Phytochrome Coordinates with a hnRNP to Regulate Alternative Splicing via an Exonic Splicing Silencer

Lin, Bou-Yun; Shih, Chueh-Ju; Hsieh, Hwey‐Lian; Chen, Hsiu-Chen; Tu, Shih-Long

doi:10.1104/pp.19.00289

Cited by 29 publications

(21 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These target genes include PIF3, whereby greater levels of P FR PHYB increased the frequency of an intron retention event in this gene, disrupting the translated protein's function [24]. In the moss Physcomitrella patens, the phytochrome protein PpPHY4 interacts directly with a splicing regulator to mediate AS in response to light [25]. Previously, the splicing factor RRC was found to mediate phytochrome response in Arabidopsis, suggesting this mechanism may be conserved in angiosperms [26].…”

Section: Introductionmentioning

confidence: 99%

Effect of phyB and phyC loss-of-function mutations on the wheat transcriptome under short and long day photoperiods

et al. 2020

View full text Add to dashboard Cite

Background: Photoperiod signals provide important cues by which plants regulate their growth and development in response to predictable seasonal changes. Phytochromes, a family of red and far-red light receptors, play critical roles in regulating flowering time in response to changing photoperiods. A previous study showed that loss-offunction mutations in either PHYB or PHYC result in large delays in heading time and in the differential regulation of a large number of genes in wheat plants grown in an inductive long day (LD) photoperiod. Results: We found that under non-inductive short-day (SD) photoperiods, phyB-null and phyC-null mutants were taller, had a reduced number of tillers, longer and wider leaves, and headed later than wild-type (WT) plants. The delay in heading between WT and phy mutants was greater in LD than in SD, confirming the importance of PHYB and PHYC in accelerating heading date in LDs. Both mutants flowered earlier in SD than LD, the inverse response to that of WT plants. In both SD and LD photoperiods, PHYB regulated more genes than PHYC. We identified subsets of differentially expressed and alternatively spliced genes that were specifically regulated by PHYB and PHYC in either SD or LD photoperiods, and a smaller set of genes that were regulated in both photoperiods. We found that photoperiod had a contrasting effect on transcript levels of the flowering promoting genes VRN-A1 and PPD-B1 in phyB and phyC mutants compared to the WT. Conclusions: Our study confirms the major role of both PHYB and PHYC in flowering promotion in LD conditions. Transcriptome characterization revealed an unexpected reversion of the wheat LD plants into SD plants in the phyB-null and phyC-null mutants and identified flowering genes showing significant interactions between phytochromes and photoperiod that may be involved in this phenomenon. Our RNA-seq data provides insight into light signaling pathways in inductive and non-inductive photoperiods and a set of candidate genes to dissect the underlying developmental regulatory networks in wheat.

show abstract

Section: Introductionmentioning

confidence: 99%

Effect of phyB and phyC loss-of-function mutations on the wheat transcriptome under short and long day photoperiods

et al. 2020

View full text Add to dashboard Cite

show abstract

“…The mechanism of phytochrome-dependent AS appears to be through direct interaction of phyB with the pre-mRNA splicing factors REDUCED RED-LIGHT RESPONSES IN CRY1CRY2 BACKGROUND1 (RRC1) and SPLICING FACTOR FOR PHYTOCHROME SIGNALING (SFPS) [161,166,168]. In Arabidopsis, the interaction between RRC1 and phyB is light-induced but independent of the Pr/Pfr conformation of phyB [161], whereas in the moss Physcomitrella patens, interaction between PpPhy4, a phyB homolog, and the splicing regulator PphnRNP-F1 is red-lightspecific, and induces interaction of PphnRNP-F1 with other spliceosome components [170,171]. In Arabidopsis, RRC1 is itself alternatively spliced in an SFPS-dependent response to light, providing a positive feedback loop [161,164,166].…”

Section: Photoreceptor-mediated Effects On Co-transcriptional Responsesmentioning

confidence: 99%

Unique and contrasting effects of light and temperature cues on plant transcriptional programs

et al. 2020

View full text Add to dashboard Cite

Plants have adapted to tolerate and survive constantly changing environmental conditions by reprogramming gene expression in response to stress or to drive developmental transitions. Among the many signals that plants perceive, light and temperature are of particular interest due to their intensely fluctuating nature which is combined with a long-term seasonal trend. Whereas specific receptors are key in the light-sensing mechanism, the identity of plant thermosensors for high and low temperatures remains far from fully addressed. This review aims at discussing common as well as divergent characteristics of gene expression regulation in plants, controlled by light and temperature. Light and temperature signaling control the abundance of specific transcription factors, as well as the dynamics of co-transcriptional processes such as RNA polymerase elongation rate and alternative splicing patterns. Additionally, sensing both types of cues modulates gene expression by altering the chromatin landscape and through the induction of long non-coding RNAs (lncRNAs). However, while light sensing is channeled through dedicated receptors, temperature can broadly affect chemical reactions inside plant cells. Thus, direct thermal modifications of the transcriptional machinery add another level of complexity to plant transcriptional regulation. Besides the rapid transcriptome changes that follow perception of environmental signals, plant developmental transitions and acquisition of stress tolerance depend on long-term maintenance of transcriptional states (active or silenced genes). Thus, the rapid transcriptional response to the signal (Phase I) can be distinguished from the long-term memory of the acquired transcriptional state (Phase IIremembering the signal). In this review we discuss recent advances in light and temperature signal perception, integration and memory in Arabidopsis thaliana, focusing on transcriptional regulation and highlighting the contrasting and unique features of each type of cue in the process.

show abstract

“…Environmental cues influence alternative splicing. Lin et al (2020) show in this issue that PHYTOCHROME4 (PpPHY4), a sensor of red and far-red light and regulator of photosynthetic capacity, interacts with a splicing regulator classified as an hnRNP in the moss Physcomitrella patens to increase its abundance. This PHY4 and PphnRNP-F1 interaction cooperatively regulates 70% of the intron retention events promoted by red light.…”

Section: Splicingmentioning

confidence: 99%

The Dynamic Kaleidoscope of RNA Biology in Plants

2020

View full text Add to dashboard Cite

ACKNOWLEDGMENTSWe thank all of the authors, reviewers, and editors, especially Sarah M. Assmann, who contributed to this Focus Issue. We thank Thanin Chantarachot and Sarah M. Assmann for comments on this editorial. LITERATURE CITEDArribas-Hernández L, Brodersen P (2020) Occurrence and functions of m 6 A and other covalent modifications in plant mRNA. Plant Physiol 182: 79-96 Bai B, van der Horst S, Cordewener J, America T, Hanson J, Bentsink L (2020) Seed stored mRNAs that are specifically associated to monosome are translationally regulated during germination. Plant Physiol 182: 378-392 Beck J, Lohscheider JN, Albert S, Andersson U, Mendgen KW, Rojas-Stütz MC, Adamska I, Funck D (2017) Small one-helix proteins are essential for photosynthesis in Arabidopsis. Front Plant Sci 8: 7 Bentley DL (2005) Rules of engagement: Co-transcriptional recruitment of pre-mRNA processing factors. Curr Opin Cell Biol 17: 251-256 Borges F, Martienssen RA (2015) The expanding world of small RNAs in plants. Nat Rev Mol Cell Biol 16: 727-741 Browning KS, Bailey-Serres J (2015) Mechanism of cytoplasmic mRNA translation. The Arabidopsis Book 13: e0176 Cao Y, Ma L (2019) To splice or to transcribe: SKIP-mediated environmental fitness and development in plants. Front Plant Sci 10: 1222 Chantarachot T, Bailey-Serres J (2018) Polysomes, stress granules, and processing bodies: A dynamic triumvirate controlling cytoplasmic mRNA fate and function. Plant Physiol 176: 254-269 Chaudhary S, Khokhar W, Jabre I, Reddy ASN, Byrne LJ, Wilson CM, Syed NH (2019) Alternative splicing and protein diversity: Plants versus animals. Front Plant Sci 10: 708 Crisp PA, Hammond R, Zhou P, Vaillancourt B, Lipzen AM, Daum C, Barry KW, de Leon N, Buell CR, Kaeppler SM, et al (2020) Variation and inheritance of small RNAs in maize inbreds and F1 hybrids. Plant

show abstract

Phytochrome Coordinates with a hnRNP to Regulate Alternative Splicing via an Exonic Splicing Silencer

Cited by 29 publications

References 54 publications

Effect of phyB and phyC loss-of-function mutations on the wheat transcriptome under short and long day photoperiods

Effect of phyB and phyC loss-of-function mutations on the wheat transcriptome under short and long day photoperiods

Unique and contrasting effects of light and temperature cues on plant transcriptional programs

The Dynamic Kaleidoscope of RNA Biology in Plants

Contact Info

Product

Resources

About