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17 pages, 5337 KiB

Open AccessArticle

Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages

by Jingyi Bai, Yu Lin, Jiaman Zhang, Ziyu Chen, Yujie Wang, Mingzhou Li and Jing Li

Int. J. Mol. Sci. 2023, 24(13), 11076; https://doi.org/10.3390/ijms241311076 - 4 Jul 2023

Cited by 2 | Viewed by 1400

Abstract

The study of chromatin accessibility across tissues and developmental stages is essential for elucidating the transcriptional regulation of various phenotypes and biological processes. However, the chromatin accessibility profiles of multiple tissues in newborn pigs and across porcine liver development remain poorly investigated. Here, [...] Read more.

The study of chromatin accessibility across tissues and developmental stages is essential for elucidating the transcriptional regulation of various phenotypes and biological processes. However, the chromatin accessibility profiles of multiple tissues in newborn pigs and across porcine liver development remain poorly investigated. Here, we used ATAC-seq and rRNA-depleted RNA-seq to profile open chromatin maps and transcriptional features of heart, kidney, liver, lung, skeletal muscle, and spleen in newborn pigs and porcine liver tissue in the suckling and adult stages, respectively. Specifically, by analyzing a union set of protein-coding genes (PCGs) and two types of transcripts (lncRNAs and TUCPs), we obtained a comprehensive annotation of consensus ATAC-seq peaks for each tissue and developmental stage. As expected, the PCGs with tissue-specific accessible promoters had active transcription and were relevant to tissue-specific functions. In addition, other non-coding tissue-specific peaks were involved in both physical activity and the morphogenesis of neonatal tissues. We also characterized stage-specific peaks and observed a close association between dynamic chromatin accessibility and hepatic function transition during liver postnatal development. Overall, this study expands our current understanding of epigenetic regulation in mammalian tissues and organ development, which can benefit both economic trait improvement and improve the biomedical usage of pigs. Full article

(This article belongs to the Special Issue Animal Genomes and Epigenomes)

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13 pages, 3273 KiB

Open AccessArticle

The Role of SOCS3 in Regulating Meat Quality in Jinhua Pigs

by Fen Wu, Zitao Chen, Zhenyang Zhang, Zhen Wang, Zhe Zhang, Qishan Wang and Yuchun Pan

Int. J. Mol. Sci. 2023, 24(13), 10593; https://doi.org/10.3390/ijms241310593 - 24 Jun 2023

Viewed by 1296

Abstract

Meat quality is an important economic trait that influences the development of the pig industry. Skeletal muscle development and glycolytic potential (GP) are two crucial aspects that significantly impact meat quality. It has been reported that abnormal skeletal muscle development and high glycogen [...] Read more.

Meat quality is an important economic trait that influences the development of the pig industry. Skeletal muscle development and glycolytic potential (GP) are two crucial aspects that significantly impact meat quality. It has been reported that abnormal skeletal muscle development and high glycogen content results in low meat quality. However, the genetic mechanisms underlying these factors are still unclear. Compared with intensive pig breeds, Chinese indigenous pig breeds, such as the Jinhua pig, express superior meat quality characteristics. The differences in the meat quality traits between Jinhua and intensive pig breeds make them suitable for uncovering the genetic mechanisms that regulate meat quality traits. In this study, the Jinhua pig breed and five intensive pig breeds, including Duroc, Landrace, Yorkshire, Berkshire, and Pietrain pig breeds, were selected as experimental materials. First, the F_ST and XP-EHH methods were used to screen the selective signatures on the genome in the Jinhua population. Then, combined with RNA-Seq data, the study further confirmed that SOCS3 could be a key candidate gene that influences meat quality by mediating myoblast proliferation and glycometabolism because of the down-regulated expression of SOCS3 in Jinhua pigs compared with Landrace pigs. Finally, through SOCS3 knockout (KO) and overexpression (OE) experiments in mouse C2C12 cells, the results showed that SOCS3 regulated the cell proliferation of myoblasts. Moreover, SOCS3 is involved in regulating glucose uptake by the IRS1/PI3K/AKT signaling pathway. Overall, these findings provide a basis for the genetic improvement of meat quality traits in the pig industry. Full article

(This article belongs to the Special Issue Animal Genomes and Epigenomes)

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24 pages, 5827 KiB

Open AccessArticle

Genome-Wide DNA Methylation and Transcriptome Integration Associates DNA Methylation Changes with Bovine Subclinical Mastitis Caused by Staphylococcus chromogenes

by Mengqi Wang, Nathalie Bissonnette, Mario Laterrière, David Gagné, Pier-Luc Dudemaine, Jean-Philippe Roy, Marc-André Sirard and Eveline M. Ibeagha-Awemu

Int. J. Mol. Sci. 2023, 24(12), 10369; https://doi.org/10.3390/ijms241210369 - 20 Jun 2023

Cited by 1 | Viewed by 1575

Abstract

Staphylococcus chromogenes (SC) is a common coagulase-negative staphylococcus described as an emerging mastitis pathogen and commonly found in dairy farms. This study investigated the potential involvement of DNA methylation in subclinical mastitis caused by SC. The whole-genome DNA methylation patterns and transcriptome profiles [...] Read more.

Staphylococcus chromogenes (SC) is a common coagulase-negative staphylococcus described as an emerging mastitis pathogen and commonly found in dairy farms. This study investigated the potential involvement of DNA methylation in subclinical mastitis caused by SC. The whole-genome DNA methylation patterns and transcriptome profiles of milk somatic cells from four cows with naturally occurring SC subclinical mastitis (SCM) and four healthy cows were characterized by next-generation sequencing, bioinformatics, and integration analyses. Comparisons revealed abundant DNA methylation changes related to SCM, including differentially methylated cytosine sites (DMCs, n = 2,163,976), regions (DMRs, n = 58,965), and methylation haplotype blocks (dMHBs, n = 53,098). Integration of methylome and transcriptome data indicated a negative global association between DNA methylation at regulatory regions (promoters, first exons, and first introns) and gene expression. A total of 1486 genes with significant changes in the methylation levels of their regulatory regions and corresponding gene expression showed significant enrichment in biological processes and pathways related to immune functions. Sixteen dMHBs were identified as candidate discriminant signatures, and validation of two signatures in more samples further revealed the association of dMHBs with mammary gland health and production. This study demonstrated abundant DNA methylation changes with possible involvement in regulating host responses and potential as biomarkers for SCM. Full article

(This article belongs to the Special Issue Animal Genomes and Epigenomes)

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19 pages, 4895 KiB

Open AccessArticle

Analysis of CircRNA Expression in Peripheral Blood of Holstein Cows in Response to Heat Stress

by Congcong Zhang, Shuhui Wang, Lirong Hu, Hao Fang, Gong Chen, Xiaojuan Ma, Ying Yu, Yachun Wang and Qing Xu

Int. J. Mol. Sci. 2023, 24(12), 10150; https://doi.org/10.3390/ijms241210150 - 15 Jun 2023

Cited by 1 | Viewed by 1316

Abstract

The present study aimed to identify key circRNAs and pathways associated with heat stress in blood samples of Holstein cows, which will provide new insights into the molecular mechanisms driving heat stress in cows. Hence, we evaluated changes in milk yield, rectal temperature, [...] Read more.

The present study aimed to identify key circRNAs and pathways associated with heat stress in blood samples of Holstein cows, which will provide new insights into the molecular mechanisms driving heat stress in cows. Hence, we evaluated changes in milk yield, rectal temperature, and respiratory rate of experimental cows between heat stress (summer) and non-heat stress (spring) conditions with two comparisons, including Sum1 vs. Spr1 (same lactation stage, different individuals, 15 cows per group) and Sum1 vs. Spr2 (same individual, different lactation stages, 15 cows per group). Compared to both Spr1 and Spr2, cows in the Sum1 group had a significantly lower milk yield, while rectal temperature and respiratory rate were significantly higher (p < 0.05), indicating that cows in the Sum1 group were experiencing heat stress. In each group, five animals were chosen randomly to undergo RNA-seq. The results reveal that 140 and 205 differentially expressed (DE) circRNAs were screened in the first and second comparisons, respectively. According to the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, these DE circRNAs were mainly enriched in five signaling pathways, including choline metabolism, the PI3K/AKT signaling pathway, the HIF-1 signaling pathway, the longevity-regulating pathway, and autophagy. Then, we obtained the top 10 hub source genes of circRNAs according to the protein–protein interaction networks. Among them, ciRNA1282 (HIF1A), circRNA4205 (NR3C1), and circRNA12923 (ROCK1) were enriched in multiple pathways and identified as binding multiple miRNAs. These key circRNAs may play an important role in the heat stress responses of dairy cows. These results provide valuable information on the involvement of key circRNAs and their expression pattern in the heat stress response of cows. Full article

(This article belongs to the Special Issue Animal Genomes and Epigenomes)

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16 pages, 1541 KiB

Open AccessArticle

A Satellite-Free Centromere in Equus przewalskii Chromosome 10

by Francesca M. Piras, Eleonora Cappelletti, Wasma A. Abdelgadir, Giulio Salamon, Simone Vignati, Marco Santagostino, Lorenzo Sola, Solomon G. Nergadze and Elena Giulotto

Int. J. Mol. Sci. 2023, 24(4), 4134; https://doi.org/10.3390/ijms24044134 - 18 Feb 2023

Cited by 2 | Viewed by 1802

Abstract

In mammals, centromeres are epigenetically specified by the histone H3 variant CENP-A and are typically associated with satellite DNA. We previously described the first example of a natural satellite-free centromere on Equus caballus chromosome 11 (ECA11) and, subsequently, on several chromosomes in other [...] Read more.

In mammals, centromeres are epigenetically specified by the histone H3 variant CENP-A and are typically associated with satellite DNA. We previously described the first example of a natural satellite-free centromere on Equus caballus chromosome 11 (ECA11) and, subsequently, on several chromosomes in other species of the genus Equus. We discovered that these satellite-free neocentromeres arose recently during evolution through centromere repositioning and/or chromosomal fusion, after inactivation of the ancestral centromere, where, in many cases, blocks of satellite sequences were maintained. Here, we investigated by FISH the chromosomal distribution of satellite DNA families in Equus przewalskii (EPR), demonstrating a good degree of conservation of the localization of the major horse satellite families 37cen and 2PI with the domestic horse. Moreover, we demonstrated, by ChIP-seq, that 37cen is the satellite bound by CENP-A and that the centromere of EPR10, the ortholog of ECA11, is devoid of satellite sequences. Our results confirm that these two species are closely related and that the event of centromere repositioning which gave rise to EPR10/ECA11 centromeres occurred in the common ancestor, before the separation of the two horse lineages. Full article

(This article belongs to the Special Issue Animal Genomes and Epigenomes)

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18 pages, 4132 KiB

Open AccessArticle

Convergent Genomic Signatures of Cashmere Traits: Evidence for Natural and Artificial Selection

by Wei Wang, Zhuohui Li, Guoxiang Xie, Xinmei Li, Zhipei Wu, Manman Li, Anguo Liu, Yan Xiong and Yu Wang

Int. J. Mol. Sci. 2023, 24(2), 1165; https://doi.org/10.3390/ijms24021165 - 6 Jan 2023

Cited by 2 | Viewed by 2302

Abstract

Convergent evolution provides powerful opportunities to investigate the genetic basis of complex traits. The Tibetan antelope (Pantholops hodgsonii) and Siberian ibex (Capra sibirica) belong to different subfamilies in Bovidae, but both have evolved similar superfine cashmere characteristics to [...] Read more.

Convergent evolution provides powerful opportunities to investigate the genetic basis of complex traits. The Tibetan antelope (Pantholops hodgsonii) and Siberian ibex (Capra sibirica) belong to different subfamilies in Bovidae, but both have evolved similar superfine cashmere characteristics to meet the cold temperature in plateau environments. The cashmere traits of cashmere goats underwent strong artificial selection, and some traces of domestication also remained in the genome. Hence, we investigated the convergent genomic signatures of cashmere traits between natural and artificial selection. We compared the patterns of convergent molecular evolution between Tibetan antelope and Siberian ibex by testing positively selected genes, rapidly evolving genes and convergent amino acid substitutions. In addition, we analyzed the selected genomic features of cashmere goats under artificial selection using whole-genome resequencing data, and skin transcriptome data of cashmere goats were also used to focus on the genes involved in regulating cashmere traits. We found that molecular convergent events were very rare, but natural and artificial selection genes were convergent enriched in similar functional pathways (e.g., ECM-receptor interaction, focal adhesion, PI3K-Akt signaling pathway) in a variety of gene sets. Type IV collagen family genes (COL4A2, COL4A4, COL4A5, COL6A5, COL6A6) and integrin family genes (ITGA2, ITGA4, ITGA9, ITGB8) may be important candidate genes for cashmere formation and development. Our results provide a comprehensive approach and perspective for exploring cashmere traits and offer a valuable reference for subsequent in-depth research on the molecular mechanisms regulating cashmere development and fineness. Full article

(This article belongs to the Special Issue Animal Genomes and Epigenomes)

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13 pages, 4609 KiB

Open AccessArticle

Temporal Expression of Myogenic Regulatory Genes in Different Chicken Breeds during Embryonic Development

by Shuang Gu, Chaoliang Wen, Junying Li, Honghong Liu, Qiang Huang, Jiangxia Zheng, Congjiao Sun and Ning Yang

Int. J. Mol. Sci. 2022, 23(17), 10115; https://doi.org/10.3390/ijms231710115 - 4 Sep 2022

Cited by 3 | Viewed by 1917

Abstract

The basic units of skeletal muscle in all vertebrates are multinucleate myofibers, which are formed from the fusion of mononuclear myoblasts during the embryonic period. In order to understand the regulation of embryonic muscle development, we selected four chicken breeds, namely, Cornish (CN), [...] Read more.

The basic units of skeletal muscle in all vertebrates are multinucleate myofibers, which are formed from the fusion of mononuclear myoblasts during the embryonic period. In order to understand the regulation of embryonic muscle development, we selected four chicken breeds, namely, Cornish (CN), White Plymouth Rock (WPR), White Leghorn (WL), and Beijing-You Chicken (BYC), for evaluation of their temporal expression patterns of known key regulatory genes (Myomaker, MYOD, and MSTN) during pectoral muscle (PM) and thigh muscle (TM) development. The highest expression level of Myomaker occurred from embryonic days E13 to E15 for all breeds, indicating that it was the crucial stage of myoblast fusion. Interestingly, the fast-growing CN showed the highest gene expression level of Myomaker during the crucial stage. The MYOD gene expression at D1 was much higher, implying that MYOD might have an important role after hatching. Histomorphology of PM and TM suggested that the myofibers was largely complete at E17, which was speculated to have occurred because of the expression increase in MSTN and the expression decrease in Myomaker. Our research contributes to lay a foundation for the study of myofiber development during the embryonic period in different chicken breeds. Full article

(This article belongs to the Special Issue Animal Genomes and Epigenomes)

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16 pages, 1057 KiB

Open AccessReview

The Molecular Impacts of Retrotransposons in Development and Diseases

by Phoebe Lut Fei Tam and Danny Leung

Int. J. Mol. Sci. 2023, 24(22), 16418; https://doi.org/10.3390/ijms242216418 - 16 Nov 2023

Viewed by 978

Abstract

Retrotransposons are invasive genetic elements that constitute substantial portions of mammalian genomes. They have the potential to influence nearby gene expression through their cis-regulatory sequences, reverse transcription machinery, and the ability to mold higher-order chromatin structures. Due to their multifaceted functions, it [...] Read more.

Retrotransposons are invasive genetic elements that constitute substantial portions of mammalian genomes. They have the potential to influence nearby gene expression through their cis-regulatory sequences, reverse transcription machinery, and the ability to mold higher-order chromatin structures. Due to their multifaceted functions, it is crucial for host fitness to maintain strict regulation of these parasitic sequences to ensure proper growth and development. This review explores how subsets of retrotransposons have undergone evolutionary exaptation to enhance the complexity of mammalian genomes. It also highlights the significance of regulating these elements, drawing on recent studies conducted in human and murine systems. Full article

(This article belongs to the Special Issue Animal Genomes and Epigenomes)

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