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Animals
Special Issues
Epigenetics in Animal Development
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Epigenetics in Animal Development

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (30 June 2024) | Viewed by 3561

Special Issue Editor

Dr. Jéssica Ispada

E-Mail Website
Guest Editor
Animal Biotechnology, AgResearch, Ruakura Research Center, Hamilton, New Zealand
Interests: embryonic development; epigenetic reprogramming; imprinting; metabolism; metaboloepigenetics; large-offspring syndrome

Special Issue Information

Dear Colleagues,

This Special Issue explores the field of epigenetics in animal development, focusing on how epigenetic mechanisms regulate gene expression and shape the development in a variety of animals. Epigenetics encompasses both heritable and environmentally induced changes in gene activity, referring to genomic modifications that do not involve alterations in the DNA sequence. During development, animals undergo a dramatic epigenetic reprogramming that both shapes cell differentiation and enables them to respond to the environment, leading to adjustments in phenotypic outcomes.

We invite original research, reviews, and short communications that cover:

  • Characterization of epigenetic mechanisms during embryonic development;
  • Epigenetic regulation of developmental plasticity and disorders in animals;
  • Embryonic stem cell establishment in animals;
  • Comparative analysis of epigenetic regulation during the development across animal species.

This Special Issue aims to provide a comprehensive overview of epigenetic regulation in animal development, serving to increase the understanding of the molecular basis of phenotypic diversity and developmental plasticity in animals. Understanding the intricate role of epigenetic mechanisms in animal development not only provides insights into the fundamental processes of cell differentiation and adaptation but also has broader implications for fields such as evolutionary biology and animal biotechnology research.

Dr. Jéssica Ispada
Guest Editor

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. Animals is an international peer-reviewed open access semimonthly 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 2400 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

  • epigenetics
  • animal development
  • DNA methylation
  • histone post-translational modifications
  • non-coding RNAs
  • environmental effects on gene expression
  • epigenetic reprogramming
  • embryonic stem cells
  • cell differentiation
  • comparative epigenetics

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

Published Papers (3 papers)

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Research

14 pages, 2900 KiB  
Article
The Whole Genome DNA Methylation Signatures of Hindlimb Muscles in Chinese Alligators during Hibernation and Active Periods
by Jihui Zhang and Xiaobing Wu
Animals 2024, 14(13), 1972; https://doi.org/10.3390/ani14131972 - 3 Jul 2024
Viewed by 1013
Abstract
Many ectotherms hibernate to increase their chances of survival during harsh winter conditions. The role of DNA methylation in regulating gene expression related to hibernation in ectotherms remains unclear. Here, we employed whole-genome bisulfite sequencing (WGBS) technology to construct a comprehensive genome-wide DNA [...] Read more.
Many ectotherms hibernate to increase their chances of survival during harsh winter conditions. The role of DNA methylation in regulating gene expression related to hibernation in ectotherms remains unclear. Here, we employed whole-genome bisulfite sequencing (WGBS) technology to construct a comprehensive genome-wide DNA methylation landscape of the hindlimb muscles in the Chinese alligator during hibernation and active periods. The results indicated that methylation modifications were most abundant at CG sites, identifying 9447 differentially methylated regions (DMRs) and 2329 differentially methylated genes (DMGs). KEGG pathway enrichment analysis of the DMGs revealed significant enrichment in major pathways such as the neurotrophin signaling pathway, the MAPK signaling pathway, the GnRH signaling pathway, the biosynthesis of amino acids, and the regulation of the actin cytoskeleton, which are closely related to lipid metabolism, energy metabolism, and amino acid metabolism. Among these, 412 differentially methylated genes were located in promoter regions, including genes related to energy metabolism such as ATP5F1C, ATP5MD, PDK3, ANGPTL1, and ANGPTL2, and genes related to ubiquitin-proteasome degradation such as FBXO28, FBXO43, KLHL40, and PSMD5. These findings suggest that methylation in promoter regions may play a significant role in regulating the adaptive hibernation mechanisms in the Chinese alligator. This study contributes to a further understanding of the epigenetic mechanisms behind the hibernation of the Chinese alligator. Full article
(This article belongs to the Special Issue Epigenetics in Animal Development)
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13 pages, 1863 KiB  
Article
Long Non-Coding RNAs Differentially Expressed in Swine Fetuses
by Francelly G. Campos, Adriana M. G. Ibelli, Maurício E. Cantão, Haniel C. Oliveira, Jane O. Peixoto, Mônica C. Ledur and Simone E. F. Guimarães
Animals 2024, 14(13), 1897; https://doi.org/10.3390/ani14131897 - 27 Jun 2024
Viewed by 844
Abstract
Long non-coding RNAs (lncRNAs) are non-coding transcripts involved in various biological processes. The Y chromosome is known for determining the male sex in mammals. LncRNAs on the Y chromosome may play important regulatory roles. However, knowledge about their action mechanisms is still limited, [...] Read more.
Long non-coding RNAs (lncRNAs) are non-coding transcripts involved in various biological processes. The Y chromosome is known for determining the male sex in mammals. LncRNAs on the Y chromosome may play important regulatory roles. However, knowledge about their action mechanisms is still limited, especially during early fetal development. Therefore, we conducted this exploratory study aiming to identify, characterize, and investigate the differential expression of lncRNAs between male and female swine fetuses at 35 days of gestation. RNA-Seq libraries from 10 fetuses were prepared and sequenced using the Illumina platform. After sequencing, a data quality control was performed using Trimmomatic, alignment with HISAT2, and transcript assembly with StringTie. The differentially expressed lncRNAs were identified using the limma package of the R software (4.3.1). A total of 871 potentially novel lncRNAs were identified and characterized. Considering differential expression, eight lncRNAs were upregulated in male fetuses. One was mapped onto SSC12 and seven were located on the Y chromosome; among them, one lncRNA is potentially novel. These lncRNAs are involved in diverse functions, including the regulation of gene expression and the modulation of chromosomal structure. These discoveries enable future studies on lncRNAs in the fetal stage in pigs. Full article
(This article belongs to the Special Issue Epigenetics in Animal Development)
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16 pages, 6350 KiB  
Article
Elucidating the Role of Transcriptomic Networks and DNA Methylation in Collagen Deposition of Dezhou Donkey Skin
by Xinrui Wang, Wei Ren, Yongdong Peng, Muhammad Zahoor Khan, Huili Liang, Yigang Zhang, Xiaotong Liu, Yinghui Chen, Xiyan Kou, Liyuan Wang, Changfa Wang and Yandong Zhan
Animals 2024, 14(8), 1222; https://doi.org/10.3390/ani14081222 - 18 Apr 2024
Cited by 1 | Viewed by 1202
Abstract
DNA methylation represents a predominant epigenetic modification with broad implications in various biological functions. Its role is particularly significant in the process of collagen deposition, a fundamental aspect of dermal development in donkeys. Despite its critical involvement, the mechanistic insights into how DNA [...] Read more.
DNA methylation represents a predominant epigenetic modification with broad implications in various biological functions. Its role is particularly significant in the process of collagen deposition, a fundamental aspect of dermal development in donkeys. Despite its critical involvement, the mechanistic insights into how DNA methylation influences collagen deposition in donkey skin remain limited. In this study, we employed whole genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) to investigate the epigenetic landscape and gene expression profiles in the dorsal skin tissues of Dezhou donkeys across three developmental stages: embryonic (YD), juvenile (2-year-old, MD), and mature (8-year-old, OD). Our analysis identified numerous differentially methylated genes that play pivotal roles in skin collagen deposition and overall skin maturation, including but not limited to COL1A1, COL1A2, COL3A1, COL4A1, COL4A2, GLUL, SFRP2, FOSL1, SERPINE1, MMP1, MMP2, MMP9, and MMP13. Notably, we observed an inverse relationship between gene expression and DNA methylation proximal to transcription start sites (TSSs), whereas a direct correlation was detected in regions close to transcription termination sites (TTSs). Detailed bisulfite sequencing analyses of the COL1A1 promoter region revealed a low methylation status during the embryonic stage, correlating with elevated transcriptional activity and gene expression levels. Collectively, our findings elucidate key genetic markers associated with collagen deposition in the skin of Dezhou donkeys, underscoring the significant regulatory role of DNA methylation. This research work contributes to the foundational knowledge necessary for the genetic improvement and selective breeding of Dezhou donkeys, aiming to enhance skin quality attributes. Full article
(This article belongs to the Special Issue Epigenetics in Animal Development)
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