Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/845560

Global transcriptome analysis reveals circadian control of splicing events in Arabidopsis thaliana

Romanowski, A.·Schlaen, R. G.·Perez-Santangelo, S.·Mancini, E.·Yanovsky, M. J.
View original source ↗Export metadata ↓

Abstract

O_LIThe circadian clock of Arabidopsis thaliana controls many physiological and molecular processes, allowing plants to anticipate daily changes in their environment. However, developing a detailed understanding of how oscillations in mRNA levels are connected to oscillations in post-transcriptional processes, such as splicing, has remained a challenge. C_LIO_LIHere we applied a combined approach using deep transcriptome sequencing and bioinformatics tools to identify novel circadian regulated genes and splicing events. C_LIO_LIUsing a stringent approach, we identified 300 intron retention, 8 exon skipping, 79 alternative 3 splice site usage, 48 alternative 5 splice site usage, and 350 multiple (more than one event type) annotated events under circadian regulation. We also found 7 and 721 novel alternative exonic and intronic events. Depletion of the circadian regulated splicing factor AtSPF30 homolog, resulted in the disruption of a subset of clock controlled splicing events. C_LIO_LIAltogether, our global circadian RNA-seq coupled with an in silico, event centred, splicing analysis tool offers a new approach for studying the interplay between the circadian clock and the splicing machinery at a global scale. The identification of many circadian regulated splicing events broadens our current understanding of the level of control that the circadian clock has over this posttranscriptional regulatory layer. C_LI

Explore related subjects

plant biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Romanowski, A., Schlaen, R. G., Perez-Santangelo, S., Mancini, E., Yanovsky, M. J.. 2019-11-17. Global transcriptome analysis reveals circadian control of splicing events in Arabidopsis thaliana. https://doi.org/10.1101/845560

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

In-cell structural analysis reveals a distinctive chloroplast ribosome in Chlamydomonas reinhardtii

Chloroplast ribosomes synthesize plastid-encoded components of photosynthetic machinery, yet their structure and organization remain poorly understood. We combined cryo-focused ion beam milling, cryo-electron tomography and subtomogram averaging to determine native chloroplast ribosomes in Chlamydomonas reinhardtii. The 4.4-4.9 [A] structure revealed a large arch-like extension on the small subunit (SSU). Comparisons with bacterial and plant chloroplast ribosomes, supported by proteomics, AlphaFold3 predictions and a recent atomic model, indicate that the arch is formed by insertions and extensions in SSU proteins. Classification resolved active, thylakoid-associated ribosomes with density adjacent to the nascent peptide exit and an arch-moved state enriched among thylakoid-associated particles, with coordinated displacement of the arch and beak. Phylogenetic analysis revealed an evolutionary mosaic: the uS3c insertion is broadly distributed across Chlorophyceae, whereas the uS2c insertion, uS5c and PSRP7 are concentrated in Chlamydomonadales, with PSRP7 also in Sphaeropleales. Nuclear-encoded components were recruited stepwise onto a plastid-encoded scaffold, with all four under comparable purifying selection. These findings link a lineage-specific SSU extension to ribosome dynamics, thylakoid association and evolution, highlighting the value of in-cell structural analysis.

plant biology↗
bioRxiv2026

Implementation and calibration of the Vaganov-Shashkin model in the virtualRings R package

Process-based tree growth models provide a mechanistic framework for investigating how climate conditions regulate tree growth across daily to annual time scales. Yet, their broader application across species and environments is constrained by the limited accessibility in open-source environments and the difficulty of estimating physiological parameters that are rarely measured directly. Here, we present virtualRings, a new R package integrating the Vaganov-Shashkin model (VSM) and the RINGS3 models, and focus on the implementation and calibration of VSM. Using tree-ring width observations from seven Northern Hemisphere sites across various environmental conditions, we compared the traditional bootstrap-based calibration approach with the Covariance Matrix Adaptation Evolution Strategy (CMA-ES). CMA-ES improved agreement between simulated and observed radial tree growth and provided an efficient approach for model parameter estimation. We further evaluated practical CMA-ES settings to balance computational cost and performance and discussed its potential limitations. The virtualRings package provides an open and reproducible platform for tree growth simulation, facilitating the application of important process-based models across species and environments and the investigation of how temperature and moisture constraints regulate daily tree-ring formation across spatial and temporal scales.

plant biology↗
bioRxiv2026

Timing of transient darkness shapes carbon-nitrogen metabolism and sugar signaling in sugarcane

Fluctuating light is common in field environments. Yet, the mechanisms by which C4 crops coordinate carbon and nitrogen metabolism during short-term carbon deprivation remain poorly understood. Here, we imposed transient darkness at different phases of the diel cycle to assess how the timing of light loss affects photosynthesis, carbohydrate turnover, amino acid dynamics, and sugar-sensing pathways in commercial sugarcane leaves. Early-day darkness significantly impaired photosynthetic induction and revealed a temporal disconnect between stomatal and metabolic limitations, whereas midday and late-day treatments caused temporary, time-specific disruptions in carbon assimilation. These shifts altered the balance between sucrose preservation and catabolic mobilization, leading to treatment-dependent changes in starch reserves and free amino acids. Core circadian components largely maintained their phase relationships, but their amplitudes varied across treatments, consistent with partial decoupling from carbon status. Darkness also reorganized energy signaling, with SnRK1 and DIN6 responses associated with greater declines in sucrose. Notably, trehalose-pathway transcripts showed marked changes in network connectivity, with ScTPSIIG consistently emerging as a highly connected candidate associated with photosynthetic performance, water-use traits, sugar sensing, and amino acid metabolism. Overall, these results indicate that the timing of carbon limitation and residual sucrose availability shape distinct metabolic responses, while trehalose metabolism provides a candidate regulatory layer coordinating carbon-nitrogen adjustment during the diel cycle, highlighting class II TPS proteins as targets for functional investigation of metabolic resilience in sugarcane.

plant biology↗