Maternal methionine supplementation during gestation alters alternative splicing and DNA methylation in bovine skeletal muscle

Abstract Background The evaluation of alternative splicing, including differential isoform expression and differential exon usage, can provide some insights on the transcriptional changes that occur in response to environmental perturbations. Maternal nutrition is considered a major intrauterine regulator of fetal developmental programming. The objective of this study was to assess potential changes in splicing events in the longissimus dorsi muscle of beef calves gestated under control or methionine-rich diets. RNA sequencing and whole-genome bisulfite sequencing were used to evaluate muscle transcriptome and methylome, respectively. Results Alternative splicing patterns were significantly altered by maternal methionine supplementation. Most of the altered genes were directly implicated in muscle development, muscle physiology, ATP activities, RNA splicing and DNA methylation, among other functions. Interestingly, there was a significant association between DNA methylation and differential exon usage. Indeed, among the set of genes that showed differential exon usage, significant differences in methylation level were detected between significant and non-significant exons, and between contiguous and non-contiguous introns to significant exons. Conclusions Overall, our findings provide evidence that a prenatal diet rich in methyl donors can significantly alter the offspring transcriptome, including changes in isoform expression and exon usage, and some of these changes are mediated by changes in DNA methylation.

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Rbfox1 is required for myofibril development and maintaining fiber type–specific isoform expression in Drosophila muscles

Life Science Alliance ◽

10.26508/lsa.202101342 ◽

2022 ◽

Vol 5 (4) ◽

pp. e202101342

Author(s):

Elena Nikonova ◽

Amartya Mukherjee ◽

Ketaki Kamble ◽

Christiane Barz ◽

Upendra Nongthomba ◽

...

Keyword(s):

Alternative Splicing ◽

Muscle Development ◽

Rna Binding ◽

Troponin I ◽

Rna Binding Proteins ◽

Fiber Type ◽

Structural Defects ◽

Specific Gene ◽

Fiber Types ◽

Isoform Expression

Protein isoform transitions confer muscle fibers with distinct properties and are regulated by differential transcription and alternative splicing. RNA-binding Fox protein 1 (Rbfox1) can affect both transcript levels and splicing, and is known to contribute to normal muscle development and physiology in vertebrates, although the detailed mechanisms remain obscure. In this study, we report that Rbfox1 contributes to the generation of adult muscle diversity in Drosophila. Rbfox1 is differentially expressed among muscle fiber types, and RNAi knockdown causes a hypercontraction phenotype that leads to behavioral and eclosion defects. Misregulation of fiber type–specific gene and splice isoform expression, notably loss of an indirect flight muscle–specific isoform of Troponin-I that is critical for regulating myosin activity, leads to structural defects. We further show that Rbfox1 directly binds the 3′-UTR of target transcripts, regulates the expression level of myogenic transcription factors myocyte enhancer factor 2 and Salm, and both modulates expression of and genetically interacts with the CELF family RNA-binding protein Bruno1 (Bru1). Rbfox1 and Bru1 co-regulate fiber type–specific alternative splicing of structural genes, indicating that regulatory interactions between FOX and CELF family RNA-binding proteins are conserved in fly muscle. Rbfox1 thus affects muscle development by regulating fiber type–specific splicing and expression dynamics of identity genes and structural proteins.

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Extensive alternative splicing transitions during postnatal skeletal muscle development are required for calcium handling functions

10.1101/124230 ◽

2017 ◽

Cited By ~ 1

Author(s):

Amy E. Brinegar ◽

Zheng Xia ◽

James A. Loehr ◽

Wei Li ◽

George G. Rodney ◽

...

Keyword(s):

Skeletal Muscle ◽

Alternative Splicing ◽

Postnatal Development ◽

Muscle Development ◽

Muscle Relaxation ◽

Calcium Handling ◽

Muscle Physiology ◽

Mouse Muscle ◽

Calcium Dependent ◽

Calcineurin A

AbstractPostnatal development of skeletal muscle is a highly dynamic period of tissue remodeling. Here we used RNA-seq to identify transcriptome changes from late embryonic to adult mouse muscle and demonstrate that alternative splicing developmental transitions impact muscle physiology. The first two weeks after birth are particularly dynamic for differential gene expression and AS transitions, and calciumhandling functions are significantly enriched among genes that undergo alternative splicing. We focused on the postnatal splicing transitions of three calcineurin A genes, calcium-dependent phosphatases that regulate multiple aspects of muscle biology. Redirected splicing of calcineurin A to the fetal isoforms in adult muscle and in differentiated C2C12 slows the timing of muscle relaxation, promotes nuclear localization of calcineurin targets Nfatc3 and Nfatc2, and affects expression of Nfatc transcription targets. The results demonstrate a previously unknown specificity of calcineurin isoforms as well as the broader impact of AS during muscle postnatal development.

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Differential network analysis of bovine muscle reveals changes in gene coexpression patterns in response to changes in maternal nutrition

BMC Genomics ◽

10.1186/s12864-020-07068-x ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Lihe Liu ◽

Rocío Amorín ◽

Philipe Moriel ◽

Nicolás DiLorenzo ◽

Phillip A. Lancaster ◽

...

Keyword(s):

Dna Methylation ◽

Network Analysis ◽

Structural Changes ◽

Maternal Nutrition ◽

Control Diet ◽

Functional Characterization ◽

Connectivity Pattern ◽

Sequencing Analysis ◽

Gene Coexpression ◽

Methionine Supplementation

Abstract Background Coexpression network analysis is a powerful tool to reveal transcriptional regulatory mechanisms, identify transcription factors, and discover gene functions. It can also be used to investigate changes in coexpression patterns in response to environmental insults or changes in experimental conditions. Maternal nutrition is considered a major intrauterine regulator of fetal developmental programming. The objective of this study was to investigate structural changes in gene coexpression networks in the muscle of bull beef calves gestated under diets with or without methionine supplementation. Both muscle transcriptome and methylome were evaluated using next generation sequencing. Results Maternal methionine supplementation significantly perturbed coexpression patterns in the offspring’s muscle. Indeed, we found that neither the connection strength nor the connectivity pattern of six modules (subnetworks) detected in the control diet were preserved in the methionine-rich diet. Functional characterization revealed that some of the unpreserved modules are implicated in myogenesis, adipogenesis, fibrogenesis, canonical Wnt/β-catenin pathway, ribosome structure, rRNA binding and processing, mitochondrial activities, ATP synthesis and NAD(P) H oxidoreductases, among other functions. The bisulfite sequencing analysis showed that nearly 2% of all evaluated cytosines were differentially methylated between maternal diets. Interestingly, there were significant differences in the levels of gene body DNA methylation between preserved and unpreserved modules. Conclusions Overall, our findings provide evidence that maternal nutrition can significantly alter gene coexpression patterns in the offspring, and some of these perturbations are mediated by changes in DNA methylation.

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Molecular Profiling of DNA Methylation and Alternative Splicing of Genes in Skeletal Muscle of Obese Rabbits

Current Issues in Molecular Biology ◽

10.3390/cimb43030110 ◽

2021 ◽

Vol 43 (3) ◽

pp. 1558-1575

Author(s):

Yanhong Li ◽

Jie Wang ◽

Mauricio A. Elzo ◽

Huimei Fan ◽

Kun Du ◽

...

Keyword(s):

Skeletal Muscle ◽

Dna Methylation ◽

Alternative Splicing ◽

Genetic Modification ◽

Muscle Development ◽

Differential Methylation ◽

Body Region ◽

Messenger Rnas ◽

Gene Body ◽

Body Regions

DNA methylation and the alternative splicing of precursor messenger RNAs (pre-mRNAs) are two important genetic modification mechanisms. However, both are currently uncharacterized in the muscle metabolism of rabbits. Thus, we constructed the Tianfu black rabbit obesity model (obese rabbits fed with a 10% high-fat diet and control rabbits from 35 days to 70 days) and collected the skeletal muscle samples from the two groups for Genome methylation sequencing and RNA sequencing. DNA methylation data showed that the promoter regions of 599 genes and gene body region of 2522 genes had significantly differential methylation rates between the two groups, of which 288 genes had differential methylation rates in promoter and gene body regions. Analysis of alternative splicing showed 555 genes involved in exon skipping (ES) patterns, and 15 genes existed in differential methylation regions. Network analysis showed that 20 hub genes were associated with ubiquitinated protein degradation, muscle development pathways, and skeletal muscle energy metabolism. Our findings suggest that the two types of genetic modification have potential regulatory effects on skeletal muscle development and provide a basis for further mechanistic studies in the rabbit.

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Nutrition during Pregnancy Impacts Offspring's Epigenetic Status—Evidence from Human and Animal Studies

Nutrition and Metabolic Insights ◽

10.4137/nmi.s29527 ◽

2015 ◽

Vol 8s1 ◽

pp. NMI.S29527 ◽

Cited By ~ 14

Author(s):

Aisling A. Geraghty ◽

Karen L. Lindsay ◽

Goiuri Alberdi ◽

Fionnuala M. McAuliffe ◽

Eileen R. Gibney

Keyword(s):

Dna Methylation ◽

Growth And Development ◽

Critical Period ◽

Animal Studies ◽

Maternal Nutrition ◽

Later Life ◽

Future Health ◽

Global Methylation ◽

Methyl Donors ◽

Methylation Patterns

Pregnancy is a vital time of growth and development during which maternal nutrition significantly influences the future health of both mother and baby. During pregnancy, the fetus experiences a critical period of plasticity. Epigenetics, specifically DNA methylation, plays an important role here. As nutrition is influential for DNA methylation, this review aims to determine if maternal nutrition during pregnancy can modify the offspring's epigenome at birth. Research focuses on micronutrients and methyl donors such as folate and B vitamins. Evidence suggests that maternal nutrition does not largely influence global methylation patterns, particularly in nutrient-replete populations; however, an important impact on gene-specific methylation is observed. A link is shown between maternal nutrition and the methylome of the offspring; however, there remains a paucity of research. With the potential to use DNA methylation patterns at birth to predict health of the child in later life, it is vital that further research be carried out.

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Extensive alternative splicing transitions during postnatal skeletal muscle development are required for calcium handling functions

eLife ◽

10.7554/elife.27192 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 23

Author(s):

Amy E Brinegar ◽

Zheng Xia ◽

James Anthony Loehr ◽

Wei Li ◽

George Gerald Rodney ◽

...

Keyword(s):

Skeletal Muscle ◽

Alternative Splicing ◽

Postnatal Development ◽

Muscle Development ◽

Muscle Relaxation ◽

Calcium Handling ◽

Muscle Physiology ◽

Mouse Muscle ◽

Calcium Dependent ◽

Calcineurin A

Postnatal development of skeletal muscle is a highly dynamic period of tissue remodeling. Here, we used RNA-seq to identify transcriptome changes from late embryonic to adult mouse muscle and demonstrate that alternative splicing developmental transitions impact muscle physiology. The first 2 weeks after birth are particularly dynamic for differential gene expression and alternative splicing transitions, and calcium-handling functions are significantly enriched among genes that undergo alternative splicing. We focused on the postnatal splicing transitions of the three calcineurin A genes, calcium-dependent phosphatases that regulate multiple aspects of muscle biology. Redirected splicing of calcineurin A to the fetal isoforms in adult muscle and in differentiated C2C12 slows the timing of muscle relaxation, promotes nuclear localization of calcineurin target Nfatc3, and/or affects expression of Nfatc transcription targets. The results demonstrate a previously unknown specificity of calcineurin isoforms as well as the broader impact of alternative splicing during muscle postnatal development.

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Methyl donor micronutrients, CD40-ligand methylation and disease activity in systemic lupus erythematosus: A cross-sectional association study

Lupus ◽

10.1177/09612033211034559 ◽

2021 ◽

pp. 096120332110345

Author(s):

Stefan Vordenbäumen ◽

Alexander Sokolowski ◽

Anna Rosenbaum ◽

Claudia Gebhard ◽

Johanna Raithel ◽

...

Keyword(s):

Systemic Lupus Erythematosus ◽

Dna Methylation ◽

T Cells ◽

Disease Activity ◽

Lupus Erythematosus ◽

Cd40 Ligand ◽

Systemic Lupus ◽

Methyl Donors ◽

Methyl Donor ◽

The Mean

Objective Hypomethylation of CD40-ligand (CD40L) in T-cells is associated with increased disease activity in systemic lupus erythematosus (SLE). We therefore investigated possible associations of dietary methyl donors and products with CD40L methylation status in SLE. Methods Food frequency questionnaires were employed to calculate methyl donor micronutrients in 61 female SLE patients (age 45.7 ± 12.0 years, disease duration 16.2 ± 8.4 years) and compared to methylation levels of previously identified key DNA methylation sites (CpG17 and CpG22) within CD40L promotor of T-cells using quantitative DNA methylation analysis on the EpiTYPER mass spectrometry platform. Disease activity was assessed by SLE Disease Activity Index (SLEDAI). Linear regression modelling was used. P values were adjusted according to Benjamini & Hochberg. Results Amongst the micronutrients assessed (g per day), methionine and cysteine were associated with methylation of CpG17 (β = 5.0 (95%CI: 0.6-9.4), p = 0.04; and β = 2.4 (0.6-4.1), p = 0.02, respectively). Methionine, choline, and cysteine were additionally associated with the mean methylation of the entire CD40L (β = 9.5 (1.0-18.0), p = 0.04; β = 1.6 (0.4-3.0), p = 0.04; and β = 4.3 (0.9-7.7), p = 0.02, respectively). Associations of the SLEDAI with hypomethylation were confirmed for CpG17 (β=-32.6 (-60.6 to -4.6), p = 0.04) and CpG22 (β=-38.3 (-61.2 to -15.4), p = 0.004), but not the mean methylation of CD40L. Dietary products with the highest impact on methylation included meat, ice cream, white bread, and cooked potatoes. Conclusions Dietary methyl donors may influence DNA methylation levels and thereby disease activity in SLE.

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Natural Antisense Transcript PEBP1P3 Regulates the RNA Expression, DNA Methylation and Histone Modification of CD45 Gene

Genes ◽

10.3390/genes12050759 ◽

2021 ◽

Vol 12 (5) ◽

pp. 759

Author(s):

Zhongjing Su ◽

Guangyu Liu ◽

Bin Zhang ◽

Ze Lin ◽

Dongyang Huang

Keyword(s):

Dna Methylation ◽

Alternative Splicing ◽

Histone Modification ◽

Antisense Rna ◽

Noncoding Rna ◽

Antisense Transcript ◽

Natural Antisense Transcript ◽

Regulation Of Expression ◽

Splicing Isoforms ◽

Intron 2

The leukocyte common antigen CD45 is a transmembrane phosphatase expressed on all nucleated hemopoietic cells, and the expression levels of its splicing isoforms are closely related to the development and function of lymphocytes. PEBP1P3 is a natural antisense transcript from the opposite strand of CD45 intron 2 and is predicted to be a noncoding RNA. The genotype-tissue expression and quantitative PCR data suggested that PEBP1P3 might be involved in the regulation of expression of CD45 splicing isoforms. To explore the regulatory mechanism of PEBP1P3 in CD45 expression, DNA methylation and histone modification were detected by bisulfate sequencing PCR and chromatin immunoprecipitation assays, respectively. The results showed that after the antisense RNA PEBP1P3 was knocked down by RNA interference, the DNA methylation of CD45 intron 2 was decreased and histone H3K9 and H3K36 trimethylation at the alternative splicing exons of CD45 DNA was increased. Knockdown of PEBP1P3 also increased the binding levels of chromatin conformation organizer CTCF at intron 2 and the alternative splicing exons of CD45. The present results indicate that the natural antisense RNA PEBP1P3 regulated the alternative splicing of CD45 RNA, and that might be correlated with the regulation of histone modification and DNA methylation.

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Role of Alternative Splicing in Regulating Host Response to Viral Infection

Cells ◽

10.3390/cells10071720 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1720

Author(s):

Kuo-Chieh Liao ◽

Mariano A. Garcia-Blanco

Keyword(s):

Innate Immunity ◽

Alternative Splicing ◽

Immune Responses ◽

Viral Infection ◽

Rna Splicing ◽

Type I ◽

Host Immune Responses ◽

Transcriptional Regulatory Mechanisms ◽

Host Virus Interactions

The importance of transcriptional regulation of host genes in innate immunity against viral infection has been widely recognized. More recently, post-transcriptional regulatory mechanisms have gained appreciation as an additional and important layer of regulation to fine-tune host immune responses. Here, we review the functional significance of alternative splicing in innate immune responses to viral infection. We describe how several central components of the Type I and III interferon pathways encode spliced isoforms to regulate IFN activation and function. Additionally, the functional roles of splicing factors and modulators in antiviral immunity are discussed. Lastly, we discuss how cell death pathways are regulated by alternative splicing as well as the potential role of this regulation on host immunity and viral infection. Altogether, these studies highlight the importance of RNA splicing in regulating host–virus interactions and suggest a role in downregulating antiviral innate immunity; this may be critical to prevent pathological inflammation.

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Profiling PRMT methylome reveals roles of hnRNPA1 arginine methylation in RNA splicing and cell growth

Nature Communications ◽

10.1038/s41467-021-21963-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Wen-juan Li ◽

Yao-hui He ◽

Jing-jing Yang ◽

Guo-sheng Hu ◽

Yi-an Lin ◽

...

Keyword(s):

Alternative Splicing ◽

Cell Growth ◽

Rna Splicing ◽

Synergistic Effects ◽

Arginine Methylation ◽

Type I ◽

Prostate Cancer Cells ◽

Cancer Cell Growth ◽

Cancer Mutations ◽

Substrate Spectrum

AbstractNumerous substrates have been identified for Type I and II arginine methyltransferases (PRMTs). However, the full substrate spectrum of the only type III PRMT, PRMT7, and its connection to type I and II PRMT substrates remains unknown. Here, we use mass spectrometry to reveal features of PRMT7-regulated methylation. We find that PRMT7 predominantly methylates a glycine and arginine motif; multiple PRMT7-regulated arginine methylation sites are close to phosphorylations sites; methylation sites and proximal sequences are vulnerable to cancer mutations; and methylation is enriched in proteins associated with spliceosome and RNA-related pathways. We show that PRMT4/5/7-mediated arginine methylation regulates hnRNPA1 binding to RNA and several alternative splicing events. In breast, colorectal and prostate cancer cells, PRMT4/5/7 are upregulated and associated with high levels of hnRNPA1 arginine methylation and aberrant alternative splicing. Pharmacological inhibition of PRMT4/5/7 suppresses cancer cell growth and their co-inhibition shows synergistic effects, suggesting them as targets for cancer therapy.

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