A chromatin-dependent mechanism regulates gene expression at the core of the<i>Arabidopsis</i>circadian clock

Malapeira, Jordi; Más, Paloma Díaz

doi:10.4161/psb.24079

Cited by 6 publications

(4 citation statements)

References 34 publications

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“…Additionally, the structure of pre-mRNAs also regulates splicing significantly (70,71). In both mammals and plants, chromatin, which carries differential DNA methylation and multiple histone modifications, may mediate pol II processivity to influence splicing outcomes (35,72–79). Hence, splicing regulation is mediated through a complex cellular network referred to as the ‘splicing code’ that fine-tunes gene expression in response to different conditions (80,81).…”

Section: Overview Of Pre-mrna Splicingmentioning

confidence: 99%

Does co-transcriptional regulation of alternative splicing mediate plant stress responses?

Jabre

Reddy

Kalyna

et al. 2019

Nucleic Acids Research

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Plants display exquisite control over gene expression to elicit appropriate responses under normal and stress conditions. Alternative splicing (AS) of pre-mRNAs, a process that generates two or more transcripts from multi-exon genes, adds another layer of regulation to fine-tune condition-specific gene expression in animals and plants. However, exactly how plants control splice isoform ratios and the timing of this regulation in response to environmental signals remains elusive. In mammals, recent evidence indicate that epigenetic and epitranscriptome changes, such as DNA methylation, chromatin modifications and RNA methylation, regulate RNA polymerase II processivity, co-transcriptional splicing, and stability and translation efficiency of splice isoforms. In plants, the role of epigenetic modifications in regulating transcription rate and mRNA abundance under stress is beginning to emerge. However, the mechanisms by which epigenetic and epitranscriptomic modifications regulate AS and translation efficiency require further research. Dynamic changes in the chromatin landscape in response to stress may provide a scaffold around which gene expression, AS and translation are orchestrated. Finally, we discuss CRISPR/Cas-based strategies for engineering chromatin architecture to manipulate AS patterns (or splice isoforms levels) to obtain insight into the epigenetic regulation of AS.

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Section: Overview Of Pre-mrna Splicingmentioning

confidence: 99%

Does co-transcriptional regulation of alternative splicing mediate plant stress responses?

Jabre

Reddy

Kalyna

et al. 2019

Nucleic Acids Research

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“…Both regulatory and non-regulatory mineral homeostasis genes including Ysl , Fro 2, Nas , Hma , bHlH 39, Irt 1, Ferritin , and many others follow light-dark cycles [ 2 ]. Most interesting, the histone methyltransferase Sdg 2 which regulates the core clock components [ 19 ] was induced by iron and zinc (see S4 File for accession numbers). Disclosed by expression changes in the oscillator master-regulator genes ( S2 Fig ), SDG2 introduces a signaling pathway by which the metals can govern the plant circadian rhythm.…”

Section: Resultsmentioning

confidence: 99%

Deciphering Mineral Homeostasis in Barley Seed Transfer Cells at Transcriptional Level

2015

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In addition to the micronutrient inadequacy of staple crops for optimal human nutrition, a global downtrend in crop-quality has emerged from intensive breeding for yield. This trend will be aggravated by elevated levels of the greenhouse gas carbon dioxide. Therefore, crop biofortification is inevitable to ensure a sustainable supply of minerals to the large part of human population who is dietary dependent on staple crops. This requires a thorough understanding of plant-mineral interactions due to the complexity of mineral homeostasis. Employing RNA sequencing, we here communicate transfer cell specific effects of excess iron and zinc during grain filling in our model crop plant barley. Responding to alterations in mineral contents, we found a long range of different genes and transcripts. Among them, it is worth to highlight the auxin and ethylene signaling factors Arfs, Abcbs, Cand1, Hps4, Hac1, Ecr1, and Ctr1, diurnal fluctuation components Sdg2, Imb1, Lip1, and PhyC, retroelements, sulfur homeostasis components Amp1, Hmt3, Eil3, and Vip1, mineral trafficking components Med16, Cnnm4, Aha2, Clpc1, and Pcbps, and vacuole organization factors Ymr155W, RabG3F, Vps4, and Cbl3. Our analysis introduces new interactors and signifies a broad spectrum of regulatory levels from chromatin remodeling to intracellular protein sorting mechanisms active in the plant mineral homeostasis. The results highlight the importance of storage proteins in metal ion toxicity-resistance and chelation. Interestingly, the protein sorting and recycling factors Exoc7, Cdc1, Sec23A, and Rab11A contributed to the response as well as the polar distributors of metal-transporters ensuring the directional flow of minerals. Alternative isoform switching was found important for plant adaptation and occurred among transcripts coding for identical proteins as well as transcripts coding for protein isoforms. We also identified differences in the alternative-isoform preference between the treatments, indicating metal-affinity shifts among isoforms of metal transporters. Most important, we found the zinc treatment to impair both photosynthesis and respiration. A wide range of transcriptional changes including stress-related genes and negative feedback loops emphasize the importance to withhold mineral contents below certain cellular levels which otherwise might lead to agronomical impeding side-effects. By illustrating new mechanisms, genes, and transcripts, this report provides a solid platform towards understanding the complex network of plant mineral homeostasis.

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“…PIF4, an integral component of clock-associated thermomorphogenesis in plants, also shows evidence of epigenetic regulation (Quint et al 2016). Histone H3 acetylation and H3K4 trimethylation (H3K4me3) serve as key regulators of the clock oscillator in plants (Malapeira et al 2012;Malapeira and Mas 2013). These chromatin modifications can work coordinately to regulate rhythmic changes in transcriptional activity, but also to influence transgenerational behaviors.…”

Section: )mentioning

confidence: 99%

Many Facets of Dynamic Plasticity in Plants

Yang

Mackenzie

2019

Cold Spring Harb Perspect Biol

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The evolutionary processes that transitioned plants to land-based habitats also incorporated a multiplicity of strategies to enhance resilience to the greater environmental variation encountered on land. The sensing of light, its quality, quantity, and duration, is central to plant survival and, as such, serves as a central network hub. Similarly, plants as sessile organisms that can encounter isolation must continually assess their reproductive options, requiring plasticity in propagation by self-and cross-pollination or asexual strategies. Irregular fluctuations and intermittent extremes in temperature, soil fertility, and moisture conditions have given impetus to genetic specializations for network resiliency, protein neofunctionalization, and internal mechanisms to accelerate their evolution. We review some of the current advancements made in understanding plant resiliency and phenotypic plasticity mechanisms. These mechanisms incorporate unusual nuclear-cytoplasmic interactions, various transposable element (TE) activities, and epigenetic plasticity of central gene networks that are broadly pleiotropic to influence resiliency phenotypes.

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A chromatin-dependent mechanism regulates gene expression at the core of theArabidopsiscircadian clock

Cited by 6 publications

References 34 publications

Does co-transcriptional regulation of alternative splicing mediate plant stress responses?

Does co-transcriptional regulation of alternative splicing mediate plant stress responses?

Deciphering Mineral Homeostasis in Barley Seed Transfer Cells at Transcriptional Level

Many Facets of Dynamic Plasticity in Plants

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