Biology subjects

Lin, W.-D.

Publications and source records attributed to Lin, W.-D..

5 recordsLinked to original sources

bioRxiv2025

Next-Generation Mapping of the ACINUS-Mediated Alternative Splicing Machinery and Its Regulation by O-glycosylation in Arabidopsis

Alternative splicing (AS) is a key mechanism of gene regulation, but the full repertoire of proteins involved and the regulatory mechanisms governing this process remain poorly understood. Using TurboID-based proximity labeling coupled with mass spectrometry (PL-MS), we comprehensively mapped the Arabidopsis AS machinery, focusing on the evolutionarily conserved splicing factor ACINUS, its paralog PININ, and the stable interactor SR45. We identified 298 high-confidence components, including both established and novel interactors, providing strong evidence that alternative splicing is coupled to transcription and that multiple RNA processing steps occur simultaneously in plants. Bioinformatic analysis reveals high redundancy, conserved mechanisms, and unique plant-specific features. Selected known and novel interactors were validated by AS readouts and phenotypic analysis, which also revealed a coordinated influence on splicing. Furthermore, a systematic evaluation of O-glycosylation double mutants revealed that SECRET AGENT (O-GlcNAc transferase) and SPINDLY (O-fucose transferase) modulate AS through both ACINUS-dependent and -independent pathways. Our results reveal the conserved as well as plant-specific AS regulatory network and highlight the global role of sugar modification in RNA processing.

plant biology↗

bioRxiv2024

Identification and functional categorization of the most stably and most variably expressed genes and retained introns in Arabidopsis thaliana seedlings

We used a large, uniform, RNA-seq dataset to investigate the stability of gene expression and intron retention in Arabidopsis thaliana seedlings. Functional classification of the most stably and most variably expressed genes was determined by GO enrichment analyses. Many variably expressed genes encoded proteins involved in photosynthesis and chloroplast structure, likely reflecting their sensitivity to changeable light intensities, and in stress responses, which allow plants to cope with environmental challenges. As revealed by GO enrichment analysis, the most stably expressed genes were involved in protein, lipid and vesicle trafficking, suggesting that fluctuations in expression of these genes are suboptimal for normal seedling development. GO analyses of genes containing either usually retained or usually spliced introns revealed no consistent enrichments for any specific functional categories. However, highly retained introns were often located in the first or last position, which may contain 5 and 3 UTRs necessary for transcriptional regulation and mRNA transport and stability. Conversely, usually spliced introns were more frequently located in internal portions of pre-mRNAs, indicating that reliable splicing in coding regions is needed to prevent the formation of premature stop codons. The large RNA-seq dataset we generated can be useful for investigating additional aspects of gene expression and pre-mRNA splicing in Arabidopsis seedlings and sets a precedent for future large scale transcriptome analyses.

plant biology↗

bioRxiv2023

Transcriptome and translatome comparison of tissues from Arabidopsis thaliana

Translation is one of the multiple complementary steps that orchestrates gene activity. In contrast to the straightforwardness of transcriptional surveys, genome-wide profiles of the translational landscape of plant cells remain technically challenging and are less well explored. Protein-coding genes are expressed at a variable degree of efficiency, resulting in pronounced discordance among the regulatory levels that govern gene activity. Ribo-Seq provides an extremely useful tool for estimating translation efficiency, but limited data sets are available for plants. Here, we provide comparative inventories of expressed and translated RNA populations, generated by mRNA sequencing (RNA-Seq) and ribosome footprinting (Ribo-Seq) of shoots and roots of Arabidopsis thaliana seedlings. Our data set provides information on the translational fitness of protein-coding mRNAs and lncRNAs that may aid in obtaining a comprehensive picture of the regulatory levels governing genes activity across the genome.

plant biology↗

bioRxiv2023

Multifaceted roles of rice ABA/stress-induced intrinsically disordered proteins in augmenting drought resistance

Water deficit stress causes devastating loss of crop yield worldwide. Improving crop drought resistance has become an urgent issue. Here we report that a group of abscisic acid (ABA)/drought stress-induced monocot-specific, intrinsically disordered, and highly proline-rich proteins, REPETITIVE PROLINE-RICH PROTEINS (RePRPs), play pivotal roles in drought resistance in rice seedlings. Rice ectopically expressing RePRPs outlived wild-type rice under extreme drought conditions primarily due to two underlying mechanisms. First, RePRP reduces water loss by decreasing stomata conductance in shoot. In addition, RePRP overexpression enhances the levels of extracellular water barriers such as lignin and suberin, primarily in the root vascular bundle. Several groups of genes involved in lignin biosynthesis, especially the wall-bound peroxidase responsible for the final assembly of the lignin network, were induced by RePRP. Second, overexpression of RePRP leads to lowered root osmotic potential. Root cell osmotic pressure was more negative in rice plants overexpressing RePRP2 than wild-type plants, and the concentration of a key osmolyte, proline, was enhanced. Furthermore, the protein levels of two aquaporins that are important for drought stress tolerance were elevated. Hence, ABA/stress-induced RePRP expression leads to several beneficial traits of drought resistance, including lower water loss rate upon dehydration and higher root water use efficiency under drought conditions. This group of unique stress proteins may be an important target for technology development in enhancing drought stress resistance in cereals.

plant biology↗

bioRxiv2018

Phosphoproteomics of Highly ABA-Induced1 identifies AT Hook Like10 phosphorylation required for growth regulation during stress

The Clade A protein phosphatase 2C Highly ABA-Induced 1 (HAI1) plays an important role in stress signaling yet little information is available on HAI1-regulated phosphoproteins. Quantitative phosphoproteomics identified phosphopeptides of increased abundance in hai1-2 in unstressed plants and in plants exposed to low water potential (drought) stress. The identity and localization of the phosphoproteins as well as enrichment of specific phosphorylation motifs indicated that these phosphorylation sites may be regulated directly by HAI1 or by HAI1-regulated kinases including Mitogen-Activated Protein Kinases (MPKs), Sucrose-non fermenting Related Kinase 2 (SnRK2s) or Casein Kinases. One of the phosphosites putatively regulated by HAI1 was S313/S314 of AT Hook-Like10 (AHL10), a DNA binding protein of unclear function. HAI1 could directly dephosphorylate AHL10 in vitro and the level of HAI1 expression affected the abundance of phosphorylated AHL10 in vivo. AHL10 S314 phosphorylation was critical for restriction of plant growth under low water potential stress and for regulation of Jasmonic Acid and Auxin-related gene expression as well as expression of developmental regulators including Shootmeristemless (STM). These genes were also mis-regulated in hai1-2. AHL10 S314 phosphorylation was required for AHL10 complexes to form foci within the nucleoplasm, suggesting that S314 phosphorylation may control AHL10 association with the nuclear matrix or with other transcriptional regulators. These data identify a set of HAI1-affected phosphorylation sites, show that HAI1-regulated phosphorylation of AHL10 S314 controls AHL10 function and localization and also indicate that HAI1-AHL10 signaling coordinates growth with stress and defense responses.

plant biology↗