Dataset Information

Transcriptome-Wide N6-Methyladenosine Methylome Alteration in the Rat Spinal Cord After Acute Traumatic Spinal Cord Injury.

ABSTRACT: Recent studies showed that RNA N6-methyladenosine (m6A) plays an important role in neurological diseases. We used methylated RNA immunoprecipitation sequencing (MeRIP-Seq) technology to generate the m6A modification map after traumatic spinal cord injury (TSCI). A total of 2,609 differential m6A peaks were identified after TSCI. Our RNA sequencing results after TSCI showed 4,206 genes with significantly altered expression. Cross-link analysis of m6A sequencing results and RNA sequencing results showed that 141 hyper-methylated genes were upregulated, 53 hyper-methylated genes were downregulated, 57 hypo-methylated genes were upregulated, and 197 hypo-methylated genes were downregulated. Among these, the important inflammatory response factor Tlr4 and the important member of the neurotrophin family Ngf were both upregulated and hyper-methylated after TSCI. This study provides that in the future, the epigenetic modifications of the genes could be used as an indicator of TSCI.

SUBMITTER: Yu J

PROVIDER: S-EPMC9189298 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Transcriptome-Wide N6-Methyladenosine Methylome Alteration in the Rat Spinal Cord After Acute Traumatic Spinal Cord Injury.

Yu Jiangtao J Chen Haihua H Ma Haoli H Zhang Zhongxiang Z Zhu Xiaolu X Wang Pengcheng P Liu Ruining R Jin Xiaoqing X Zhao Yan Y

Frontiers in neuroscience 20220530

Recent studies showed that RNA N6-methyladenosine (m6A) plays an important role in neurological diseases. We used methylated RNA immunoprecipitation sequencing (MeRIP-Seq) technology to generate the m6A modification map after traumatic spinal cord injury (TSCI). A total of 2,609 differential m6A peaks were identified after TSCI. Our RNA sequencing results after TSCI showed 4,206 genes with significantly altered expression. Cross-link analysis of m6A sequencing results and RNA sequencing results ...[more]

PMID: 35706691

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Project description:BackgroundHeat stress has a substantial negative economic impact on the dairy industry. N6-methyladenosine (m6A) is the most common internal RNA modification in eukaryotes and plays a key role in regulating heat stress response in animals. In dairy cows, however, this modification remains largely unexplored. Therefore, we examined the effects of heat stress on the m6A modification and gene expression in bovine mammary epithelial cells to elucidate the mechanism of heat stress response. In this study, Mammary alveolar cells-large T antigen (MAC-T) cells were incubated at 37 °C (non-heat stress group, NH) and 40 °C (heat stress group, H) for 2 hours, respectively. HSP70, HSF1, BAX and CASP3 were up regulated in H group compared with those in the NH group.ResultsMethylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) were conducted to identify m6A peaks and to produce gene expression data of MAC-T cells in the H and NH groups. In total, we identified 17,927 m6A peaks within 9355 genes in the H group, and 18,974 peaks within 9660 genes in the NH groups using MeRIP-seq. Compared with the NH group, 3005 significantly differentially enriched m6A peaks were identified, among which 1131 were up-regulated and 1874 were down-regulated. In addition, 1502 significantly differentially expressed genes were identified using RNA-seq, among which 796 were up-regulated and 706 were down-regulated in the H group compared to the NH group. Furthermore, 199 differentially expressed and synchronously differentially methylated genes were identified by conjoint analysis of the MeRIP-seq and RNA-seq data, which were subsequently divided into four groups: 47 hyper-up, 53 hyper-down, 59 hypo-up and 40 hypo-down genes. In addition, GO enrichment and KEGG analyses were used to analyzed the potential functions of the genes in each section.ConclusionThe comparisons of m6A modification patterns and conjoint analyses of m6A modification and gene expression profiles suggest that m6A modification plays a critical role in the heat stress response by regulating gene expression.

Project description:In mammals, skeletal muscle development is a complex biological process regulated by many factors. N6-methyladenosine (m6A) RNA modification plays an important role in many biological processes. However, the regulation of m6A on skeletal muscle growth and development in adult goats remains unclear. In this study, Duan goats (DA) and Nubia goats (NBY), both female and 12 months old, were selected as the research objects, and m6A-Seq and RNA-Seq were mainly used to detect the difference of m6A modification and gene expression during the development of the longissimus dorsi (LD) muscle in the two breeds. The results showed that compared with DA, the meat production performance of NBY was better than that of DA, and the modification level of m6A was higher than that of DA in LD. The m6A-Seq of LD indicated m6A peaks were mainly enriched in the coding sequence (CDS) and stop codon. A total of 161 differentially methylated genes (DMGs) and 1294 differentially expressed genes (DEGs) were identified in two breeds. GO and KEGG analysis showed that DMGs were closely related to cellular metabolism, and most of DMGs were enriched in pathways related to energy metabolism, muscle growth and development, mainly MAPK signaling pathway, Wnt signaling pathway and CGMP-PKG signaling pathway. The DEGs were significantly enriched in actin binding, calcium ion binding, angiogenesis, and other biological processes, and most of them were enriched in PI3K-Akt and CGMP-PKG signaling pathways. Combined analysis of m6A-Seq and RNA-Seq data revealed a negative correlation between differentially methylated m6A levels and mRNA abundance, and mRNA expression of the gene with m6A peak near 3'UTR will decrease. In addition, 11 DMGs regulating cell differentiation, muscle growth and development were identified. This study displayed the m6A profiles and distribution patterns in the goat transcriptome, determined the potential role of m6A modification in muscle growth and provided a new reference for the further study of goat skeletal muscle development.

Project description:BackgroundCucumber green mottle mosaic virus (CGMMV) causes substantial global losses in cucurbit crops, especially watermelon. N6-methyladenosine (m6A) methylation in RNA is one of the most important post-transcriptional modification mechanisms in eukaryotes. It has been shown to have important regulatory functions in some model plants, but there has been no research regarding m6A modifications in watermelon.ResultsWe measured the global m6A level in resistant watermelon after CGMMV infection using a colorimetric method. And the results found that the global m6A level significantly decreased in resistant watermelon after CGMMV infection. Specifically, m6A libraries were constructed for the resistant watermelon leaves collected 48 h after CGMMV infection and the whole-genome m6A-seq were carried out. Numerous m6A modified peaks were identified from CGMMV-infected and control (uninfected) samples. The modification distributions and motifs of these m6A peaks were highly conserved in watermelon transcripts but the modification was more abundant than in other reported crop plants. In early response to CGMMV infection, 422 differentially methylated genes (DMGs) were identified, most of which were hypomethylated, and probably associated with the increased expression of watermelon m6A demethylase gene ClALKBH4B. Gene Ontology (GO) analysis indicated quite a few DMGs were involved in RNA biology and stress responsive pathways. Combined with RNA-seq analysis, there was generally a negative correlation between m6A RNA methylation and transcript level in the watermelon transcriptome. Both the m6A methylation and transcript levels of 59 modified genes significantly changed in response to CGMMV infection and some were involved in plant immunity.ConclusionsOur study represents the first comprehensive characterization of m6A patterns in the watermelon transcriptome and helps to clarify the roles and regulatory mechanisms of m6A modification in watermelon in early responses to CGMMV.

Dataset Information

Transcriptome-Wide N6-Methyladenosine Methylome Alteration in the Rat Spinal Cord After Acute Traumatic Spinal Cord Injury.

Publications

Transcriptome-Wide N6-Methyladenosine Methylome Alteration in the Rat Spinal Cord After Acute Traumatic Spinal Cord Injury.

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