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Integrated analysis of the transcriptome wide m6A methylome in Peripheral nerve injury

ABSTRACT: Integrated analysis of the transcriptome wide m6A methylome in Peripheral nerve injury

PROVIDER: PRJNA721213 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14209280_1.fastq.gz	Fastqsanger.gz
	SRR14209280_2.fastq.gz	Fastqsanger.gz
	SRR14209281_1.fastq.gz	Fastqsanger.gz
	SRR14209281_2.fastq.gz	Fastqsanger.gz
	SRR14209282_1.fastq.gz	Fastqsanger.gz

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Integrated analysis of the transcriptome wide m6A methylome in Peripheral nerve injury

Project description:N6-methyladenosine(m6A) is the most plentiful internal RNA modification, especially in eukaryotic messenger RNA (mRNA), which plays pivotal roles in mRNA life cycle and nerve development processes. In this study, samples were collected from Sciatic Nerve Injury (SNI) after 7 days and control rats. Altered peaks of m6A-modified transcripts were mainly related to immune system process, cell activation and nervous system development. KEGG pathway analyses highlighted the Axon guidance pathway, Calcium signaling pathway and B cell receptor signaling pathway. These data further enrich the contents of epigenetics in Peripheral Nerve Injury and provide a new opinion to promote the function recovery

2021-06-27 | GSE171866 | GEO

Epitranscriptomic Analysis of m6A Methylome After Peripheral Nerve Injury.

Project description:N6-methyladenosine (m6A) is one of the most plentiful internal RNA modifications, especially in eukaryotic messenger RNA (mRNA), which plays pivotal roles in the regulation of mRNA life cycle and nerve development. However, the mRNA m6A methylation pattern in peripheral nervous injury (PNI) has not been investigated. In this study, sciatic nerve samples were collected from 7 days after sciatic nerve injury (SNI) and control rats. Quantitative real-time PCR demonstrated that m6A-related methyltransferase/demethylase genes were remarkably upregulated in SNI group compared with control group. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) was performed to reveal the m6A methylation landscape. The results showed that 4,014 m6A peaks were significantly altered, including 2,144 upregulated and 1,870 downregulated m6A peaks, which were corresponded to 1,858 genes. Moreover, 919 differentially expressed genes were identified by the conjoint analysis of MeRIP-seq and RNA-seq. GO and KEGG pathway analyses were performed to determine the biological functions and signaling pathways of the m6A-modified genes. Notably, these genes were mainly related to the immune system process, cell activation, and nervous system development in GO analysis. KEGG pathway analysis revealed that these genes were involved in the cell cycle, B cell receptor signaling pathway, axon guidance pathway, and calcium signaling pathway. Furthermore, the m6A methylation and protein expression levels of autophagy-related gene (Atg7) were increased, together with the activation of autophagy. These findings shed some light on the epigenetic regulation of gene expression, which may provide a new opinion to promote functional recovery after PNI.

| S-EPMC8301379 | biostudies-literature

Decoding the m6A expression profiling of spinal cord after spared nerve injury at three time points with RIP-Seq

Project description:We performed gene expression profiling analysis using data obtained from RNA-seq and m6A peaks profiling analysis using data obtained from RIP-Seq of spared nerve injury model at 3rd, 7th, 14th postoperative day and sham group. To investigate the differential m6A expression profiling, we established spared nerve injury model at 3rd, 7th, 14th postoperative day and sham group.

2022-05-06 | GSE202166 | GEO

Enhancer Analysis in Peripheral Nerve Injury

Project description:ChIP-seq of H3K27acetylation in sham and injured nerve. Schwann cells play an important role in the response of peripheral nerve to injury. This study was designed to identify enhancers that are altered in sciatic nerve at 3 days post-injury to help identify pathways that mediate the gene expression reprogramming that occurs in Schwann cells after nerve injury. We employed ChIP-seq analysis of H3K27 acetylation as a mark of actively engaged enhancers, and compared enhancers in the distal stump of transected sciatic nerve compared to contralateral (sham) condition.

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Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors

Project description:Aberrant DNA methylation (DNAm) was first linked to cancer over 25 years ago. Since then, many studies have associated hypermethylation of tumour suppressor genes and hypomethylation of oncogenes to the tumourigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs). Recently, new technologies for whole-genome DNAm (methylome) analysis have been developed, enabling unbiased analysis of cancer methylomes. Using MeDIP-seq, we report a sequencing-based comparative methylome analysis of malignant peripheral nerve sheath tumours (MPNST), benign Neurofibromas and normal Schwann cells. Analysis of these methylomes revealed a complex landscape of DNAm alterations. Contrary to the current dogma, significant global hypomethylation was not observed in the MPNST methylome. However, a highly significant (P<10-100) directional difference in DNAm was found in satellite repeats, suggesting these repeats to be the main target for hypomethylation in MPNST. Comparative analysis of the MPNST and Schwann cell methylomes identified 101,466 cancer-associated differentially methylated regions (cDMRs). Analysis showed these cDMRs to be significantly enriched for two satellite repeat types (SATR1 and ARLM-NM-1) and suggests an association between aberrant DNAm of these sequences and transition from healthy cells to malignant disease. Significant enrichment of hypermethylated cDMRs in CGI shores (P<10-60), non-CGI-associated promoters (P<10-4) and hypomethylated cDMRs in SINE repeats (P<10-100) was also identified. Integration of DNAm and gene expression data showed that the expression pattern of genes associated with CGI shore cDMRs was able to discriminate between disease phenotypes. This study establishes MeDIP-seq as an effective method to analyse cancer methylomes. Examination of methylation profiles in malignant, benign and normal tissue

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RNA m6A methylome of Caenorhabditis elegans

Project description:RNA m6A methylome of Caenorhabditis elegans

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RNA-seq of mouse sciatic peripheral nerve of uninjured mouse against implantation of a silicon device or peripheral nerve injury.

Project description:Foreign body reaction is one of the most important limiting factors to the clinical translation of implantable bioelectronics. The experiment compares the process of foreign body reaction, following the implantation of a silicon device in a mouse peripheral nerve, to that of peripheral nerve injury, following nerve crushing. Both processes are also compared to a naïve peripheral nerve from an uninjured mouse. The endpoints are day 1, 4, 7, 14 and 28 days.

2022-04-30 | E-MTAB-10294 | biostudies-arrayexpress

m6A-Label-seq directly reports m6A methylome at base resolution

Project description:m6A-Label-seq directly reports m6A methylome at base resolution

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