[Shu-Hsing Wu] Splicing variants constitutes new regulators in de-etiolation

Light is a crucial environmental signal ensuring a successful growth and development of a young plant seedling. Light triggers multiple layers of gene expression regulation in plants to produce RNAs and proteins for autotrophic growth. The advances of next-generation sequencing have enabled the detection of multiple transcript variants from one single gene, but not the actual configurations of the transcript variants, such as the transcription start sites, splicing site selections and polyadenylation sites etc. By integrating cDNA normalization and single-molecule real-time (SMRT) long-read sequencing, Shu-Hsing Wu’s team has reported a unprecedent repertoire of full-length (FL) transcriptomes in developing young seedlings. Greater than 30,000 gene models from ~16,500 loci were detected, including ~12,000 new splicing models and ~700 new genes. Among the light-regulated transcription factor genes, intron-retained variants for 2 BBX transcription factor genes were experimentally confirmed to be biologically functional by working synergically or antagonistically with their annotated cognates. This report provides a comprehensive portrait of full-length transcripts, offering opportunities to improve the genome annotation and to address the biological relevance of the splicing variants in de-etiolating seedlings.

Huang CK, Lin WD and Wu SH* (2022) An improved repertoire of splicing variants and their potential roles in Arabidopsis photomorphogenic development. Genome Biol 23:50

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02620-2