Acute Depletion of METTL3 Implicates -methyladenosine in Alternative Intron/exon Inclusion in the Nascent Transcriptome

Overview

Journal Genome Res

Specialty Genetics

Date 2021 Jun 16

PMID 34131006

Citations 30

Authors

Guifeng Wei

Mafalda Almeida

Greta Pintacuda

Heather Coker

Joseph S Bowness

Jernej Ule

Neil Brockdorff

Affiliations

Soon will be listed here.

Abstract

RNA -methyladenosine (mA) modification plays important roles in multiple aspects of RNA regulation. mA is installed cotranscriptionally by the METTL3/14 complex, but its direct roles in RNA processing remain unclear. Here, we investigate the presence of mA in nascent RNA of mouse embryonic stem cells. We find that around 10% of mA peaks are located in alternative introns/exons, often close to 5' splice sites. mA peaks significantly overlap with RBM15 RNA binding sites and the histone modification H3K36me3. Acute depletion of METTL3 disrupts inclusion of alternative introns/exons in the nascent transcriptome, particularly at 5' splice sites that are proximal to mA peaks. For terminal or variable-length exons, mA peaks are generally located on or immediately downstream from a 5' splice site that is suppressed in the presence of mA and upstream of a 5' splice site that is promoted in the presence of mA. Genes with the most immediate effects on splicing include several components of the mA pathway, suggesting an autoregulatory function. Collectively, our findings demonstrate crosstalk between the mA machinery and the regulation of RNA splicing.

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References

Wang P, Doxtader K, Nam Y . Structural Basis for Cooperative Function of Mettl3 and Mettl14 Methyltransferases. Mol Cell. 2016; 63(2):306-317. PMC: 4958592. DOI: 10.1016/j.molcel.2016.05.041. View

Lee J, Skalnik D . Rbm15-Mkl1 interacts with the Setd1b histone H3-Lys4 methyltransferase via a SPOC domain that is required for cytokine-independent proliferation. PLoS One. 2012; 7(8):e42965. PMC: 3424240. DOI: 10.1371/journal.pone.0042965. View

Wang X, Zhao B, Roundtree I, Lu Z, Han D, Ma H . N(6)-methyladenosine Modulates Messenger RNA Translation Efficiency. Cell. 2015; 161(6):1388-99. PMC: 4825696. DOI: 10.1016/j.cell.2015.05.014. View

Roundtree I, Luo G, Zhang Z, Wang X, Zhou T, Cui Y . YTHDC1 mediates nuclear export of N-methyladenosine methylated mRNAs. Elife. 2017; 6. PMC: 5648532. DOI: 10.7554/eLife.31311. View

Moindrot B, Cerase A, Coker H, Masui O, Grijzenhout A, Pintacuda G . A Pooled shRNA Screen Identifies Rbm15, Spen, and Wtap as Factors Required for Xist RNA-Mediated Silencing. Cell Rep. 2015; 12(4):562-72. PMC: 4534822. DOI: 10.1016/j.celrep.2015.06.053. View

Liu J, Yue Y, Han D, Wang X, Fu Y, Zhang L . A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat Chem Biol. 2013; 10(2):93-5. PMC: 3911877. DOI: 10.1038/nchembio.1432. View

Zhang Y, Liu T, Meyer C, Eeckhoute J, Johnson D, Bernstein B . Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008; 9(9):R137. PMC: 2592715. DOI: 10.1186/gb-2008-9-9-r137. View

Sledz P, Jinek M . Structural insights into the molecular mechanism of the m(6)A writer complex. Elife. 2016; 5. PMC: 5023411. DOI: 10.7554/eLife.18434. View

Wang X, Lu Z, Gomez A, Hon G, Yue Y, Han D . N6-methyladenosine-dependent regulation of messenger RNA stability. Nature. 2013; 505(7481):117-20. PMC: 3877715. DOI: 10.1038/nature12730. View

10.

Patil D, Chen C, Pickering B, Chow A, Jackson C, Guttman M . m(6)A RNA methylation promotes XIST-mediated transcriptional repression. Nature. 2016; 537(7620):369-373. PMC: 5509218. DOI: 10.1038/nature19342. View

11.

Knuckles P, Lence T, Haussmann I, Jacob D, Kreim N, Carl S . Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the mA machinery component Wtap/Fl(2)d. Genes Dev. 2018; 32(5-6):415-429. PMC: 5900714. DOI: 10.1101/gad.309146.117. View

12.

PERRY R, Kelley D, Friderici K, Rottman F . The methylated constituents of L cell messenger RNA: evidence for an unusual cluster at the 5' terminus. Cell. 1975; 4(4):387-94. DOI: 10.1016/0092-8674(75)90159-2. View

13.

Linder B, Grozhik A, Olarerin-George A, Meydan C, Mason C, Jaffrey S . Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. Nat Methods. 2015; 12(8):767-72. PMC: 4487409. DOI: 10.1038/nmeth.3453. View

14.

Wei G, Brockdorff N, Zhang T . The PWWP2A Histone Deacetylase Complex Represses Intragenic Spurious Transcription Initiation in mESCs. iScience. 2020; 23(11):101741. PMC: 7670215. DOI: 10.1016/j.isci.2020.101741. View

15.

Zhang Z, Chen L, Zhao Y, Yang C, Roundtree I, Zhang Z . Single-base mapping of mA by an antibody-independent method. Sci Adv. 2019; 5(7):eaax0250. PMC: 6609220. DOI: 10.1126/sciadv.aax0250. View

16.

Geula S, Moshitch-Moshkovitz S, Dominissini D, AlFatah Mansour A, Kol N, Salmon-Divon M . Stem cells. m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation. Science. 2015; 347(6225):1002-6. DOI: 10.1126/science.1261417. View

17.

Ke S, Alemu E, Mertens C, Gantman E, Fak J, Mele A . A majority of m6A residues are in the last exons, allowing the potential for 3' UTR regulation. Genes Dev. 2015; 29(19):2037-53. PMC: 4604345. DOI: 10.1101/gad.269415.115. View

18.

Fish L, Navickas A, Culbertson B, Xu Y, Nguyen H, Zhang S . Nuclear TARBP2 Drives Oncogenic Dysregulation of RNA Splicing and Decay. Mol Cell. 2019; 75(5):967-981.e9. PMC: 6731133. DOI: 10.1016/j.molcel.2019.06.001. View

19.

Garcia-Campos M, Edelheit S, Toth U, Safra M, Shachar R, Viukov S . Deciphering the "mA Code" via Antibody-Independent Quantitative Profiling. Cell. 2019; 178(3):731-747.e16. DOI: 10.1016/j.cell.2019.06.013. View

20.

Barbieri I, Tzelepis K, Pandolfini L, Shi J, Millan-Zambrano G, Robson S . Promoter-bound METTL3 maintains myeloid leukaemia by mA-dependent translation control. Nature. 2017; 552(7683):126-131. PMC: 6217924. DOI: 10.1038/nature24678. View