m6A Methylation Analysis of Differentially Expressed Genes in Skin Tissues of Coarse and Fine Type Liaoning Cashmere Goats

Comprehensive analysis of the expression profiles of mRNA, lncRNA, circRNA, and miRNA in primary hair follicles of coarse sheep fetal skin

BACKGROUND

The Qinghai Tibetan sheep, a local breed renowned for its long hair, has experienced significant deterioration in wool characteristics due to the absence of systematic breeding practices. Therefore, it is imperative to investigate the molecular mechanisms underlying follicle development in order to genetically enhance wool-related traits and safeguard the sustainable utilization of valuable germplasm resources. However, our understanding of the regulatory roles played by coding and non-coding RNAs in hair follicle development remains largely elusive.

RESULTS

A total of 20,874 mRNAs, 25,831 circRNAs, 4087 lncRNAs, and 794 miRNAs were annotated. Among them, we identified 58 DE lncRNAs, 325 DE circRNAs, 924 DE mRNAs, and 228 DE miRNAs during the development of medullary primary hair follicle development. GO and KEGG functional enrichment analyses revealed that the JAK-STAT, TGF-β, Hedgehog, PPAR, cGMP-PKG signaling pathway play crucial roles in regulating fibroblast and epithelial development during skin and hair follicle induction. Furthermore, the interactive network analysis additionally identified several crucial mRNA, circRNA, and lncRNA molecules associated with the process of primary hair follicle development. Ultimately, by investigating DEmir's role in the ceRNA regulatory network mechanism, we identified 113 circRNA-miRNA pairs and 14 miRNA-mRNA pairs, including IGF2BP1-miR-23-x-novel-circ-01998-MSTRG.7111.3, DPT-miR-370-y-novel-circ-005802-MSTRG.14857.1 and TSPEAR-oar-miR-370-3p-novel-circ-005802- MSTRG.10527.1.

CONCLUSIONS

Our study offers novel insights into the distinct expression patterns of various transcription types during hair follicle morphogenesis, establishing a solid foundation for unraveling the molecular mechanisms that drive hair development and providing a scientific basis for selectively breeding desirable wool-related traits in this specific breed.

Biological methylation: redefining the link between genotype and phenotype

The central dogma of molecular biology is responsible for the crucial flow of genetic information from DNA to protein through the transcription and translation process. Although the sequence of DNA is constant in all organs, the difference in protein and variation in the phenotype is mainly due to the quality and quantity of tissue-specific gene expression and methylation pattern. The term methylation has been defined and redefined by various scientists in the last fifty years. There is always huge excitement around this field because the inheritance of something is beyond its DNA sequence. Advanced gene methylation studies have redefined molecular genetics and these tools are considered de novo in alleviating challenges of animal disease and production. Recent emerging evidence has shown that the impact of DNA, RNA, and protein methylation is crucial for embryonic development, cell proliferation, cell differentiation, and phenotype production. Currently, many researchers are focusing their work on methylation to understand its significant role in expression, disease-resistant traits, productivity, and longevity. The main aim of the present review is to provide an overview of DNA, RNA, and protein methylation, current research output from different sources, methodologies, factors responsible for methylation of genes, and future prospects in animal genetics.

Multi-omics analysis of functional substances and expression verification in cashmere fineness

BACKGROUND

Numerous factors influence the growth and development of cashmere. Existing research on cashmere has predominantly emphasized a single omics level. Integrating multi-omics analyses can offer a more comprehensive understanding by encompassing the entire spectrum. This study more accurately and comprehensively identified the key factors influencing cashmere fineness using multi-omics analysis.

METHODS

This study used skin tissues of coarse cashmere type (CT_LCG) and fine cashmere type Liaoning cashmere goats (FT_LCG) for the analysis. This study employed an integrated approach involving transcriptomics, translatomics, proteomics, and metabolomics to identify substances associated with cashmere fineness. The findings were validated using parallel reaction monitoring (PRM) and multiple reaction monitoring (MRM) techniques.

RESULTS

The GO functional enrichment analysis identified three common terms: multicellular organismal process, immune system process, and extracellular region. Furthermore, the KEGG enrichment analysis uncovered the involvement of the arachidonic acid metabolic pathway. Protein expression trends were verified using PRM technology. The expression trends of KRT79, as confirmed by PRM, were consistent with those observed in TMT proteomics and exhibited a positive regulatory effect on cashmere fineness. Metabolite expression trends were confirmed using MRM technology. The expression trends of 9 out of 15 validated metabolites were in agreement with those identified in the non-targeted metabolomics analysis.

CONCLUSIONS

This study employed multi-omics analysis to identify key regulators of cashmere fineness, including PLA2G12A, KRT79, and prostaglandin B2. The findings of this study offer valuable data and establish a theoretical foundation for conducting comprehensive investigations into the molecular regulatory mechanisms and functional aspects of cashmere fineness.

Identification of N6-Methyladenosine-Related Factors and the Prediction of the Regulatory Mechanism of Hair Follicle Development in Rex and Hycole Rabbits

Hair follicle development directly affects the development of the rabbit fur industry. The growth and development of a hair follicle is modified and regulated by many genes and mechanisms. M6A is an important RNA modification. However, there are few studies on the effects of the regulation of m6A on hair follicle growth and development. In this study, hematoxylin-eosin (HE) staining was used to explore the difference in hair follicle development between Rex rabbits and Hycole rabbits, and we performed m6A sequencing to identify the key genes with m6A modification in hair follicle growth. The results showed that the hair length, coarse hair percentage, primary hair follicle ratio, and skin thickness of Hycole rabbits were significantly higher than those of Rex rabbits. However, the proportion of secondary hair follicles in Hycole rabbits was significantly lower than that in Rex rabbits. In addition, we found five differential methylases, 20 differential genes, and 24 differential signaling pathways related to hair growth and development. The results of the Sankey diagram showed that 12 genes were related to 13 signal pathways. Finally, we found that five methylases regulated the development of hair follicles through differential genes/signal pathways. These findings laid a molecular foundation for the function of m6A modification in hair development.

Genome-wide DNA methylation and transcriptome analyses reveal the key gene for wool type variation in sheep

BACKGROUND

Wool fibers are valuable materials for textile industry. Typical wool fibers are divided into medullated and non-medullated types, with the former generated from primary wool follicles and the latter by either primary or secondary wool follicles. The medullated wool is a common wool type in the ancestors of fine wool sheep before breeding. The fine wool sheep have a non-medullated coat. However, the critical period determining the type of wool follicles is the embryonic stage, which limits the phenotypic observation and variant contrast, making both selection and studies of wool type variation fairly difficult.

RESULTS

During the breeding of a modern fine (MF) wool sheep population with multiple-ovulation and embryo transfer technique, we serendipitously discovered lambs with ancestral-like coarse (ALC) wool. Whole-genome resequencing confirmed ALC wool lambs as a variant type from the MF wool population. We mapped the significantly associated methylation locus on chromosome 4 by using whole genome bisulfite sequencing signals, and in turn identified the SOSTDC1 gene as exons hypermethylated in ALC wool lambs compare to their half/full sibling MF wool lambs. Transcriptome sequencing found that SOSTDC1 was expressed dozens of times more in ALC wool lamb skin than that of MF and was at the top of all differentially expressed genes. An analogy with the transcriptome of coarse/fine wool breeds revealed that differentially expressed genes and enriched pathways at postnatal lamb stage in ALC/MF were highly similar to those at the embryonic stage in the former. Further experiments validated that the SOSTDC1 gene was specifically highly expressed in the nucleus of the dermal papilla of primary wool follicles.

CONCLUSION

In this study, we conducted genome-wide differential methylation site association analysis on differential wool type trait, and located the only CpG locus that strongly associated with primary wool follicle development. Combined with transcriptome analysis, SOSTDC1 was identified as the only gene at this locus that was specifically overexpressed in the primary wool follicle stem cells of ALC wool lamb skin. The discovery of this key gene and its epigenetic regulation contributes to understanding the domestication and breeding of fine wool sheep.

Transcriptome-wide analysis of RNA m6A methylation regulation of muscle development in Queshan Black pigs

BACKGROUND

N⁶-methyladenosine (m⁶A) refers to the methylation modification of N⁶ position of RNA adenine, a dynamic reversible RNA epigenetic modification that plays an important regulatory role in a variety of life processes. In this study, we used MeRIP-Seq and RNA-Seq of the longissimus dorsi (LD) muscle of adult (QA) and newborn (QN) Queshan Black pigs to screen key genes with m⁶A modification involved in muscle growth by bioinformatics analysis.

RESULTS

A total of 23,445 and 25,465 m⁶A peaks were found in the whole genomes of QA and QN, respectively. Among them, 613 methylation peaks were significantly different (DMPs) and 579 genes were defined as differentially methylated genes (DMGs). Compared with the QN group, there were 1,874 significantly differentially expressed genes (DEGs) in QA group, including 620 up-regulated and 1,254 down-regulated genes. In order to investigate the relationship between m⁶A and mRNA expression in the muscle of Queshan Black pigs at different periods, a combined analysis of MeRIP-Seq and RNA-Seq showed that 88 genes were significantly different at both levels. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes results showed that DEGs and DMGs were mainly involved in skeletal muscle tissue development, FoxO signaling pathway, MAPK signaling pathway, insulin signaling pathway, PI3K-Akt signaling pathway, and Wnt signaling pathway. Four DEGs (IGF1R, CCND2, MYOD1 and FOS) and four DMGs (CCND2, PHKB, BIN1 and FUT2), which are closely related to skeletal muscle development, were selected as candidate genes for verification, and the results were consistent with the sequencing results, which indicated the reliability of the sequencing results.

CONCLUSIONS

These results lay the foundation for understanding the specific regulatory mechanisms of growth in Queshan Black pigs, and provide theoretical references for further research on the role of m⁶A in muscle development and breed optimization selection.

The Characterization and Differential Analysis of m6A Methylation in Hycole Rabbit Muscle and Adipose Tissue and Prediction of Regulatory Mechanism about Intramuscular Fat

N6-methyladenosine (m⁶A) widely participates in various life processes of animals, including disease, memory, growth and development, etc. However, there is no report on m⁶A regulating intramuscular fat deposition in rabbits. In this study, m⁶A modification of Hycole rabbit muscle and adipose tissues were detected by MeRIP-Seq. In this case, 3 methylases and 12 genes modified by m⁶A were found to be significantly different between muscle and adipose tissues. At the same time, we found 3 methylases can regulate the expression of 12 genes in different ways and the function of 12 genes is related to fat deposition base on existing studies. 12 genes were modified by m⁶A methylase in rabbit muscle and adipose tissues. These results suggest that 3 methylases may regulate the expression of 12 genes through different pathways. In addition, the analysis of results showed that 6 of the 12 genes regulated eight signaling pathways, which regulated intramuscular fat deposition. RT-qPCR was used to validate the sequencing results and found the expression results of RT-qPCR and sequencing results are consistent. In summary, METTL4, ZC3H13 and IGF2BP2 regulated intramuscular fat by m⁶A modified gene/signaling pathways. Our work provided a new molecular basis and a new way to produce rabbit meat with good taste.

Research Progress of m6A RNA Methylation in Skin Diseases

N⁶-Methyladenosine (m⁶A) is the most common mRNA modification in eukaryotes and is a dynamically reversible posttranscriptional modification. The enzymes involved in m⁶A modification mainly include methyltransferases (writers), demethylases (erasers), and methylated readers (Readers). m⁶A modification is mainly catalyzed by m⁶A methyltransferase and removed by m⁶A demethylase. The modified RNA can be specifically recognized and bound by m⁶A recognition protein. This protein complex then mediates RNA splicing, maturation, nucleation, degradation, and translation. m⁶A also alters gene expression and regulates cellular processes such as self-renewal, differentiation, invasion, and apoptosis. An increasing body of evidence indicates that the m⁶A methylation modification process is closely related to the occurrence of various skin diseases. In this review, we discuss the role of m⁶A methylation in skin development and skin diseases including psoriasis, melanoma, and cutaneous squamous cell carcinoma.

Transcriptome-Wide Study of mRNAs and lncRNAs Modified by m6A RNA Methylation in the Longissimus Dorsi Muscle Development of Cattle-Yak

Cattle-yak is a hybrid F₁ generation of cattle and yak, which has a history of more than 3000 years and has shown better production performance and higher economic benefits than those of yaks. However, up to now, there has been no study on the transcriptome-wide m⁶A methylation profile of bovine skeletal muscle and its potential biological function during muscle development. Here, we observed significant changes in the expression levels of muscle-related marker genes and methylation-related enzymes during the development of cattle-yak, and the overall m⁶A content in the Longissimus dorsi muscle of 18-month-old cattle-yak decreased significantly. A total of 36,602 peaks, 11,223 genes and 8388 lncRNAs were identified in the two groups, including 2989 differential peaks (427 up-regulated peaks and 2562 down-regulated peaks), 1457 differentially expressed genes (833 up-regulated genes and 624 down-regulated genes) and 857 differentially expressed lncRNAs (293 up-regulated lncRNAs and 564 down-regulated lncRNAs). GO and KEGG analysis revealed that they were significantly enriched in some muscle-related pathways (Wnt signaling pathway and MAPK signaling pathway) and high-altitude adaptation-related pathway (HIF-1 signaling pathway). Moreover, m⁶A abundance was positively correlated with gene expression levels, while it was negatively correlated with lncRNA expression levels. This indicates that m⁶A modification played an important role in the Longissimus dorsi muscle development of cattle-yak; however, the regulation mechanism of m⁶A-modified mRNA and lncRNA may be different. This study was the first report of transcriptome-wide m⁶A-modified mRNAs and lncRNAs atlas in the Longissimus dorsi muscle development of cattle-yak, one which will provide new perspectives for genetic improvement in bovines.

Identification and functional analysis of m6A in the mammary gland tissues of dairy goats at the early and peak lactation stages

N6-methyladenosine (m⁶A) is the most common reversible epigenetic RNA modification in the mRNA of all higher eukaryotic organisms and plays an important role in the regulation of gene expression and cell function. In this study, m⁶A-modified methylated RNA immunoprecipitation sequencing (MeRIP-seq) and transcriptome sequencing (RNA-seq) were used to identify the key genes with m⁶A modification during mammary gland development and lactation in dairy goats. The results showed that m⁶A methylation occurred at 3,927 loci, which were significantly enriched in the 3′ untranslated region (3′UTR) and the termination codon region. In the early stage and peak stage of lactation, m⁶A methylation occurred extensively in mammary tissues, and a total of 725 differentially expressed m⁶A-modified genes were obtained, all negatively correlated with mRNA expression. In addition, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that different methylated genes were mainly involved in the growth and apoptosis of mammary epithelial cells through signaling pathways, such as the mitogen-activated protein kinase (MAPK) and phospholipase D pathways, and then affected the development and lactation of mammary gland. All in all, we identified and analyzed the methylation events related to the development and lactation regulation of mammary gland at the early and peak lactation stages, and provided a theoretical basis to reveal the physiological regulatory system of mammary gland development and lactation in dairy goats.

m6A modification of mRNA in skin diseases

N6-methyladenosine (m6A) is the predominant post-transcriptional modification for eukaryotic mRNA. It's regulated by methyltransferases, demethylases, and m6A binding proteins, and plays an important role in regulating splicing, translation, and degradation of mRNA. Skin diseases, especially immune skin diseases and skin tumors, have a complicated pathogenesis and are refractory to treatment, seriously affecting the patient quality of life. Recent studies have revealed that m6A and its regulatory proteins can affect the development of numerous skin diseases. The m6A modification was found to be involved in skin accessory development, including hair follicle and sweat gland formation. The level of m6A modification was significantly altered in a variety of skin diseases including melanoma, cutaneous squamous cell carcinoma, Merkel cell carcinoma, and psoriasis, and affected a variety of biological processes including cell proliferation and differentiation migration. The m6A and its regulatory proteins may become potential molecular markers or therapeutic targets for skin diseases, and have promising clinical applications in early diagnosis, efficacy determination, prognosis prediction, and gene therapy of skin diseases.

N6-Methyladenosine Methylome Profiling of Muscle and Adipose Tissues Reveals Methylase-mRNA Metabolic Regulatory Networks in Fat Deposition of Rex Rabbits

N6-methyladenosine (m6A) is the most prevalent internal form of modification in messenger RNA in higher eukaryotes and plays an important role in cancer, immunity, reproduction, development, and fat deposition. Intramuscular fat is the main factor used to measure the meat quality of an animal. The deposition of intramuscular fat and perirenal fat increases with age. However, there is no data on m6A modification of Rex rabbits and its potential biological roles in adipose deposition and muscle growth. Here, we performed two high-throughput sequencing methods, m6A-modified RNA immunoprecipitation sequence (MeRIP-seq) and RNA sequence (RNA-seq), to identify key genes with m6A modification on fat deposition in the muscle and adipose tissues of Rex rabbits. Then, qRT-PCR was used to identify the differently methylated genes related to fat deposition. Our findings showed that there were 12,876 and 10,973 m6A peaks in the rabbit muscle and adipose tissue transcriptomes, respectively. Stop codons, 3′-untranslated regions, and coding regions were found to be mainly enriched for m6A peaks. In addition, we found 5 differential methylases and 12 key genes of methylation modification related to fat deposition between muscle and adipose tissues samples. The expression levels of six random key genes were significantly higher in the fat than that in the muscle of Rex rabbits at different stages (p < 0.01). Finally, five differential methylases were found to regulate adipogenesis by affecting the expression of screened genes in different ways. These findings provided a theoretical basis for our future research on the function of m6A modification during the growth of fat deposits.

Transcriptome-Wide m6A Methylome and m6A-Modified Gene Analysis in Asthma

N6-methyladenosine (m6A) modification is one of the most prevalent RNA modification forms and is an important posttranscriptional mechanism for regulating genes. In previous research, we found that m6A regulator–mediated RNA methylation modification was involved in asthma; however, the specific modified genes are not clear. In this study, we systematically evaluated the transcriptome-wide m6A methylome and m6A-modified genes in asthma. Here, we performed two high-throughput sequencing methods, methylated RNA immunoprecipitation sequencing (MeRIP-seq), and RNA sequencing (RNA-seq) to identify key genes with m6A modification in asthma. Through difference analysis, we found that 416 methylation peaks were significantly upregulated and 152 methylation peaks were significantly downregulated, and it was mainly distributed in 3′ UTR. Furthermore, compared with the control group, there were 2,505 significantly upregulated genes and 4,715 significantly downregulated genes in the asthma group. Next, through a combined analysis of transcriptome and differential peaks, 14 differentially expressed genes related to RNA methylation modification were screened. Finally, through 87 health controls and 411 asthma cases from the U-BIOPRED (Unbiased Biomarkers for the Prediction of Respiratory Disease Outcomes) program, we verified three m6A-modified key genes (BCL11A, MATK, and CD300A) and found that they were mainly distributed in exons and enriched in 3' UTR. Our findings suggested that intervening in m6A-modified genes may provide a new idea for the treatment of asthma.

The m6A methylation regulates gonadal sex differentiation in chicken embryo

Background

As a ubiquitous reversible epigenetic RNA modification, N6-methyladenosine (m6A) plays crucial regulatory roles in multiple biological pathways. However, its functional mechanisms in sex determination and differentiation during gonadal development of chicken embryos are not clear. Therefore, we established a transcriptome-wide m6A map in the female and male chicken left gonads of embryonic day 7 (E7) by methylated RNA immunoprecipitation sequencing (MeRIP-seq) to offer insight into the landscape of m6A methylation and investigate the post-transcriptional modification underlying gonadal differentiation.

Results

The chicken embryonic gonadal transcriptome was extensively methylated. We found 15,191 and 16,111 m6A peaks in the female and male left gonads, respectively, which were mainly enriched in the coding sequence (CDS) and stop codon. Among these m6A peaks, we identified that 1013 and 751 were hypermethylated in females and males, respectively. These differential peaks covered 281 and 327 genes, such as BMP2, SMAD2, SOX9 and CYP19A1, which were primarily associated with development, morphogenesis and sex differentiation by functional enrichment. Further analysis revealed that the m6A methylation level was positively correlated with gene expression abundance. Furthermore, we found that YTHDC2 could regulate the expression of sex-related genes, especially HEMGN and SOX9, in male mesonephros/gonad mingle cells, which was verified by in vitro experiments, suggesting a regulatory role of m6A methylation in chicken gonad differentiation.

Conclusions

This work provided a comprehensive m6A methylation profile of chicken embryonic gonads and revealed YTHDC2 as a key regulator responsible for sex differentiation. Our results contribute to a better understanding of epigenetic factors involved in chicken sex determination and differentiation and to promoting the future development of sex manipulation in poultry industry.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-022-00710-6.

Global Landscape of m6A Methylation of Differently Expressed Genes in Muscle Tissue of Liaoyu White Cattle and Simmental Cattle

Liaoyu white cattle (LYWC) is a local breed in Liaoning Province, China. It has the advantages of grow quickly, high slaughter ratew, high meat quality and strong anti-stress ability. N⁶ methyladenosine (m6A) is a methylation modification of N⁶ position of RNA adenine, which is an important modification mechanism affecting physiological phenomena. In this study, we used the longissimus dorsi muscle of LYWC and SIMC for m6A-seq and RNA-seq high-throughput sequencing, and identified the key genes involved in muscle growth and m6A modification development by bioinformatics analysis. There were 31532 m6A peaks in the whole genome of LYWC and 47217 m6A peaks in the whole genome of SIMC. Compared with Simmental cattle group, LYWC group had 17,351 differentially expressed genes: 10,697 genes were up-regulated, 6,654 genes were down regulated, 620 differentially expressed genes were significant, while 16,731 differentially expressed genes were not significant. Among the 620 significantly differentially expressed genes, 295 genes were up-regulated and 325 genes were down regulated. In order to explore the relationship between m6A and mRNA expression in the muscles of LYWC and SIMC, the combined analysis of MeRIP-seq and RNA-seq revealed that 316 genes were m6A modified with mRNA expression. To identify differentially methylated genes related to muscle growth, four related genes were selected for quantitative verification in LYWC and SIMC. GO enrichment and KEGG analysis showed that the differentially expressed genes modified by m6A are mainly involved in skeletal muscle contraction, steroid biosynthesis process, redox process, PPAR pathway and fatty acid metabolism, and galactose metabolism. These results provide a theoretical basis for further research on the role of m6A in muscle growth and development.

Comprehensive analysis of differences in N6-methyladenosine RNA methylomes in the rat adenohypophysis after GnRH treatment

N6-methyladenosine is considered to be the most common and abundant internal chemical modification among the more than 150 identified chemical RNA modifications. It is involved in most biological processes and actively participates in the regulation of animal reproduction. However, the potential function of m⁶ A in the pituitaries of mammals is not yet clear. It is also unknown whether m⁶ A is involved in the secretion and regulation of FSH by GnRH, which in turn affects mammalian reproduction. In this study, rats were treated with gonadorelin to simulate physiological GnRH-mediated regulation of FSH synthesis and secretion, and m⁶ A-seq was used to analyze the differential m⁶ A modification of the rat pituitary after gonadorelin treatment. A whole-transcriptome map of m⁶ A in the rat pituitary gland before and after gonadorelin treatment was successfully created. A total of 6413 differential peaks were identified, of which 3764 m⁶ A peaks were upregulated and 2649 m⁶ A peaks were downregulated. Among the 709 differentially expressed genes, 250 genes were discovered with differential methylation modifications. Intriguingly, the altered m⁶ A peaks within mRNAs were enriched in steroid biosynthetic processes and responses to cAMP. The results of the study will lay a foundation for further exploration of the potential role of m⁶ A modification in the regulation of reproductive hormone secretion and provide a theoretical basis for the application of GnRH analogs in mammalian artificial reproduction.

Function of m6A and its regulation of domesticated animals' complex traits

N6-methyladenosine (m6A) is the most functionally important epigenetic modification in RNA. The m6A modification widely exists in mRNA and noncoding RNA, influences the mRNA processing, and regulates the secondary structure and maturation of noncoding RNA. Studies showed the important regulatory roles of m6A modification in animal's complex traits, such as development, immunity, and reproduction-related traits. As an important intermediate stage from animal genome to phenotype, the function of m6A in the complex trait formation of domestic animals cannot be neglected. This review discusses recent research advances on m6A modification in well-studied organisms, such as human and model organisms, and introduces m6A detection technologies, small-molecule inhibitors of m6A-related enzymes, interaction between m6A and other biological progresses, and the regulation mechanisms of m6A in domesticated animals' complex traits.

Analysis of N6-Methyladenosine Methylome in Adenocarcinoma of Esophagogastric Junction

Background: From previous studies, we found that there are more than 100 types of RNA modifications in RNA molecules. m⁶A methylation is the most common. The incidence rate of adenocarcinoma of the esophagogastric junction (AEG) at home and abroad has increased faster than that of stomach cancer at other sites in recent years. Here, we systematically analyze the modification pattern of m⁶A mRNA in adenocarcinoma at the esophagogastric junction.

Methods: m⁶A sequencing, RNA sequencing, and bioinformatics analysis were used to describe the m⁶A modification pattern in adenocarcinoma and normal tissues at the esophagogastric junction.

Results: In AEG samples, a total of 4,775 new m⁶A peaks appeared, and 3,054 peaks disappeared. The unique m6A-related genes in AEG are related to cancer-related pathways. There are hypermethylated or hypomethylated m⁶A peaks in AEG in differentially expressed mRNA transcripts.

Conclusion: This study preliminarily constructed the first m⁶A full transcriptome map of human AEG. This has a guiding role in revealing the mechanism of m⁶A-mediated gene expression regulation.

The role of RNA m6A methylation in lipid metabolism

The m6A methylation is the most numerous modification of mRNA in mammals, coordinated by RNA m6A methyltransferases, RNA m6A demethylases, and RNA m6A binding proteins. They change the RNA m6A methylation level in their specific manner. RNA m6A modification has a significant impact on lipid metabolic regulation. The "writer" METTL3/METTL14 and the "eraser" FTO can promote the accumulation of lipids in various cells by affecting the decomposition and synthesis of lipids. The "reader" YTHDF recognizes m6A methylation sites of RNA and regulates the target genes' translation. Due to this function that regulates lipid metabolism, RNA m6A methylation plays a pivotal role in metabolic diseases and makes it a great potential target for therapy.

Transcriptome-Wide m6A Analysis Provides Novel Insights Into Testicular Development and Spermatogenesis in Xia-Nan Cattle

Testis is the primary organ of the male reproductive tract in mammals that plays a substantial role in spermatogenesis. Improvement of our knowledge regarding the molecular mechanisms in testicular development and spermatogenesis will be reflected in producing spermatozoa of superior fertility. Evidence showed that N6-Methyladenosine (m6A) plays a dynamic role in post-transcription gene expression regulation and is strongly associated with production traits. However, the role of m6A in bovine testis has not been investigated yet. In this study, we conducted MeRIP-Seq analysis to explore the expression profiles of the m6A and its potential mechanism underlying spermatogenesis in nine bovine testes at three developmental stages (prepuberty, puberty and postpuberty). The experimental animals with triplicate in each stage were chosen based on their semen volume and sperm motility except for the prepuberty bulls and used for testes collection. By applying MeRIP-Seq analysis, a total of 8,774 m6A peaks and 6,206 m6A genes among the studied groups were identified. All the detected peaks were found to be mainly enriched in the coding region and 3'- untranslated regions. The cross-analysis of m6A and mRNA expression exhibited 502 genes with concomitant changes in the mRNA expression and m6A modification. Notably, 30 candidate genes were located in the largest network of protein-protein interactions. Interestingly, four key node genes (PLK4, PTEN, EGR1, and PSME4) were associated with the regulation of mammal testis development and spermatogenesis. This study is the first to present a map of RNA m6A modification in bovine testes at distinct ages, and provides new insights into m6A topology and related molecular mechanisms underlying bovine spermatogenesis, and establishes a basis for further studies on spermatogenesis in mammals.

Integrated Study of Transcriptome-wide m6A Methylome Reveals Novel Insights Into the Character and Function of m6A Methylation During Yak Adipocyte Differentiation

Yak (Bos grunniens) is considered an iconic symbol of Tibet and high altitude, but they suffer from malnutrition during the cold season that challenges the metabolism of energy. Adipocytes perform a crucial role in maintaining the energy balance, and adipocyte differentiation is a complex process involving multiple changes in the expression of genes. N ⁶-methyladenosine (m⁶A) plays a dynamic role in post-transcription gene expression regulation as the most widespread mRNA modification of the higher eukaryotes. However, currently there is no research existing on the m⁶A transcriptome-wide map of bovine animals and their potential biological functions in adipocyte differentiation. Therefore, we performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) to determine the distinctions in m⁶A methylation and gene expression during yak adipocyte differentiation. In yak adipocyte and preadipocyte the content of m⁶A and m⁶A-associated enzymes was substantially different. In the two groups, a total of 14,710 m⁶A peaks and 13,388 m⁶A peaks were identified. For the most part, m⁶A peaks were enriched in stop codons, 3'-untranslated regions, and coding regions with consensus motifs of GGACU. The functional enrichment exploration displayed that differentially methylated genes participated in some of the pathways associated with adipogenic metabolism, and several candidate genes (KLF9, FOXO1, ZNF395, and UHRF1) were involved in these pathways. In addition to that, there was a positive association between m⁶A abundance and levels of gene expression, which displayed that m⁶A may play a vital role in modulating gene expression during yak adipocyte differentiation. Further, in the adipocyte group, several methylation gene protein expression levels were significantly higher than in preadipocytes. In short, it can be concluded that the current study provides a comprehensive explanation of the m⁶A features in the yak transcriptome, offering in-depth insights into m⁶A topology and associated molecular mechanisms underlying bovine adipocyte differentiation, which might be helpful for further understanding its mechanisms.

Screening of cashmere fineness-related genes and their ceRNA network construction in cashmere goats

Competitive endogenous RNA (ceRNA) is a transcript that can be mutually regulated at the post-transcriptional level by competing shared miRNAs. The ceRNA network connects the function of protein-encoded mRNA with the function of non-coding RNA, such as microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA). However, compared with the ceRNA, the identification and combined analysis of lncRNAs, mRNAs, miRNAs, and circRNAs in the cashmere fineness have not been completed. Using RNA-seq technology, we first identified the miRNAs presented in Liaoning Cashmere Goat (LCG) skin, and then analyzed the mRNAs, lncRNAs, circRNAs expressed in LCG and Inner Mongolia cashmere goat (MCG) skin. As a result, 464 known and 45 new miRNAs were identified in LCG skin. In LCG and MCG skin, 1222 differentially expressed mRNAs were identified, 170 differentially expressed lncRNAs and 32 differentially expressed circRNAs were obtained. Then, qRT-PCR was used to confirm further the representative lncRNAs, mRNAs, circRNAs and miRNAs. In addition, miRanda predicted the relationships of ceRNA regulatory network among lncRNAs, circRNAs, miRNAs and mRNAs, the potential regulatory effects were investigated by Go and KEGG analysis. Through the screening and analysis of the results, the ceRNA network regulating cashmere fineness was constructed. LncRNA MSTRG14109.1 and circRNA452 were competed with miRNA-2330 to regulated the expression of TCHH, KRT35 and JUNB, which may provide a potential basis for further research on the process of regulating the cashmere fineness.

Association analysis for SNPs of KRT26 and TCHH genes with cashmere production performance, body measurement traits and milk production traits in Liaoning cashmere goats

Cashmere fineness is getting thicker, which is one of the key problems in cashmere breeding, however, there have been no systematic studies on the molecular regulation of cashmere fineness. The aim of this study was to investigate the relationship between KRT26 and TCHH gene polymorphism and production performance in Liaoning cashmere goats (LCG). The potential single nucleotide polymorphisms (SNPs) of LCG were detected by sequence alignment and PCR-Seq polymorphism of KRT26 and TCHH genes and analyzed the effect of SNPs on production performance by SPSS software. Two SNPs sites (A559T and A6839G) of two genes were detected. The AA genotype of KRT26 A559T locus was the dominant genotype. AG and GG at TCHH A6839G locus were the dominant genotypes. AAAA was the dominant haplotype combination. The results showed that KRT26 and TCHH genes were associated with cashmere fineness of LCG, and A559T (AA) and A6839G (GG) genotypes were the preferred marker genotypes for cashmere fineness, which provided more theoretical basis for further research on cashmere fineness.

Multiomics landscape of the autosomal dominant osteopetrosis type II disease-specific induced pluripotent stem cells

BACKGROUND

Autosomal dominant osteopetrosis type II (ADO2) is a genetically and phenotypically metabolic bone disease, caused by osteoclast abnormalities. The pathways dysregulated in ADO2 could lead to the defects in osteoclast formation and function. However, the mechanism remains elusive.

MATERIALS AND METHODS

To systematically explore the molecular characterization of ADO2, we performed a multi-omics profiling from the autosomal dominant osteopetrosis type II iPSCs (ADO2-iPSCs) and healthy normal control iPSCs (NC-iPSCs) using whole genome re-sequencing, DNA methylation and N6-methyladenosine (m6A) analysis in this study.

RESULTS

Totally, we detected 7,095,817 single nucleotide polymorphisms (SNPs) and 1,179,573 insertion and deletions (InDels), 1,001,943 differentially methylated regions (DMRs) and 2984 differential m6A peaks, and the comprehensive multi-omics profile was generated from the two cells. Interestingly, the ISG15 m6A level in ADO2-iPSCs is higher than NC-iPSCs by IGV software, and the differentially expressed m6A-modified genes (DEMGs) were highly enriched in the osteoclast differentiation and p53 signaling pathway, which associated with the development of osteopetrosis. In addition, combining our previously published transcriptome and proteome datasets, we found that the change in DNA methylation levels correlates inversely with some gene expression levels.

CONCLUSION

Our results indicate that the global multi-omics landscape not only provides a high-quality data resource but also reveals a dynamic pattern of gene expression, and found that the pathogenesis of ADO2 may begin early in life.

Comprehensive Analysis of Transcriptome-wide m6A Methylome Upon Clostridium perfringens Beta2 Toxin Exposure in Porcine Intestinal Epithelial Cells by m6A Sequencing

Piglet diarrhea is a swine disease responsible for serious economic impacts in the pig industry. Clostridium perfringens beta2 toxin (CPB2), which is a major toxin of C. perfringens type C, may cause intestinal diseases in many domestic animals. N6-methyladenosine (m6A) RNA methylation plays critical roles in many immune and inflammatory diseases in livestock and other animals. However, the role of m6A methylation in porcine intestinal epithelial (IPEC-J2) cells exposed to CPB2 has not been studied. To address this issue, we treated IPEC-J2 cells with CPB2 toxin and then quantified methylation-related enzyme expression by RT-qPCR and assessed the m6A methylation status of the samples by colorimetric N6-methyladenosine quantification. The results showed that the methylation enzymes changed to varying degrees while the m6A methylation level increased (p < 0.01). On this basis, we performed N6-methyladenosine sequencing (m6A-seq) and RNA sequencing (RNA-seq) to examine the detailed m6A modifications and gene expression of the IPEC-J2 cells following CPB2 toxin exposure. Our results indicated that 1,448 m6A modification sites, including 437 up-regulated and 1,011 down-regulated, differed significantly between CPB2 toxin exposed cells and non-exposed cells (p < 0.05). KEGG pathway analysis results showed that m6A peaks up-regulated genes (n = 394) were mainly enriched in cancer, Cushing syndrome and Wnt signaling pathways, while m6A peaks down-regulated genes (n = 920) were mainly associated with apoptosis, small cell lung cancer, and the herpes simplex virus 1 infection signaling pathway. Furthermore, gene expression (RNA-seq data) analysis identified 1,636 differentially expressed genes (DEGs), of which 1,094 were up-regulated and 542 were down-regulated in the toxin exposed group compared with the control group. In addition, the down-regulated genes were involved in the Hippo and Wnt signaling pathways. Interestingly, the combined results of m6A-seq and RNA-seq identified genes with up-regulated m6A peaks but with down-regulated expression, here referred to as "hyper-down" genes (n = 18), which were mainly enriched in the Wnt signaling pathway. Therefore, we speculate that the genes in the Wnt signaling pathway may be modified by m6A methylation in CPB2-induced IPEC-J2 cells. These findings provide new insights enabling further exploration of the mechanisms underlying piglet diarrhea caused by CPB2 toxin.

Systematic detection of m6A-modified transcripts at single-molecule and single-cell resolution

Epigenetic modifications control the stability and translation of mRNA molecules. Here, we present a microscopy-based platform for quantifying modified RNA molecules and for relating the modification patterns to single-cell phenotypes. We directly capture mRNAs from cell lysates on oligo-dT-coated coverslips, then visually detect and sequence individual m6A-immunolabled transcripts without amplification. Integration of a nanoscale device enabled us to isolate single cells on the platform, and thereby relate single-cell m6A modification states to gene expression signatures and cell surface markers. Application of the platform to MUTZ3 leukemia cells revealed a marked reduction in cellular m6A levels as CD34+ leukemic progenitors differentiate to CD14+ myeloid cells. We then coupled single-molecule m6A detection with fluorescence in situ hybridization (FISH) to relate mRNA and m6A levels of individual genes to single-cell phenotypes. This single-cell multi-modal assay suite can empower investigations of RNA modifications in rare populations and single cells.

Parallel Independent Losses of G-Type Lysozyme Genes in Hairless Aquatic Mammals

Lysozyme enzymes provide classic examples of molecular adaptation and parallel evolution, however, nearly all insights to date come from chicken-type (c-type) lysozymes. Goose-type (g-type) lysozymes occur in diverse vertebrates, with multiple independent duplications reported. Most mammals possess two g-type lysozyme genes (Lyg1 and Lyg2), the result of an early duplication, although some lineages are known to have subsequently lost one copy. Here we examine g-type lysozyme evolution across >250 mammals and reveal widespread losses of either Lyg1 or Lyg2 in several divergent taxa across the mammal tree of life. At the same time, we report strong evidence of extensive losses of both gene copies in cetaceans and sirenians, with an additional putative case of parallel loss in the tarsier. To validate these findings, we inspected published short-read data and confirmed the presence of loss of function mutations. Despite these losses, comparisons of selection pressures between intact g- and c-type lysozyme genes showed stronger purifying selection in the former, indicative of conserved function. Although the reasons for the evolutionary loss of g-type lysozymes in fully aquatic mammals are not known, we suggest that this is likely to at least partially relate to their hairlessness. Indeed, although Lyg1 does not show tissue-specific expression, recent studies have linked Lyg2 expression to anagen hair follicle development and hair loss. Such a role for g-type lysozyme would explain why the Lyg2 gene became obsolete when these taxa lost their body hair.

Analysis of m6A methylation in skin tissues of different sex Liaoning cashmere goats

N⁶-methyladenosine (m⁶A) is the most frequent internal modification of mRNA and lncRNA in eukaryotes. We used two high-throughput sequencing method, m⁶A-seq and RNA-seq to identify pivotal m⁶A-modified genes in cashmere fineness and fiber growth. 8062 m⁶A peaks were detected by m⁶A-seq, including 2157 upregulated and 6445 downregulated. Furthermore, by comparing m⁶A-modified genes of the male Liaoning Cashmere Goat (M-LCG) and female Liaoning Cashmere Goat (F-LCG) skin tissues, we get 862 differentially expressed m⁶A-modified genes. To identify differently expressed m⁶A genes associated with cashmere fineness, 11 genes were selected for validation using real time fluorescent quantitative PCR in M-LCG and F-LCG. This study provides an acadamic basis on the molecular regulation mechanism of m⁶A modification in cashmere growth process.

METTL3-mediated m6A modification regulates cell cycle progression of dental pulp stem cells

Background

Dental pulp stem cells (DPSCs) are a promising cell source in endodontic regeneration and tissue engineering with limited self-renewal and pluripotency capacity. N⁶-methyladenosine (m⁶A) is the most prevalent, reversible internal modification in RNAs associated with stem cell fate determination. In this study, we aim to explore the biological effect of m⁶A methylation in DPSCs.

Methods

m⁶A immunoprecipitation with deep sequencing (m⁶A RIP-seq) demonstrated the features of m⁶A modifications in DPSC transcriptome. Lentiviral vectors were constructed to knockdown or overexpress methyltransferase like 3 (METTL3). Cell morphology, viability, senescence, and apoptosis were analyzed by β-galactosidase, TUNEL staining, and flow cytometry. Bioinformatic analysis combing m⁶A RIP and shMETTL3 RNA-seq functionally enriched overlapped genes and screened target of METTL3. Cell cycle distributions were assayed by flow cytometry, and m⁶A RIP-qPCR was used to confirm METTL3-mediated m⁶A methylation.

Results

Here, m⁶A peak distribution, binding area, and motif in DPSCs were first revealed by m⁶A RIP-seq. We also found a relatively high expression level of METTL3 in immature DPSCs with superior regenerative potential and METTL3 knockdown induced cell apoptosis and senescence. A conjoint analysis of m⁶A RIP and RNA sequencing showed METTL3 depletion associated with cell cycle, mitosis, and alteration of METTL3 resulted in cell cycle arrest. Furthermore, the protein interaction network of differentially expressed genes identified Polo-like kinase 1 (PLK1), a critical cycle modulator, as the target of METTL3-mediated m⁶A methylation in DPSCs.

Conclusions

These results revealed m⁶A methylated hallmarks in DPSCs and a regulatory role of METTL3 in cell cycle control. Our study shed light on therapeutic approaches in vital pulp therapy and served new insight into stem cell-based tissue engineering.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13287-021-02223-x.

Impacts of Epigenetic Processes on the Health and Productivity of Livestock

The dynamic changes in the epigenome resulting from the intricate interactions of genetic and environmental factors play crucial roles in individual growth and development. Numerous studies in plants, rodents, and humans have provided evidence of the regulatory roles of epigenetic processes in health and disease. There is increasing pressure to increase livestock production in light of increasing food needs of an expanding human population and environment challenges, but there is limited related epigenetic data on livestock to complement genomic information and support advances in improvement breeding and health management. This review examines the recent discoveries on epigenetic processes due to DNA methylation, histone modification, and chromatin remodeling and their impacts on health and production traits in farm animals, including bovine, swine, sheep, goat, and poultry species. Most of the reports focused on epigenome profiling at the genome-wide or specific genic regions in response to developmental processes, environmental stressors, nutrition, and disease pathogens. The bulk of available data mainly characterized the epigenetic markers in tissues/organs or in relation to traits and detection of epigenetic regulatory mechanisms underlying livestock phenotype diversity. However, available data is inadequate to support gainful exploitation of epigenetic processes for improved animal health and productivity management. Increased research effort, which is vital to elucidate how epigenetic mechanisms affect the health and productivity of livestock, is currently limited due to several factors including lack of adequate analytical tools. In this review, we (1) summarize available evidence of the impacts of epigenetic processes on livestock production and health traits, (2) discuss the application of epigenetics data in livestock production, and (3) present gaps in livestock epigenetics research. Knowledge of the epigenetic factors influencing livestock health and productivity is vital for the management and improvement of livestock productivity.

Cultivation of Hair Matrix Cells from Cashmere Goat Skins and Exemplified Applications

Simple Summary

A large scale of sequencing data pertaining to cashmere growth on cashmere goats have not been cost-effectively used due to the lack of in vitro cellular models, especially for hair matrix cells (HMCs)—the precursors of hair-forming keratinocytes, causing an enormous waste of data resources. Herein, we successfully isolated and cultivated previously unreported HMCs from cashmere goat skins and identified them morphologically and molecularly via their distinct appearance and signature genes’ expression from spatially adjacent dermal papilla cells. Through monitoring the effects of calcium and all-trans retinoic acid on HMCs using various biological techniques, we displayed that the cells are useful models to explore unsolved issues in hair fiber growth on goats. Therefore, our present success paves the road for further utilizing currently deposited data to unveil the secrets of cashmere growth and, ultimately, improve the quantity and quality of animal fibers.

Abstract

A functional interpretation of filtered candidates and predicted regulatory pathways related to cashmere growth from sequencing trials needs available cell models, especially for hair matrix cells (HMCs), whose continual proliferation and differentiation result in rapid hair growth. To fulfill such goals, we herein obtained primary goat HMCs via a microdissection-based method; optimized the selection of the culture medium and coating substances for better cell maintenance; and exemplified their usefulness through examining the effects of calcium and all-trans retinoic acid (ATRA) on cells using immunoblotting, flow cytometry, and other techniques. As a result, we successfully acquired primary and passaged goat HMCs with typical keratinocyte morphology. Calcium-free RPMI (Roswell Park Memorial Institute) 1640 and MEM (minimum Eagle’s medium) outperformed normal DMEM/F12 (Dulbecco’s modified Eagle’s medium/Nutrient Mixture F-12) on long-term cell maintenance, whereas serum-free media K-SFM and EpiLife failed to support cell growth. HMCs differed molecularly and morphologically from their neighbor dermal papilla cells on expressions of feature genes, such as HOXC13, and on characteristic keratinocyte-like appearances versus fibroblast shapes, respectively. Higher calcium concentrations significantly stimulated the expression of the genes (e.g., KRT1 and IVL) involved in keratinocyte differentiation and, promoted cell proliferation. Moreover, 10⁻⁵ M ATRA obviously boosted goat HMC expansions and changed their cell cycle distributions compared to the controls. Our study shines a light on researches exploring the mechanisms underlying the growth of cashmere.

Transcriptome Profiling and Differential Gene Expression in Canine Microdissected Anagen and Telogen Hair Follicles and Interfollicular Epidermis

The transcriptome profile and differential gene expression in telogen and late anagen microdissected hair follicles and the interfollicular epidermis of healthy dogs was investigated by using RNAseq. The genes with the highest expression levels in each group were identified and genes known from studies in other species to be associated with structure and function of hair follicles and epidermis were evaluated. Transcriptome profiling revealed that late anagen follicles expressed mainly keratins and telogen follicles expressed GSN and KRT15. The interfollicular epidermis expressed predominately genes encoding for proteins associated with differentiation. All sample groups express genes encoding for proteins involved in cellular growth and signal transduction. The expression pattern of skin-associated genes in dogs is similar to humans. Differences in expression compared to mice and humans include BMP2 expression mainly in telogen and high KRT17 expression in the interfollicular epidermis of dogs. Our data provide the basis for the investigation of the structure and function of canine skin or skin disease and support the use of dogs as a model for human cutaneous disease by assigning gene expression to specific tissue states.