Comparative analysis of DNA methylome and transcriptome of skeletal muscle in lean-, obese-, and mini-type pigs

Yang, Yalan; Liang, Guoming; Niu, Guanglin; Zhang, Yuanyuan; Zhou, Rong; Wang, Yanfang; Mu, Yulian; Tang, Zhonglin; Li, Kui

doi:10.1038/srep39883

Cited by 40 publications

(45 citation statements)

References 102 publications

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“…Previous researchers found that the myoblast proliferation phases of LD in TC pigs were longer than that those in WZS pigs [4], and it was predicted that cell proliferation may contribute to differences in muscle mass and body size between these two breeds [6]. In the current study, GO analysis showed that cell proliferation was at a higher level in LW than in HN pigs at 78 dpc.…”

Section: Discussionsupporting

confidence: 51%

“…They found 547, 5566, and 4360 differentially expressed mRNAs, lncRNAs, and circRNAs, respectively, and constructed 26 ceRNA interactions [5]. DNA methylation, mRNA, lncRNA and miRNA pro les in the LD muscle of TC, LR and Wuzhishan (WZS) pigs at the age of 240 days were compared, and differentially methylated genes were associated with lipid metabolism, oxidative stress, muscle development, and the p38 MAPK signaling pathway [6]. Differences in meat quality between fat-and lean-type pigs were mainly due to muscle development and lipid metabolism, and mRNA, miRNA, lncRNA, circRNA, and methylation were all involved in the regulation of meat quality.…”

Section: Introductionmentioning

confidence: 99%

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LncRNA IMFlnc1 promotes porcine intramuscular adipocyte differentiation by sponging miR-199a-5p to up-regulate CAV-1

Wang

Chen

et al. 2020

Preprint

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Background Local Chinese local pig breeds have better meat quality, such as thinner muscle fiber and higher intramuscular-fat (IMF) content. However, its molecular regulation mechanism has not been discussed in-depth. Studies indicated that long non coding RNAs (lncRNAs) participate in the regulation of muscle and fat development. The expressional differences of lncRNAs in the longissimus dorsi (LD) muscle were identified between Huainan pigs (local Chinese pigs, fat-type, HN) and Large White pigs (lean-type, LW) at 38, 58, and 78 days post conception (dpc).Results In total, 2131 novel lncRNAs were identified in 18 samples, and 291, 305, and 683 differentially expressed lncRNAs (DELs) were found between these two breeds at three stages, respectively. GO and KEGG analysis of the DEL co expressed mRNAs showed that muscle development and energy metabolism were more active at 58 dpc in HN, but at 78 dpc in LW pigs. Muscle cell differentiation and myofibril assembly might contribute to earlier myogenesis and primary-muscle-fiber assembly in HN, and cell proliferation, insulin, and the mitogen-activated protein kinase (MAPK) pathway might contribute to longer proliferation in LW pigs. The PI3K/Akt and cAMP pathways were associated with higher IMF deposition in HN. IMFlnc1 was selected for functional verification, and results indicated that it regulated the expressional level of caveolin-1 (CAV-1) as a competing endogenous RNA (ceRNA) for miR-199a-5p.Conclusion Our data contributed to understanding lncRNAs in porcine-muscle development and IMF deposition, and provided valuable information for improving pig-meat quality.

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Section: Discussionsupporting

confidence: 51%

Section: Introductionmentioning

confidence: 99%

LncRNA IMFlnc1 promotes porcine intramuscular adipocyte differentiation by sponging miR-199a-5p to up-regulate CAV-1

Wang

Chen

et al. 2020

Preprint

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“…In order to examine expression of the short H2A variants, we analyzed publicly available transcriptome data from human, opossum, and platypus (Brawand et al 2011), dog (Broad Institute), and pig (Wageningen University's FAANG project) (Yang et al 2017). SRA identifiers are listed in Supplemental Table S3.…”

Section: Rna-seq Analysismentioning

confidence: 99%

Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals

Molaro¹,

Young²,

Malik³

2018

Genome Res.

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Eukaryotic genomes must accomplish both compact packaging for genome stability and inheritance, as well as accessibility for gene expression. They do so using post-translational modifications of four ancient canonical histone proteins (H2A, H2B, H3, and H4) and by deploying histone variants with specialized chromatin functions. Some histone variants are conserved across all eukaryotes, whereas others are lineage-specific. Here, we performed detailed phylogenomic analyses of "short H2A histone" variants found in mammalian genomes. We discovered a previously undescribed typically-sized H2A variant in monotremes and marsupials, , which may represent the common ancestor of the short H2As. We also discovered a novel class of short H2A histone variants in eutherian mammals, We show that short H2A variants arose on the X Chromosome in the common ancestor of all eutherian mammals and diverged into four evolutionarily distinct clades: ,, , and However, the repertoires of short histone H2A variants vary extensively among eutherian mammals due to lineage-specific gains and losses. Finally, we show that all four short H2As are subject to accelerated rates of protein evolution relative to both canonical and other variant H2A proteins including H2A.R. Our analyses reveal that short H2As are a unique class of testis-restricted histone variants displaying an unprecedented evolutionary dynamism. Based on their X-Chromosomal localization, genetic turnover, and testis-specific expression, we hypothesize that short H2A variants may participate in genetic conflicts involving sex chromosomes during reproduction.

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“…In order to examine expression of the short H2A variants, we analyzed publically available transcriptome data. Human, opossum and platypus data have been published (Brawand, et al 2011), dog data are from the Broad Institute (unpublished) and pig data are from Wageningen University's FAANG project or as published (Yang, et al 2017). SRA identifiers are listed in Supp Table 3.…”

Section: Rna-seq Analysismentioning

confidence: 99%

Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals

Molaro

Young

Malik

2017

Preprint

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Eukaryotic genomes must accomplish the tradeoff between compact packaging for genome stability and inheritance, and accessibility for gene expression. They do so using post-translational modifications of four ancient canonical histone proteins (H2A, H2B, H3 and H4), and by deploying histone variants with specialized chromatin functions. While some histone variants are highly conserved across eukaryotes, others carry out lineage-specific functions. Here, we characterize the evolution of male germline-specific "short H2A variants", which wrap shorter DNA fragments than canonical H2A. In addition to three previously described H2A.B, H2A.L and H2A.P variants, we describe a novel, extremely short H2A histone variant: H2A.Q. We show that H2A.B, H2A.L, H2A.P and H2A.Q are most closely related to a novel, more canonical mmH2A variant found only in monotremes and marsupials. Using phylogenomics, we trace the origins and early diversification of short histone variants into four distinct clades to the ancestral X chromosome of placental mammals. We show that short H2A variants further diversified by repeated lineage-specific amplifications and losses, including pseudogenization of H2A.L in many primates. We also uncover evidence for concerted evolution of H2A.B and H2A.L genes by gene conversion in many species, involving loci separated by large distances. Finally, we find that short H2As evolve more rapidly than any other histone variant, with evidence that positive selection has acted upon H2A.P in primates. Based on their X chromosomal location and pattern of genetic innovation, we speculate that short H2A histone variants are engaged in a form of genetic conflict involving the mammalian sex chromosomes. IntroductionNucleosomes are the basic unit of chromatin in practically all eukaryotes. A typical nucleosome particle wraps 150bp of DNA around an octamer of four histone proteins: H3, H4, H2A and H2B (Kornberg 1974;Kornberg and Thomas 1974;Malik and Henikoff 2003). These four canonical "core" histone proteins have a stereotypical structure characterized by alpha-helices comprising a "histone fold domain" (HFD) (Luger, et al. 1997). During nucleosome assembly, the HFD mediates dimerization of H3 with H4, and that of H2A with H2B, and contains the nucleosome-DNA interface. Nucleosomes thus comprise a central core of a H3-H4 tetramer, flanked by two H2A-H2B dimers. In contrast to their HFD, the N-and C-terminal tails of canonical histones are far less structured and remain solvent-exposed in the nucleosome.. CC-BY-NC 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/165936 doi: bioRxiv preprint first posted online Jul. 20, 2017; 3 Nucleosomes can prevent other cellular factors, such as transcription factors, from interacting with DNA. While the post-translational modification of histone tails play an important role in regulating these interactions, eukaryotic genomes also establish diverse chroma...

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Comparative analysis of DNA methylome and transcriptome of skeletal muscle in lean-, obese-, and mini-type pigs

Cited by 40 publications

References 102 publications

LncRNA IMFlnc1 promotes porcine intramuscular adipocyte differentiation by sponging miR-199a-5p to up-regulate CAV-1

LncRNA IMFlnc1 promotes porcine intramuscular adipocyte differentiation by sponging miR-199a-5p to up-regulate CAV-1

Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals

Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals

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