Deposition of 5-Methylcytosine on Enhancer RNAs Enables the Coactivator Function of PGC-1α

Aguiló, Francesca; Li, SiDe; Balasubramaniyan, Natarajan; Sancho, Ana; Benko, Sabina; Zhang, Fan; Vashisht, Ajay A.; Rengasamy, Madhumitha; Andino, Blanca; Chen, Chih‐Hung; Zhou, Felix; Qian, Chengyuan; Zhou, Ming‐Ming; Wohlschlegel, James A.; Zhang, Weijia; Suchy, Frederick J.; Walsh, Martin J.

doi:10.1016/j.celrep.2015.12.043

Cited by 138 publications

(106 citation statements)

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“…This observation raises the possibility that m5C may be involved in the splicing process or may mark transcripts for degradation. Another intriguing possibility is that m5C may decorate regulatory RNAs, such as promoter- or enhancer-derived transcripts [43], which was indeed demonstrated by Aguilo et al in a recent work [44]. …”

Section: Discussionmentioning

confidence: 99%

Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain

et al. 2017

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BackgroundRecent work has identified and mapped a range of posttranscriptional modifications in mRNA, including methylation of the N6 and N1 positions in adenine, pseudouridylation, and methylation of carbon 5 in cytosine (m5C). However, knowledge about the prevalence and transcriptome-wide distribution of m5C is still extremely limited; thus, studies in different cell types, tissues, and organisms are needed to gain insight into possible functions of this modification and implications for other regulatory processes.ResultsWe have carried out an unbiased global analysis of m5C in total and nuclear poly(A) RNA of mouse embryonic stem cells and murine brain. We show that there are intriguing differences in these samples and cell compartments with respect to the degree of methylation, functional classification of methylated transcripts, and position bias within the transcript. Specifically, we observe a pronounced accumulation of m5C sites in the vicinity of the translational start codon, depletion in coding sequences, and mixed patterns of enrichment in the 3′ UTR. Degree and pattern of methylation distinguish transcripts modified in both embryonic stem cells and brain from those methylated in either one of the samples. We also analyze potential correlations between m5C and micro RNA target sites, binding sites of RNA binding proteins, and N6-methyladenosine.ConclusionOur study presents the first comprehensive picture of cytosine methylation in the epitranscriptome of pluripotent and differentiated stages in the mouse. These data provide an invaluable resource for future studies of function and biological significance of m5C in mRNA in mammals.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1139-1) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain

et al. 2017

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“…One explanation for their complex biology might be that these MTases modify additional substrates outside of the tRNA and rRNA realm. Indeed, NSUN7 was recently identified as a modifier of enhancer RNAs [44], but NSUN2 has also repeatedly been found to methylate sites outside of its purview [9,[45][46][47][48][49][50]. Two 'readers' of m 5 C have been reported, the mRNA export adapter ALYREF (Aly/REF export factor) [49] and the DNA/RNA-binding protein YBX1 (Y-box binding protein 1) [47,51], implying certain molecular functions (see below).…”

Section: Introductionmentioning

confidence: 99%

Multiple links between 5-methylcytosine content of mRNA and translation

et al. 2020

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Background: 5-Methylcytosine (m 5 C) is a prevalent base modification in tRNA and rRNA but it also occurs more broadly in the transcriptome, including in mRNA, where it serves incompletely understood molecular functions. In pursuit of potential links of m 5 C with mRNA translation, we performed polysome profiling of human HeLa cell lysates and subjected RNA from resultant fractions to efficient bisulfite conversion followed by RNA sequencing (bsRNA-seq). Bioinformatic filters for rigorous site calling were devised to reduce technical noise.Results: We obtained~1000 candidate m 5 C sites in the wider transcriptome, most of which were found in mRNA. Multiple novel sites were validated by amplicon-specific bsRNA-seq in independent samples of either human HeLa, LNCaP and PrEC cells. Furthermore, RNAi-mediated depletion of either the NSUN2 or TRDMT1 m 5 C:RNA methyltransferases showed a clear dependence on NSUN2 for the majority of tested sites in both mRNAs and noncoding RNAs. Candidate m 5 C sites in mRNAs are enriched in 5′UTRs and near start codons and are embedded in a local context reminiscent of the NSUN2-dependent m 5 C sites found in the variable loop of tRNA. Analysing mRNA sites across the polysome profile revealed that modification levels, at bulk and for many individual sites, were inversely correlated with ribosome association. Conclusions: Our findings emphasise the major role of NSUN2 in placing the m 5 C mark transcriptome-wide. We further present evidence that substantiates a functional interdependence of cytosine methylation level with mRNA translation. Additionally, we identify several compelling candidate sites for future mechanistic analysis.

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“…One explanation for their complex biology might be that these MTases modify additional substrates outside of the tRNA and rRNA realm. Indeed, NSUN7 was recently identified as a modifier of enhancer RNAs (Aguilo et al 2016), but NSUN2 has also repeatedly been found to methylate sites outside of its purview (Squires et al 2012;Hussain et al 2013b;Khoddami and Cairns 2013;Yang et al 2017;Chen et al 2019;Huang et al 2019;Sun et al 2019). Two 'readers' of m 5 C have been reported, the mRNA export adapter ALYREF (Aly/REF export factor) (Yang et al 2017) and the DNA/RNAbinding protein YBX1 (Y-box binding protein 1) Yang et al 2019b), implying certain molecular functions (see below).…”

Section: Introductionmentioning

confidence: 99%

Multiple links between 5-methylcytosine content of mRNA and translation

Schümann

Zhang²,

Sibbritt

et al. 2020

Preprint

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Abstract5-methylcytosine (m5C) is a prevalent base modification in tRNA and rRNA but it also occurs more broadly in the transcriptome, including in mRNA, where it serves incompletely understood molecular functions. In pursuit of potential links of m5C with mRNA translation, we performed polysome profiling of human HeLa cell lysates and subjected RNA from resultant fractions to efficient bisulfite conversion followed by RNA sequencing (bsRNA-seq). Bioinformatic filters for rigorous site calling were devised to reduce technical noise. We obtained ∼1,000 candidate m5C sites in the wider transcriptome, most of which were found in mRNA. Multiple novel sites were validated by amplicon-specific bsRNA-seq in independent samples of either human HeLa, LNCaP and PrEC cells. Furthermore, RNAi-mediated depletion of either the NSUN2 or TRDMT1 m5C:RNA methyltransferases showed a clear dependence on NSUN2 for the majority of tested sites in both mRNAs and noncoding RNAs. Candidate m5C sites in mRNAs are enriched in 5’UTRs and near start codons, and are commonly embedded in a local context reminiscent of the NSUN2-dependent m5C sites found in the variable loop of tRNA. Analysing mRNA sites across the polysome profile revealed that modification levels, at bulk and for many individual sites, were inversely correlated with ribosome association. Altogether, these findings emphasise the major role of NSUN2 in making this mark transcriptome-wide and further substantiate a functional interdependence of cytosine methylation level with mRNA translation.

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Deposition of 5-Methylcytosine on Enhancer RNAs Enables the Coactivator Function of PGC-1α

Cited by 138 publications

References 54 publications

Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain

Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain

Multiple links between 5-methylcytosine content of mRNA and translation

Multiple links between 5-methylcytosine content of mRNA and translation

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