Cap‐binding complex assists RNA polymerase II transcription in plant salt stress response

Abstract

Adaptive response to stress involves an extensive reprogramming of gene expression. Under stressful conditions, the induction of efficient changes in messenger RNA (mRNA) production is crucial for maximized plant survival. Transcription and pre‐mRNA processing are two closely related steps in mRNA biogenesis, yet how they are controlled in plant stress response remains elusive. Here, we show that the Arabidopsis nuclear cap‐binding complex (CBC) component CBP20 directly interacts with ELF7, a subunit of the transcription elongation factor RNA Pol II‐associated factor 1 complex (PAF1c) to promote RNA Pol II transcription in plant response to salt stress. CBP20 and ELF7 coregulate the expression of a large number of genes including those crucial for salt tolerance. Both CBP20 and ELF7 are required for enhanced RNA Pol II elongation at salt‐activated genes. Though CBP20 also regulates intron splicing, this function is largely independent of ELF7. Our study reveals the function of an RNA processing regulator CBC in assisting efficient RNA Pol II transcription and pinpoints the complex roles of CBC on mRNA production in plant salt stress resistance.

Coordinated histone variant H2A.Z eviction and H3.3 deposition control plant thermomorphogenesis

“…Arabidopsis thaliana ino80‐5 (Zhang et al ., 2015), elf7‐3 , elf8‐1 (He et al ., 2004), h3.3kd (Wollmann et al ., 2012), hira‐1 (Nie et al ., 2014), asf1a;asf1b (Zhu et al ., 2011), HTR5‐GFP (Wollmann et al ., 2012), and ELF7‐Myc (Zhang et al ., 2022) were reported previously. In the h2a.z mutant, the expression of two of the three H2A.Z coding genes HTA8 and HTA11 was not detected, while another gene HTA9 was expressed at lower levels compared with wild‐type (WT; Coleman‐Derr & Zilberman, 2012).…”

“…It consists of several evolutionarily conserved components including EARLY FLOWERING7 (ELF7)/VERNALIZATION INDEPENDENCE2 (VIP2), VIP3, VIP4, VIP5, ELF8/VIP6, and CDC73, which are homologs of the yeast Paf1, Ski8, Leo1, Rtf1, Ctr1, and Cdc73, respectively (He et al ., 2004; Oh et al ., 2004; Yu & Michaels, 2010). We recently reported that PAF1c facilitates enhanced RNA Pol II elongation at salt‐responsive genes (Zhang et al ., 2022).…”

A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning-expressed responses

“…Based on our synthetic data, spike-in normalization provides more accurate results, especially in cases where global transcription and proportional shares of the RNA pool are affected by experimental conditions. Several environmental changes have been shown to have effects on global transcription in plants (Branco-Price et al 2005; Szádeczky-Kardoss et al 2022; Rymen et al 2007; T. Zhang et al 2012; H. Zhang et al 2022; Koiwa 2006; Thatcher et al 2018). Although artificial spike-in controls have been used in microarray and some RNA-Seq data, their application in plant RNA-Seq data has been relatively limited.…”

Elongation factor 1 is a component of the Arabidopsis RNA polymerase II elongation complex and associates with a subset of transcribed genes

“…The observation that the elf1‐1 mutation does not cause significant growth defects, resembles the situation with tfIIs mutant plants that also grow similar to wild‐type under standard conditions (Grasser et al ., 2009), but exhibit a striking sensitivity when exposed to elevated temperatures (Szádeczky‐Kardoss et al ., 2022). Moreover, Arabidopsis plants defective in PAF1C subunits display reduced tolerance to increased salt concentrations and are affected in the response to mechanical stimulation (Jensen et al ., 2017; Obermeyer et al ., 2022; Zhang et al ., 2022). Likewise, expression of ELF1 may prove relevant under certain environmental conditions, since ELF1 associates preferentially with genes that are responsive to biotic and abiotic stress responses.…”