Transcriptional and Post-Transcriptional Regulation and Transcriptional Memory of Chromatin Regulators in Response to Low Temperature

Abstract

Chromatin regulation ensures stable repression of stress-inducible genes under nonstress conditions and transcriptional activation and memory of stress-related genes after stress exposure. However, there is only limited knowledge on how chromatin genes are regulated at the transcriptional and post-transcriptional level upon stress exposure and relief from stress. We reveal that the repressive modification histone H3 lysine 27 trimethylation (H3K27me3) targets genes which are quickly activated upon cold exposure, however, H3K27me3 is not necessarily lost during a longer time in the cold. In addition, we have setup a quantitative reverse transcription polymerase chain reactionbased platform for high-throughput transcriptional profiling of a large set of chromatin genes. We find that the expression of many of these genes is regulated by cold. In addition, we reveal an induction of several DNA and histone demethylase genes and certain histone variants after plants have been shifted back to ambient temperature (deacclimation), suggesting a role in the memory of cold acclimation. We also re-analyze large scale transcriptomic datasets for transcriptional regulation and alternative splicing (AS) of chromatin genes, uncovering an unexpected level of regulation of these genes, particularly at the splicing level. This includes several vernalization regulating genes whose AS may result in cold-regulated protein diversity. Overall, we provide a profiling platform for the analysis of chromatin regulatory genes and integrative analyses of their regulation, suggesting a dynamic regulation of key chromatin genes in response to low temperature stress.

The Crosstalk Between Epigenetic Mechanisms and Alternative RNA Processing Regulation

“…quickly activated under cold stress and differentially expressed at the splicing level, were found to be modified by H3K27me3 in non-stress conditions (Vyse et al, 2020). These reports suggest a dynamic regulation of temperature stress-responsive genes by alternative RNA processing and histone modification.…”

“…An recent study indicated that temperature variation is memorized by chromatin via H3K36me3 modification, resulting in a specific splicing pattern, which enables a feasible adaptation to stress conditions ( Pajoro et al, 2017 ). Another study showed that genes which are quickly activated under cold stress and differentially expressed at the splicing level, were found to be modified by H3K27me3 in non-stress conditions ( Vyse et al, 2020 ). These reports suggest a dynamic regulation of temperature stress-responsive genes by alternative RNA processing and histone modification.…”

Multi-omics network-based functional annotation of unknown Arabidopsis genes

“…Several explanations can be found for the latter observation: (1) a process can be well modeled on the co-expression level, resulting in high quality functional hypotheses, which fail to be validated due to a lack of experimentally profiled protein-DNA/-protein interactions. Alternatively, several stress-related processes are known to be regulated at the post-transcriptional level by regulation of mRNA processing and/or stability (Floris et al 2009;Vyse et al 2020). Such processes are potentially difficult to validate using PDI data, as interactions where the target is a protein coding gene might be rare or non-existing.…”

Breeding for Climate Change Resilience: A Case Study of Loblolly Pine (Pinus taeda L.) in North America

“…The epigenome can be defined as all the chemical compounds that are "on or attached" to DNA and cause modification in its function without altering the sequence (Riggs et al, 1996). An increasing number of publications provide evidence of mitotically and/or meiotically heritable traits in gene function attributed to epigenetic mechanisms and associated with changes in the environmental conditions (Vyse et al, 2020). The environmental cues experienced by parent trees during the reproductive process can affect growth and adaptive traits of their progeny as a result of epigenetic changes.…”