Episo: quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite

Abstract

Motivation RNA 5-methylcytosine (m5C) is a type of post-transcriptional modification that may be involved in numerous biological processes and tumorigenesis. RNA m5C can be profiled at single-nucleotide resolution by high-throughput sequencing of RNA treated with bisulfite (RNA-BisSeq). However, the exploration of transcriptome-wide profile and potential function of m5C in splicing remains to be elucidated due to lack of isoform level m5C quantification tool. Results We developed a computational package to quantify Epitranscriptomal RNA m5C at the transcript isoform level (named Episo). Episo consists of three tools: mapper, quant and Bisulfitefq, for mapping, quantifying and simulating RNA-BisSeq data, respectively. The high accuracy of Episo was validated using an improved m5C-specific methylated RNA immunoprecipitation (meRIP) protocol, as well as a set of in silico experiments. By applying Episo to public human and mouse RNA-BisSeq data, we found that the RNA m5C is not evenly distributed among the transcript isoforms, implying the m5C may subject to be regulated at isoform level. Availability and implementation Episo is released under the GNU GPLv3+ license. The resource code Episo is freely accessible from https://github.com/liujunfengtop/Episo (with Tophat/cufflink) and https://github.com/liujunfengtop/Episo/tree/master/Episo_Kallisto (with Kallisto). Supplementary information Supplementary data are available at Bioinformatics online.

Epitranscriptomic regulation of transcriptome plasticity in development and diseases of the brain

“…Several epitranscriptome mapping studies showed that the embryonic and adult tissues that build up the mammalian CNS contain relatively higher abundance of RNA modifications than other organs. For example, higher level of m 6 A and m 6 Am in mRNA exist both in human and mouse brain tissues compared to non-brain tissues ( 7 , 8 ), and it was also reported that either m 5 C or ψ level was significantly higher in the brain than those in other tissues ( 9 , 10 ). These results imply that fine-tuning of gene expression by RNA modifications may regulate development and function of the CNS.…”

Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics

“… R https://cran.r-project.org/web/packages/BisRNA [191] Episo Bowtie Episo is the only computational tool available to quantify the RNA m 5 C modification at the transcript isoform level, which distinguish m 5 C level between isoforms of the same gene. GNU GPLv3 + license https://github.com/liujunfengtop/Episo [192] …”

5-methylcytonsine profiles in mouse transcriptomes suggest the randomness of m5C formation catalyzed by RNA methyltransferase

“…To explore the profiles of m 5 C in mouse transcriptomes, I applied Episo [7] to published RNA-BisSeq data in mouse (liver, kidney, heart and brain). According to the mapping results from Episo, I computed the methylation rate of cytosine and the methylation rate of reads (Table 1).…”

“…The alignment procedure was performed by using Episo [7], which maps RNA-BisSeq reads to the reference genome and reference transcriptome. Episo can convert the m…”

“…However, only partial m sites were analyzed in the above studies. The methylation level of candidate cytosine positions should be no less than 0.2 [8] and 0.1[7, 9], respectively.In this study, I mapped m globally in human HeLa cells and multiple mouse tissues using RNA-BidSeq and deeply analyzed the relationship among global methylation rate, methylation level at single-nucleotide resolution and at gene resolution. Collectively, these data suggest that the m formation catalyzed by RNA methyltransferase is random.…”