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Dynamic m6A mRNA methylation directs translational control of heat shock response

Abstract

The most abundant mRNA post-transcriptional modification is N6-methyladenosine (m6A), which has broad roles in RNA biology1,2,3,4,5. In mammalian cells, the asymmetric distribution of m6A along mRNAs results in relatively less methylation in the 5′ untranslated region (5′UTR) compared to other regions6,7. However, whether and how 5′UTR methylation is regulated is poorly understood. Despite the crucial role of the 5′UTR in translation initiation, very little is known about whether m6A modification influences mRNA translation. Here we show that in response to heat shock stress, certain adenosines within the 5′UTR of newly transcribed mRNAs are preferentially methylated. We find that the dynamic 5′UTR methylation is a result of stress-induced nuclear localization of YTHDF2, a well-characterized m6A ‘reader’. Upon heat shock stress, the nuclear YTHDF2 preserves 5′UTR methylation of stress-induced transcripts by limiting the m6A ‘eraser’ FTO from demethylation. Remarkably, the increased 5′UTR methylation in the form of m6A promotes cap-independent translation initiation, providing a mechanism for selective mRNA translation under heat shock stress. Using Hsp70 mRNA as an example, we demonstrate that a single m6A modification site in the 5′UTR enables translation initiation independent of the 5′ end N7-methylguanosine cap. The elucidation of the dynamic features of 5′UTR methylation and its critical role in cap-independent translation not only expands the breadth of physiological roles of m6A, but also uncovers a previously unappreciated translational control mechanism in heat shock response.

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Figure 1: YTHDF2 changes cellular localization and expression levels in response to heat shock stress.
Figure 2: Altered m6A profiles in MEF cells in response to heat shock stress.
Figure 3: m6A modification promotes selective translation under heat shock stress.
Figure 4: Selective 5′UTR m6A modification mediates cap-independent translation.

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Primary accessions

Sequence Read Archive

Data deposits

Sequencing data have been deposited at NCBI Sequence Read Archive under accession number SRA280261.

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Acknowledgements

We would like to thank Qian laboratory members for helpful discussions and Cornell University Life Sciences Core Laboratory Center for performing deep sequencing. This work was supported by grants from the US National Institutes of Health DP2 OD006449 and R01AG042400 (to S.-B.Q.) and NIDA DA037150 (to S.R.J.) and the US Department of Defense (W81XWH-14-1-0068) (to S.-B.Q.).

Author information

Authors and Affiliations

Authors

Contributions

J.Z. and S.-B.Q. conceived the project. J.Z. performed most experiments. J.W. analysed the sequencing data. X.G. performed Ribo-seq. X.Z. assisted heat shock assays. S.R.J. helped with original FTO ideas. S.-B.Q. wrote the manuscript. All authors discussed the results and edited the manuscript.

Corresponding author

Correspondence to Shu-Bing Qian.

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Competing interests

The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Subcellular localization of the m6A machinery in cells before and after heat shock stress.

a, MEF cells before or 2 h after heat shock (HS; 42 °C, 1 h) were immunostanied with indicated antibodies. DAPI was used for nuclear staining. b, MEF (left panel) and HeLa cells (right panel) were subject to heat shock stress (42 °C, 1 h) followed by recovery at 37 °C for various times. Anti-YTHDF2 immunostaining was counterstained by DAPI. Images are representative of at least 50 cells. Bar, 10 µm.

Extended Data Figure 2 mRNA stability and induction in response to heat shock stress.

a, Effects of heat shock stress on mRNA stability. MEF cells without heat shock stress (No HS), immediately after heat shock stress (42 °C, 1 h) (Post HS 0 h), or 2 h recovery at 37 °C (Post HS 2 h) were subject to further incubation in the presence of 5 µg ml−1 ActD. At the indicated times, mRNA levels were determined by qPCR. Error bars, mean ± s.e.m.; n = 3 biological replicates. b, MEF cells were collected at indicated times after heat shock stress (42 °C, 1 h) followed by RNA extraction and real-time PCR. Relative levels of indicated transcripts are normalized to β-actin. Error bars, mean ± s.e.m.; n = 3 biological replicates. c, HSF1 wild-type (WT) and knockout (KO) cells were subject to heat shock stress (42 °C, 1 h) followed by recovery at 37 °C for various times. Real-time PCR was conducted to quantify transcripts encoding Hsp70 and YTHDF2. Relative levels of transcripts are normalized to β-actin. Error bars, mean ± s.e.m.; *P < 0.05, **P < 0.01, unpaired two-tailed t-test; n = 3 biological replicates.

Extended Data Figure 3 Characterization of m6A sites in MEF cells with or without heat shock stress.

a, b, m6A profiling was conducted on MEF cells before (a) or 2 h after (b) heat shock (42 °C, 1 h). Left, pie chart presenting fractions of m6A peaks in different transcript segments. Right, sequence logo representing the consensus motif relative to m6A. CDS, coding sequence region.

Extended Data Figure 4 m6A profiling of HSPA8 in MEF cells with or without heat shock stress.

An example of constitutively expressed transcript HSPA8 in MEF cells with or without heat shock stress. Coverage of m6A immunoprecipitation and control reads (input) are indicated in red and grey, respectively. The transcript architecture is shown below the x axis.

Extended Data Figure 5 Dynamic m6A modification of HSPA1A by YTHDF2 and FTO.

An example of stress-induced transcript HSPA1A in post-stressed MEF cells with either YTHDF2 or FTO knockdown. Coverage of m6A immunoprecipitation and control reads (input) are indicated in red and blue, respectively. The transcript architecture is shown below the x axis.

Extended Data Figure 6 Direct competition between YTHDF2 and FTO in m6A binding.

a, Synthesized mRNA with m6A was incubated with FTO (2 µg) in the presence of an increasing amount of YTHDF2 (0, 0.5, 1 and 2 µg), followed by RNA pull-down and immunoblotting. b, Synthesized mRNA with m6A was incubated with FTO (1 µg in top panel and 2 µg in bottom panel) in the absence of presence of YTHDF2 (4 µg), followed by m6A dot blotting.

Extended Data Figure 7 YTHDF2 knockdown does not affect Hsp70 transcription after stress.

MEF cells with or without YTHDF2 knockdown were subject to heat shock stress (42 °C, 1 h) followed by recovery at 37 °C for various times. Real-time PCR was conducted to quantify Hsp70 mRNA levels. Error bars, mean ± s.e.m.; n = 3 biological replicates. sh-Scram, scrambled shRNA.

Extended Data Figure 8 FTO knockdown promotes Hsp70 synthesis.

a, m6A blotting of purified HSPA1A in MEF with or without FTO knockdown. Messenger RNAs synthesized by in vitro transcription in the absence or presence of m6A were used as control. RNA staining is shown as loading control. Representative of two biological replicates. b, MEF cells with or without FTO knockdown were collected at indicated times after heat shock stress (42 °C, 1 h) followed by immunoblotting using antibodies indicated. N, no heat shock. Representative of three biological replicates.

Extended Data Figure 9 m6A modification promotes cap-independent translation.

a, Fluc reporter mRNAs with or without 5′UTR was synthesized in the absence or presence of m6A. The transfected MEFs were incubation in the presence of 5 µg ml−1 ActD. At the indicated times, mRNA levels were determined by qPCR. Error bars, mean ± s.e.m.; n = 3 biological replicates. b, Fluc reporter mRNAs with or without Hsp70 5′UTR was synthesized in the absence of presence of m6A, followed by addition of a non-functional cap analogue ApppG. Fluc activity in transfected MEF cells was recorded using real-time luminometry. c, Constructs expressing Fluc reporter bearing 5′UTR from Hsc70 or Hsp105 are depicted on the top. Fluc activities in transfected MEF cells were quantified and normalized to the control containing normal A. Error bars, mean ± s.e.m.; *P < 0.05, unpaired two-tailed t-test; n = 3 biological replicates.

Extended Data Figure 10 Site-specific detection of m6A modification on HSPA1A.

a, Sequences of HSPA1A template and the DNA primer used for site-specific detection. Synthesized mRNAs containing a single m6A site (red) or A (blue) are used as positive and negative controls, respectively. The red shading in the HSPA1A sequence indicates predicted m6A sites. Autoradiogram shows primer extension of controls (left panel) and endogenous HSPA1A (right panel). b, Fluc mRNAs with or without m6A incorporation were incubated in the rabbit reticulocyte lysate system (RRL) at 30 °C for up to 60 min. Messenger RNA levels were determined by qPCR. Error bars, mean ± s.e.m.; n = 3 biological replicates.

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Zhou, J., Wan, J., Gao, X. et al. Dynamic m6A mRNA methylation directs translational control of heat shock response. Nature 526, 591–594 (2015). https://doi.org/10.1038/nature15377

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