H3K36me2 is highly correlated with m<sup>6</sup>A modifications in plants

Shim, Sangrea; Lee, Hong Gil; Lee, Hong-Woo; Seo, Pil Joon

doi:10.1111/jipb.12917

Cited by 31 publications

(17 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Indeed, previously, it was shown that salinity‐responsive m 6 A peak containing transcripts of Arabidopsis were more stable under salt stress (Anderson et al., 2018). There are other potential mechanisms leading to increased transcript abundance such as possible interactions of m 6 A writer or reader complexes with histone modifications to affect RNA transcription (Huang et al., 2009; Shim et al., 2020). Based on our data alone, it is hard to predict whether this change in mRNA abundance of the cold‐enriched m6A containing transcripts is the result of an increased stability or enhanced transcription, or a combination of both, and this needs further investigation.…”

Section: Discussionmentioning

confidence: 99%

mRNA N⁶‐methyladenosine is critical for cold tolerance in Arabidopsis

Govindan

Sharma

et al. 2022

The Plant Journal

View full text Add to dashboard Cite

Plants respond to low temperatures by altering the mRNA abundance of thousands of genes contributing to numerous physiological and metabolic processes that allow them to adapt. At the post-transcriptional level, these cold stress-responsive transcripts undergo alternative splicing, microRNA-mediated regulation and alternative polyadenylation, amongst others. Recently, m 6 A, m 5 C and other mRNA modifications that can affect the regulation and stability of RNA were discovered, thus revealing another layer of posttranscriptional regulation that plays an important role in modulating gene expression. The importance of m 6 A in plant growth and development has been appreciated, although its significance under stress conditions is still underexplored. To assess the role of m 6 A modifications during cold stress responses, methylated RNA immunoprecipitation sequencing was performed in Arabidopsis seedlings esposed to low temperature stress (4°C) for 24 h. This transcriptome-wide m 6 A analysis revealed large-scale shifts in this modification in response to low temperature stress. Because m 6 A is known to affect transcript stability/ degradation and translation, we investigated these possibilities. Interestingly, we found that cold-enriched m 6 A-containing transcripts demonstrated the largest increases in transcript abundance coupled with increased ribosome occupancy under cold stress. The significance of the m 6 A epitranscriptome on plant cold tolerance was further assessed using the mta mutant in which the major m 6 A methyltransferase gene was mutated. Compared to the wild-type, along with the differences in CBFs and COR gene expression levels, the mta mutant exhibited hypersensitivity to cold treatment as determined by primary root growth, biomass, and reactive oxygen species accumulation. Furthermore, and most importantly, both non-acclimated and cold-acclimated mta mutant demonstrated hypersensitivity to freezing tolerance. Taken together, these findings suggest a critical role for the epitranscriptome in cold tolerance of Arabidopsis.

show abstract

Section: Discussionmentioning

confidence: 99%

mRNA N⁶‐methyladenosine is critical for cold tolerance in Arabidopsis

Govindan

Sharma

et al. 2022

The Plant Journal

View full text Add to dashboard Cite

show abstract

“…m 6 A refers to the methylation of the adenosine base at the nitrogen‐6 position, which is the most prevalent internal modification of eukaryotic mRNAs (Dominissini et al, 2012, 2013; Yue et al, 2015; Arribas‐Hernandez et al, 2018). m 6 A regulates almost every aspect of mRNA processing and metabolism, of which alternative polyadenylation (APA) is an important post‐transcriptional regulatory mechanism that can generate different mRNA isoforms (Jia et al, 2011; Zheng et al, 2013; Liu et al, 2014; Ping et al, 2014; Wang et al, 2014, 2015; Shim et al, 2020). Cleavage and Polyadenylation Specificity Factor 30 (CPSF30) is a key polyadenylation factor which has two isoforms, the short one named CPSF30‐S and the longer one termed CPSF30‐L, which contains an additional YT512B Homolog (YTH) domain that is established as a m 6 A binding domain.…”

Section: Emerging Roles Of Phase Separation In Plantsmentioning

confidence: 99%

Phase separation in plants: New insights into cellular compartmentalization

Zheng

et al. 2021

JIPB

View full text Add to dashboard Cite

A fundamental challenge for cells is how to coordinate various biochemical reactions in space and time. To achieve spatiotemporal control, cells have developed organelles that are surrounded by lipid bilayer membranes. Further, membraneless compartmentalization, a process induced by dynamic physical association of biomolecules through phase transition offers another efficient mechanism for intracellular organization. While our understanding of phase separation was predominantly dependent on yeast and animal models, recent findings have provided compelling evidence for emerging roles of phase separation in plants. In this review, we first provide an overview of the current knowledge of phase separation, including its definition, biophysical principles, molecular features and regulatory mechanisms. Then we summarize plant-specific phase separation phenomena and describe their functions in plant biological processes in great detail. Moreover, we propose that phase separation is an evolutionarily conserved and efficient mechanism for cellular compartmentalization which allows for distinct metabolic processes and signaling pathways, and is especially beneficial for the sessile lifestyle of plants to quickly and efficiently respond to the changing environment.

show abstract

“…I n eukaryotic cells, histones and DNA are packed and ordered into highly structured units called nucleosomes. Nucleosomal histones are subject to multiple posttranslational modifications, such as methylation, acetylation, phosphorylation, and ubiquitination, which play critical roles in various biological processes that include transcriptional regulation, chromosome packaging, and repair of DNA damage (Bannister and Kouzarides, 2011;Zhao et al, 2019;Shim et al, 2020). Acetylation of histones occurs at specific lysine residues on their N-terminal tails and is associated with transcriptional activation (Struhl, 1998).…”

Section: Introductionmentioning

confidence: 99%

A domesticated Harbinger transposase forms a complex with HDA6 and promotes histone H3 deacetylation at genes but not TEs in Arabidopsis

Zhou

Velanis

et al. 2021

JIPB

View full text Add to dashboard Cite

In eukaryotes, histone acetylation is a major modification on histone N-terminal tails that is tightly connected to transcriptional activation. HDA6 is a histone deacetylase involved in the transcriptional regulation of genes and transposable elements (TEs) in Arabidopsis thaliana. HDA6 has been shown to participate in several complexes in plants, including a conserved SIN3 complex. Here, we uncover a novel protein complex containing HDA6, several Harbinger transposon-derived proteins (HHP1, SANT1,

show abstract

H3K36me2 is highly correlated with m⁶A modifications in plants

Cited by 31 publications

References 15 publications

mRNA N⁶‐methyladenosine is critical for cold tolerance in Arabidopsis

mRNA N⁶‐methyladenosine is critical for cold tolerance in Arabidopsis

Phase separation in plants: New insights into cellular compartmentalization

A domesticated Harbinger transposase forms a complex with HDA6 and promotes histone H3 deacetylation at genes but not TEs in Arabidopsis

Contact Info

Product

Resources

About

H3K36me2 is highly correlated with m6A modifications in plants

Cited by 31 publications

References 15 publications

mRNA N6‐methyladenosine is critical for cold tolerance in Arabidopsis

mRNA N6‐methyladenosine is critical for cold tolerance in Arabidopsis

Phase separation in plants: New insights into cellular compartmentalization

A domesticated Harbinger transposase forms a complex with HDA6 and promotes histone H3 deacetylation at genes but not TEs in Arabidopsis

Contact Info

Product

Resources

About

H3K36me2 is highly correlated with m⁶A modifications in plants

mRNA N⁶‐methyladenosine is critical for cold tolerance in Arabidopsis

mRNA N⁶‐methyladenosine is critical for cold tolerance in Arabidopsis