Freese, N. | bioRxiv Science

bioRxiv2020

AINTEGUMENTA and AINTEGUMENTA-LIKE6 directly regulate floral homeotic and growth genes in young flowers

Arabidopsis flower primordia give rise to floral organ primordia in stereotypical positions within four concentric whorls. Floral organ primordia in each whorl undergo distinct developmental programs to become one of four organ types (sepals, petals, stamens, and carpels). The Arabidopsis transcription factors AINTEGUMENTA (ANT) and AINTEGUMENTA-LIKE6 (AIL6) play critical and partially overlapping roles during floral organogenesis. They are required for correct positioning of floral organ initiation, contribute to the specification of floral organ identity, and regulate the growth and morphogenesis of developing floral organs. To gain insight into the molecular means by which ANT and AIL6 contribute to floral organogenesis, we identified the genome-wide binding sites of both ANT and AIL6 in stage 3 flower primordia, the developmental stage at which sepal primordia become visible and class B and C floral homeotic genes are first expressed. AIL6 binds to a subset of ANT sites, suggesting that AIL6 regulates some but not all of the same target genes as ANT. ANT and AIL6 binding sites are associated with genes involved in many biological processes related to meristem and flower organ development. Comparison of genes associated with both ANT and AIL6 ChIP-Seq peaks and those differentially expressed after perturbation of ANT or AIL6 activity identified likely direct targets of ANT and AIL6 regulation. These include the floral homeotic genes APETALA3 (AP3) and AGAMOUS (AG) and four growth regulatory genes: BIG BROTHER (BB), ROTUNDIFOLIA3 (ROT3), ANGUSTIFOLIA3/GRF INTERACTING FACTOR (AN3/GIF1), and XYLOGLUCAN ENDOTRANSGLUCOLSYLASE/HYDROLASE9 (XTH9). One Sentence SummaryThe transcription factors ANT and AIL6 directly regulate genes involved in different aspects of flower development including genes that specify floral organ identity and those that regulate growth.

plant biology↗

bioRxiv2018

Cytokinin treatment of rice induces minimal effect on differential splicing compared to splicing between tissues

Alternatively spliced genes produce multiple spliced isoforms, called transcript variants. In differential alternative splicing, the relative abundance of transcript variants differs across sample types. Differential alternative splicing is common in animal systems and influences cellular development in many processes, but its extent and significance is not as well known in plants. To investigate alternative splicing in plants, we examined rice seedling RNA-Seq data that included approximately 40 million sequence alignments per library, three libraries per sample type, and four sample types: roots and shoots, each treated with exogenous cytokinin delivered hydroponically, plus mock-treated controls. Cytokinin treatment triggered expression changes in thousands of genes, but had minimal effect on alternative splicing. However, there were many splicing differences between roots and shoots. Analysis of a similar (but less deeply sequenced) mRNA-Seq data set from Arabidopsis showed the same pattern. Quantitative fragment analysis of reverse transcriptase-PCR products made from newly prepared rice samples confirmed nine of ten differential splicing events between rice roots and shoots. In both the Arabidopsis and rice mRNA-Seq data sets, most genes annotated as alternatively spliced had small minor variant frequencies, i.e., the less frequently observed forms were supported by fewer than 20% of informative mRNA-Seq sequences. Of splicing choices where there was more abundant support for minor forms, most alternative splicing events were located within the protein-coding sequence and also maintained the annotated reading frame. A tool for visualizing protein annotations in the context of genomic sequence (ProtAnnot) together with a genome browser (Integrated Genome Browser) were used to visualize and assess effects of differential splicing on gene function. In general, differentially spliced regions coincided with conserved regions in the encoded proteins, indicating that differential alternative splicing is likely to affect protein function between root and shoot tissue in rice.

molecular biology↗