Transcriptome-Wide -Methyladenosine (mA) Methylome Profiling of Heat Stress in Pak-choi ( Ssp. )

Overview

Journal Plants (Basel)

Date 2020 Aug 27

PMID 32842619

Citations 20

Authors

Gaofeng Liu

Jin Wang

Xilin Hou

Affiliations

Soon will be listed here.

Abstract

In higher eukaryotes, -methyladenosine (mA) is the most common internal form of messenger RNA modification. By mapping the mA methyl genome in multiple species, the potential regulatory function of reversible mA methylation on mRNA is revealed. Recent studies have shown that RNA mA modification influences mRNA transcription, location, translation, stability, splicing, and nuclear export. However, there are not enough data on the mA transcriptome-wide map and its potential biological role in the heat stress of Pak-choi ( ssp. ). In this work, MeRIP-seq was used to obtain the first transcriptome-wide profiling of RNA mA modification in Pak-choi. Meanwhile, the transcriptome data were obtained by analyzing the input samples' sequencing data. Our research indicated that with three replicates, there were 11,252 common mA peaks and 9729 common mA-containing genes identified in the normal (CK) and heat stress (T43) groups. It was found that mA peaks were highly enriched in the 3' untranslated region in both CK and T43 groups. About 80% of the genes have one mA site. The consensus sequence of mA peaks was also enriched, which showed as AAACCV (V: U/A/G). In addition, association analysis found that there is a certain relationship between the degree of mA methylation and the transcription level, indicating that mA plays a certain regulatory role in gene expression. This comprehensive map in the study may provide a solid basis for determining the potential function of RNA mA modification in Pak-choi under normal (CK) and heat stress (T43) conditions.

Citing Articles

Epitranscriptome profiles reveal participation of the RNA methyltransferase gene OsMTA1 in rice seed germination and salt stress response.

Li Y, Yin M, Wang J, Zhao X, Xu J, Wang W BMC Plant Biol. 2025; 25(1):115.

PMID: 39865266 PMC: 11771074. DOI: 10.1186/s12870-025-06134-4.

RNA modifications in plant adaptation to abiotic stresses.

Cai J, Shen L, Kang H, Xu T Plant Commun. 2024; 6(2):101229.

PMID: 39709520 PMC: 11897461. DOI: 10.1016/j.xplc.2024.101229.

mA demethylase CpALKBH regulates mRNA stability to modulate the development and virulence of chestnut blight fungus.

Zhao L, Wei X, Chen F, Chen B, Li R mBio. 2024; 16(1):e0184424.

PMID: 39611846 PMC: 11708048. DOI: 10.1128/mbio.01844-24.

N6-methyladenosine RNA methyltransferase CpMTA1 mediates CpAphA mRNA stability through a YTHDF1-dependent m6A modification in the chestnut blight fungus.

Zhao L, Wei X, Chen F, Yuan L, Chen B, Li R PLoS Pathog. 2024; 20(8):e1012476.

PMID: 39159278 PMC: 11361730. DOI: 10.1371/journal.ppat.1012476.

Untranslated yet indispensable-UTRs act as key regulators in the environmental control of gene expression.

Hardy E, Balcerowicz M J Exp Bot. 2024; 75(14):4314-4331.

PMID: 38394144 PMC: 11263492. DOI: 10.1093/jxb/erae073.

References

Zheng H, Li S, Zhang X, Sui N . Functional Implications of Active N-Methyladenosine in Plants. Front Cell Dev Biol. 2020; 8:291. PMC: 7202093. DOI: 10.3389/fcell.2020.00291. View

Ahuja I, de Vos R, Bones A, Hall R . Plant molecular stress responses face climate change. Trends Plant Sci. 2010; 15(12):664-74. DOI: 10.1016/j.tplants.2010.08.002. View

Huang D, Sherman B, Lempicki R . Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009; 4(1):44-57. DOI: 10.1038/nprot.2008.211. View

Kotak S, Vierling E, Baumlein H, von Koskull-Doring P . A novel transcriptional cascade regulating expression of heat stress proteins during seed development of Arabidopsis. Plant Cell. 2007; 19(1):182-95. PMC: 1820961. DOI: 10.1105/tpc.106.048165. View

Zhou J, Wan J, Gao X, Zhang X, Jaffrey S, Qian S . Dynamic m(6)A mRNA methylation directs translational control of heat shock response. Nature. 2015; 526(7574):591-4. PMC: 4851248. DOI: 10.1038/nature15377. View

Meyer K, Patil D, Zhou J, Zinoviev A, Skabkin M, Elemento O . 5' UTR m(6)A Promotes Cap-Independent Translation. Cell. 2015; 163(4):999-1010. PMC: 4695625. DOI: 10.1016/j.cell.2015.10.012. View

Robinson M, McCarthy D, Smyth G . edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009; 26(1):139-40. PMC: 2796818. DOI: 10.1093/bioinformatics/btp616. View

Meyer K, Saletore Y, Zumbo P, Elemento O, Mason C, Jaffrey S . Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. Cell. 2012; 149(7):1635-46. PMC: 3383396. DOI: 10.1016/j.cell.2012.05.003. View

Yu J, Li Y, Wang T, Zhong X . Modification of N6-methyladenosine RNA methylation on heat shock protein expression. PLoS One. 2018; 13(6):e0198604. PMC: 6002042. DOI: 10.1371/journal.pone.0198604. View

10.

Nakashima K, Yamaguchi-Shinozaki K, Shinozaki K . The transcriptional regulatory network in the drought response and its crosstalk in abiotic stress responses including drought, cold, and heat. Front Plant Sci. 2014; 5:170. PMC: 4032904. DOI: 10.3389/fpls.2014.00170. View

11.

Schwartz S, Agarwala S, Mumbach M, Jovanovic M, Mertins P, Shishkin A . High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell. 2013; 155(6):1409-21. PMC: 3956118. DOI: 10.1016/j.cell.2013.10.047. View

12.

Shen L, Liang Z, Gu X, Chen Y, Teo Z, Hou X . N(6)-Methyladenosine RNA Modification Regulates Shoot Stem Cell Fate in Arabidopsis. Dev Cell. 2016; 38(2):186-200. PMC: 6364302. DOI: 10.1016/j.devcel.2016.06.008. View

13.

Li J, Lin X, Chen A, Peterson T, Ma K, Bertzky M . Global priority conservation areas in the face of 21st century climate change. PLoS One. 2013; 8(1):e54839. PMC: 3554607. DOI: 10.1371/journal.pone.0054839. View

14.

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley D . Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012; 7(3):562-78. PMC: 3334321. DOI: 10.1038/nprot.2012.016. View

15.

Niu Y, Zhao X, Wu Y, Li M, Wang X, Yang Y . N6-methyl-adenosine (m6A) in RNA: an old modification with a novel epigenetic function. Genomics Proteomics Bioinformatics. 2013; 11(1):8-17. PMC: 4357660. DOI: 10.1016/j.gpb.2012.12.002. View

16.

Dominissini D, Moshitch-Moshkovitz S, Salmon-Divon M, Amariglio N, Rechavi G . Transcriptome-wide mapping of N(6)-methyladenosine by m(6)A-seq based on immunocapturing and massively parallel sequencing. Nat Protoc. 2013; 8(1):176-89. DOI: 10.1038/nprot.2012.148. View

17.

Anderson S, Kramer M, Gosai S, Yu X, Vandivier L, Nelson A . N-Methyladenosine Inhibits Local Ribonucleolytic Cleavage to Stabilize mRNAs in Arabidopsis. Cell Rep. 2018; 25(5):1146-1157.e3. DOI: 10.1016/j.celrep.2018.10.020. View

18.

Cui X, Zhang L, Meng J, Rao M, Chen Y, Huang Y . MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-Seq Data. IEEE/ACM Trans Comput Biol Bioinform. 2018; 15(2):526-534. DOI: 10.1109/TCBB.2015.2403355. View

19.

Wang Z, Tang K, Zhang D, Wan Y, Wen Y, Lu Q . High-throughput m6A-seq reveals RNA m6A methylation patterns in the chloroplast and mitochondria transcriptomes of Arabidopsis thaliana. PLoS One. 2017; 12(11):e0185612. PMC: 5683568. DOI: 10.1371/journal.pone.0185612. View

20.

Pertea M, Pertea G, Antonescu C, Chang T, Mendell J, Salzberg S . StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015; 33(3):290-5. PMC: 4643835. DOI: 10.1038/nbt.3122. View