A G(enomic)P(ositioning)S(ystem) for Plant RNAPII Transcription

Leng, Xueyuan; Thomas, Quentin; Rasmussen, Simon; Marquardt, Sebastian

doi:10.1016/j.tplants.2020.03.005

Cited by 34 publications

(34 citation statements)

References 236 publications

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“…It remains an open question whether this recruitment occurs through direct protein-protein interactions or through other proteins, e. g. components of the general transcriptional machinery. H3K4 methylation is deposited by the COMPASS complex and is required for efficient transcriptional elongation 45 – 48 . This is critical for transcriptional regulation in development and stress response in animals, where release of paused RNA Pol II into elongation is a limiting step 49 , 50 .…”

Section: Discussionmentioning

confidence: 99%

Heteromeric HSFA2/HSFA3 complexes drive transcriptional memory after heat stress in Arabidopsis

et al. 2021

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Adaptive plasticity in stress responses is a key element of plant survival strategies. For instance, moderate heat stress (HS) primes a plant to acquire thermotolerance, which allows subsequent survival of more severe HS conditions. Acquired thermotolerance is actively maintained over several days (HS memory) and involves the sustained induction of memory-related genes. Here we show that FORGETTER3/ HEAT SHOCK TRANSCRIPTION FACTOR A3 (FGT3/HSFA3) is specifically required for physiological HS memory and maintaining high memory-gene expression during the days following a HS exposure. HSFA3 mediates HS memory by direct transcriptional activation of memory-related genes after return to normal growth temperatures. HSFA3 binds HSFA2, and in vivo both proteins form heteromeric complexes with additional HSFs. Our results indicate that only complexes containing both HSFA2 and HSFA3 efficiently promote transcriptional memory by positively influencing histone H3 lysine 4 (H3K4) hyper-methylation. In summary, our work defines the major HSF complex controlling transcriptional memory and elucidates the in vivo dynamics of HSF complexes during somatic stress memory.

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Section: Discussionmentioning

confidence: 99%

Heteromeric HSFA2/HSFA3 complexes drive transcriptional memory after heat stress in Arabidopsis

et al. 2021

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“…Another layer of H3K4me complexity is its occurrence in three states (mono-, di-, and trimethylation; me1, me2 and me3, respectively). Generally, H3K4me3 and H3K4me2 are found on the first several nucleosomes of genes, while H3K4me1 is found in downstream regions within the gene bodies [10][11][12] . Our previous genetic and genomic studies in Arabidopsis thaliana (hereafter Arabidopsis) have demonstrated key roles of gene body H3K4me1 in the control of transcription; a putative H3K4me1 demethylase, LYSINE-SPECIFIC DEMETHYLASE1-LIKE2 (LDL2), mediates transcriptional silencing induced by gene body H3K9me2 13 , while a related demethylase, FLOWERING LOCUS D (FLD), coordinates convergent overlapping transcription by removing H3K4me1 14 .…”

Section: Introductionmentioning

confidence: 99%

Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation

Oya

Takáhashi

Takashima

et al. 2021

Preprint

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Mono-, di-, and trimethylation of histone H3 lysine 4 (H3K4me1/2/3) are associated with transcription, yet it remains controversial whether H3K4me1/2/3 promote or result from transcription. Our previous characterizations of Arabidopsis H3K4 demethylases suggest roles for H3K4me1 in transcription. However, the control of H3K4me1 remains unexplored in Arabidopsis, in which no methylase for H3K4me1 has been identified. Here, we identified three Arabidopsis methylases that direct H3K4me1. Analyses of their genome-wide localization using ChIP-seq and machine learning revealed that one of the enzymes cooperates with the transcription machinery, while the other two are associated with specific histone modifications and DNA sequences. Importantly, these two types of localization patterns are also found for the other H3K4 methylases in Arabidopsis and mice. These results suggest that H3K4me1/2/3 are established and maintained via interplay with transcription as well as inputs from other chromatin features, presumably enabling elaborate gene control.

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“…RNAPII elongation rate can be modulated by different actors. These can include chromatin remodelling factors [38,103], DNA topology [104,105], or RNAPII elongation factors [106]. Among these last, TFIIS -as mentioned above-, is required for correct RNAPII elongation and is needed for alternative splicing decisions in response to light [90].…”

Section: Transcription and Splicing Factors That Could Be Acting As Coupling Factorsmentioning

confidence: 99%

Light in the transcription landscape: chromatin, RNA polymerase II and splicing throughout Arabidopsis thaliana’s life cycle

et al. 2020

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Plants have a high level of developmental plasticity that allows them to respond and adapt to changes in the environment. Among the environmental cues, light controls almost every aspect of A. thaliana's life cycle, including seed maturation, seed germination, seedling de-etiolation and flowering time. Light signals induce massive reprogramming of gene expression, producing changes in RNA polymerase II transcription, alternative splicing, and chromatin state. Since splicing reactions occur mainly while transcription takes place, the regulation of RNAPII transcription has repercussions in the splicing outcomes. This cotranscriptional nature allows a functional coupling between transcription and splicing, in which properties of the splicing reactions are affected by the transcriptional process. Chromatin landscapes influence both transcription and splicing. In this review, we highlight, summarize and discuss recent progress in the field to gain a comprehensive insight on the cross-regulation between chromatin state, RNAPII transcription and splicing decisions in plants, with a special focus on light-triggered responses. We also introduce several examples of transcription and splicing factors that could be acting as coupling factors in plants. Unravelling how these connected regulatory networks operate, can help in the design of better crops with higher productivity and tolerance.

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A G(enomic)P(ositioning)S(ystem) for Plant RNAPII Transcription

Cited by 34 publications

References 236 publications

Heteromeric HSFA2/HSFA3 complexes drive transcriptional memory after heat stress in Arabidopsis

Heteromeric HSFA2/HSFA3 complexes drive transcriptional memory after heat stress in Arabidopsis

Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation

Light in the transcription landscape: chromatin, RNA polymerase II and splicing throughout Arabidopsis thaliana’s life cycle

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