331 lncRNAs, and 61 circRNAs were differentially expressed. The protein–protein interaction network analysis revealed that among these DEGs, the genes GNGT1, ANXA1, and CDC20 related to cellular developmental processes and blood vessel development were the key genes associated with the development of IUGR. A total of 495,870 differentially methylated regions were identified between the N_IUGR and H_IUGR groups, which included 25,053 differentially methylated genes (DMEs); moreover, the overall methylation level was higher in the H_IUGR group than in the N_IUGR group. Combined analysis showed an inverse correlation between methylation levels and gene expression. A total of 1375 genes involved in developmental processes, tissue development, and immune system regulation exhibited methylation differences in gene expression levels in the promoter regions and gene ontology regions. Five genes, namely, ANXA1, ADM, NRP2, SHH, and SMAD1, with high methylation levels were identified as potential contributors to IUGR development. These findings provide valuable insights that DNA methylation plays a crucial role in the epigenetic regulation of gene expression and mammalian development and that DNA-hypermethylated genes contribute to IUGR development in Rongchang pigs. Full article
(This article belongs to the Special Issue Animal Genomes and Epigenomes 2.0)
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18 pages, 10118 KiB  
Article
Integration of ATAC-Seq and RNA-Seq Analysis to Identify Key Genes in the Longissimus Dorsi Muscle Development of the Tianzhu White Yak
by Jingsheng Li, Zongchang Chen, Yanbin Bai, Yali Wei, Dashan Guo, Zhanxin Liu, Yanmei Niu, Bingang Shi, Xiaolan Zhang, Yuan Cai, Zhidong Zhao, Jiang Hu, Jiqing Wang, Xiu Liu, Shaobin Li and Fangfang Zhao
Int. J. Mol. Sci. 2024, 25(1), 158; https://doi.org/10.3390/ijms25010158 - 21 Dec 2023
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Abstract
During the postnatal stages, skeletal muscle development undergoes a series of meticulously regulated alterations in gene expression. However, limited studies have employed chromatin accessibility to unravel the underlying molecular mechanisms governing muscle development in yak species. Therefore, we conducted an analysis of both [...] Read more.
During the postnatal stages, skeletal muscle development undergoes a series of meticulously regulated alterations in gene expression. However, limited studies have employed chromatin accessibility to unravel the underlying molecular mechanisms governing muscle development in yak species. Therefore, we conducted an analysis of both gene expression levels and chromatin accessibility to comprehensively characterize the dynamic genome-wide chromatin accessibility during muscle growth and development in the Tianzhu white yak, thereby elucidating the features of accessible chromatin regions throughout this process. Initially, we compared the differences in chromatin accessibility between two groups and observed that calves exhibited higher levels of chromatin accessibility compared to adult cattle, particularly within ±2 kb of the transcription start site (TSS). In order to investigate the correlation between alterations in chromatin accessible regions and variations in gene expression levels, we employed a combination of ATAC-seq and RNA-seq techniques, leading to the identification of 18 central transcriptional factors (TFs) and 110 key genes with significant effects. Through further analysis, we successfully identified several TFs, including Sp1, YY1, MyoG, MEF2A and MEF2C, as well as a number of candidate genes (ANKRD2, ANKRD1, BTG2 and LMOD3) which may be closely associated with muscle growth and development. Moreover, we constructed an interactive network program encompassing hub TFs and key genes related to muscle growth and development. This innovative approach provided valuable insights into the molecular mechanism underlying skeletal muscle development in the postnatal stages of Tianzhu white yaks while also establishing a solid theoretical foundation for future research on yak muscle development. Full article
(This article belongs to the Special Issue Animal Genomes and Epigenomes 2.0)
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Review

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21 pages, 1742 KiB  
Review
Cis-Regulatory Elements in Mammals
by Xingyu Liu, Mengjie Chen, Xiuwen Qu, Wenjing Liu, Yuting Dou, Qingyou Liu, Deshun Shi, Mingsheng Jiang and Hui Li
Int. J. Mol. Sci. 2024, 25(1), 343; https://doi.org/10.3390/ijms25010343 - 26 Dec 2023
Cited by 1 | Viewed by 1473
Abstract
In cis-regulatory elements, enhancers and promoters with complex molecular interactions are used to coordinate gene transcription through physical proximity and chemical modifications. These processes subsequently influence the phenotypic characteristics of an organism. An in-depth exploration of enhancers and promoters can substantially enhance our [...] Read more.
In cis-regulatory elements, enhancers and promoters with complex molecular interactions are used to coordinate gene transcription through physical proximity and chemical modifications. These processes subsequently influence the phenotypic characteristics of an organism. An in-depth exploration of enhancers and promoters can substantially enhance our understanding of gene regulatory networks, shedding new light on mammalian development, evolution and disease pathways. In this review, we provide a comprehensive overview of the intrinsic structural attributes, detection methodologies as well as the operational mechanisms of enhancers and promoters, coupled with the relevant novel and innovative investigative techniques used to explore their actions. We further elucidated the state-of-the-art research on the roles of enhancers and promoters in the realms of mammalian development, evolution and disease, and we conclude with forward-looking insights into prospective research avenues. Full article
(This article belongs to the Special Issue Animal Genomes and Epigenomes 2.0)
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