Dynamic control of chromatin-associated m6A methylation regulates nascent RNA synthesis

Xu, Wenqi; He, Chenxi; Kaye, Emily G; Li, Jiahui; Mu, Mandi; Nelson, Geoffrey M.; Dong, Li; Jia-hua, Wang; Wu, Feizhen; Shi, Yujiang Geno; Adelman, Karen; Lan, Fei; Shi, Yang; Shen, Hongjie

doi:10.1016/j.molcel.2022.02.006

Cited by 93 publications

(73 citation statements)

References 55 publications

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“…This question is intricately related to the relative timing of m6A deposition with respect to mRNA splicing, which is not fully understood. On the one hand, m6A appears to be present at near steady-state levels already on chromatin-associated RNA (Ke et al, 2017), is present on nascent RNA (Xu et al, 2022), and was found by one study to be widespread on introns (Louloupi et al, 2018), suggesting that it is deposited prior to splicing. Yet, most studies have found the modification to be strongly depleted from introns (Chen-Kiang et al, 1979; Ke et al, 2017; Wei et al, 2021), suggesting that it may be installed following splicing.…”

Section: Discussionmentioning

confidence: 99%

Exon-intron architecture determines mRNA stability by dictating m6A deposition

Uzonyi

Slobodin

Schwartz

2022

Preprint

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N6-methyladenosine (m6A), a widespread destabilizing mark on mRNA, is non-uniformly distributed across the transcriptome, yet the basis for its selective deposition is unknown. Here, we uncover that m6A deposition is not selective. Instead, m6A distribution is exclusion-based: m6A-consensus harboring sites are methylated by default, unless they are within a window of up to ∼200 nt from an exon-intron junction. A simple model, relying exclusively on presence of m6A motifs and exon-intron architecture allows high accuracy recapitulation of experimentally-measured m6A profiles and of all m6A hallmarks. We further establish that m6A serves as the long-sought mechanism underlying the strong association between exon-intron architecture and mRNA stability. Our findings establish a mechanism by which the memory of nuclear RNA splicing is covalently etched on an mRNA, in the form of m6A, and determines its cytoplasmic stability, with broad implications on the regulation, function, and evolution of both m6A and mRNA stability.

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Section: Discussionmentioning

confidence: 99%

Exon-intron architecture determines mRNA stability by dictating m6A deposition

Uzonyi

Slobodin

Schwartz

2022

Preprint

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“…For example, METTL3 is recruited to promoters of highly expressed genes in Drosophila cells in a transcription-dependent manner where it regulates the release of RNA polymerase II (RNAPII) from its paused state [ 5 ]. Also consistent with a role on the regulation of transcription, METTL3 modifies nascent RNAs derived from promoters and enhancers, protecting them from premature transcription termination [ 6 ]. In addition, earlier work on human cells suggested an inverse relationship between transcription efficiency and m6A levels [ 7 ].…”

Section: Introductionmentioning

confidence: 80%

Slow RNAPII Transcription Elongation Rate, Low Levels of RNAPII Pausing, and Elevated Histone H1 Content at Promoters Associate with Higher m6A Deposition on Nascent mRNAs

Gallego

Fernández-Justel

Martín-Vírgala

et al. 2022

Genes

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N6-methyladenosine modification (m6A) fine-tunes RNA fate in a variety of ways, thus regulating multiple fundamental biological processes. m6A writers bind to chromatin and interact with RNA polymerase II (RNAPII) during transcription. To evaluate how the dynamics of the transcription process impact m6A deposition, we studied RNAPII elongation rates in mouse embryonic stem cells with altered chromatin configurations, due to reductions in linker histone H1 content. We found that genes transcribed at slow speed are preferentially methylated and display unique signatures at their promoter region, namely high levels of histone H1, together with marks of bivalent chromatin and low RNAPII pausing. They are also highly susceptible to m6A loss upon histone H1 reduction. These results indicate that RNAPII velocity links to chromatin structure and the deposition of m6A, highlighting the intricate relationship between different regulatory layers on nascent mRNA molecules.

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“…As such, METTL3 would have more contact time with the 5' end of RNA, the region where m6A is predominantly found in Drosophila 35 . METTL3 itself has been found to promote productive RNAPolII elongation, which suggests that there may be two-way communication between m6A and RNAPolII processivity 25,36 . An alternative explanation for the discrepancy between METTL3 binding and m6A levels is that methylation may occur at all MET-TL3 bound transcripts but not be retained.…”

Section: Discussionmentioning

confidence: 99%

Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation

Khyzha

Henikoff

Ahmad

2022

Preprint

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Whereas techniques to map chromatin-bound proteins are well-developed, mapping chromatin-associated RNAs remains a challenge. Here we describe Reverse Transcribe & Tagment (RT&Tag), in which RNAs associated with a chromatin epitope are targeted by an antibody followed by a protein A-Tn5 transposome. Localized reverse transcription generates RNA/cDNA hybrids that are subsequently tagmented for sequencing by Tn5. We demonstrate the utility of RT&Tag in Drosophila cells for capturing the noncoding RNA roX2 with the dosage compensation complex and maturing transcripts associated with silencing histone modifications. We also show that RT&Tag can detect N6-methyladenosine (m6A)-modified mRNAs, and show that genes producing methylated transcripts are characterized by extensive promoter pausing of RNA polymerase II. The high efficiency of in situ antibody tethering and tagmentation makes RT&Tag especially suitable for rapid low-cost profiling of chromatin-associated RNAs from small samples.

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Dynamic control of chromatin-associated m6A methylation regulates nascent RNA synthesis

Cited by 93 publications

References 55 publications

Exon-intron architecture determines mRNA stability by dictating m6A deposition

Exon-intron architecture determines mRNA stability by dictating m6A deposition

Slow RNAPII Transcription Elongation Rate, Low Levels of RNAPII Pausing, and Elevated Histone H1 Content at Promoters Associate with Higher m6A Deposition on Nascent mRNAs

Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation

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