Biology subjects

Spillane, C.

Publications and source records attributed to Spillane, C..

3 recordsLinked to original sources

bioRxiv2026

Cytoplasmic genomes change allelic expression bias in plant seeds independently of parental imprinting: evidence for cytonuclear regulatory epistasis in Arabidopsis thaliana

Cytoplasmic genomes play critical roles in plant cells, yet their potential contribution to regulation of the nuclear genome remains largely unexplored. Here, we examine how cytoplasmic genotype affects allelic dominance at nuclear loci by identifying allele-specific expression in hybrid plant lines in which cytoplasmic genomes have been swapped between accessions. After developing a bias-free ASE analysis pipeline based on dual pseudo-genome alignment, we determined ASE across 48 RNA-seq datasets of the model plant, Arabidopsis thaliana and distinguished between allelic bias under the control of the genotype and or the cytoplasm. Of 7,997 nuclear genes for which informative SNPs could be mapped, 2,702 displayed allelic imbalances, the great majority controlled by the nuclear background. However cytoplasmic interactions with nuclear genotype were found to regulate ASE at 24 genes. We also tested interactions with genomic imprinting, a specific form of ASE in which parental inheritance determines expression state, within seed transcriptomes: while we detected both novel and previously-reported imprinted genes, only three genes (VFB1, ANNAT3, ENODL2) exhibited both parent-of-origin bias and cytoplasm-responsiveness. This indicates that these two parental inheritance mechanisms are largely independent, with implications for maternal-cytoplasmic coadaptation theories. Interestingly, genes subject to cytoplasmic ASE were enriched in the ascorbate and aldarate metabolism pathway, with the highest ASE biases found in GAE4 and UGD3. We conclude that cytoplasmic variation can selectively alter expression of nuclear-encoded alleles and that this may represent a novel source of control of cellular energy balance and metabolic signalling pathways.

genetics↗

bioRxiv2026

A genetic network coordinated by TCP16 and LHY integrates regulation of the vegetative-reproductive phase transition in Arabidopsis thaliana

The transition to flowering in Arabidopsis thaliana is a complex process governed by many biological and environmental stimuli. Although many of the genes which regulate this process have been identified over the past 30 years, it remains unclear how these networks are integrated. In this study, we used the transcriptional responses of Col-0, Ler-1, and three mutant lines, to build a genome wide regulatory network of Arabidopsis thaliana during the flowering transition. The expression profiles of 22,810 genes across five genotypes were collected from the GEO database Series GSE57 from which we assigned flowering-time genes to different interacting modules by an adapted form of Hierarchical Complete Linkage Clustering (HCLC) after reconstruction of regulatory networks according to the Position Weight Matrix (PWM)-based method. Within these modules, we identified 77 core genes and 31 controller or driver genes. We identify two genes, LHY and, less expectedly, the transcription factor TCP16, to be topographically positioned at the regulatory hubs a nine-gene transcriptional control unit, implying they have the capacity to integrate information from across the flowering time pathways which interpret different environmental or endogenous cues during the vegetative-reproductive transition. Interrogating their behaviour across transcriptional datasets, we show that both LHY and TCP16 show transcriptional oscillations during the flowering transition, with a wavelength that varies depending on environmental conditions. We suggest that the transcriptional responses of LHY and TCP16 allow them to regulate the flow of information through the genetic networks which integrates different floral transition cues, and that genetic modelling approaches can provide new insights into the regulation of well-studied biological processes such as the flowering transition. Author summaryHow plants decide when to flower is a critical stage for completing their life cycles. It is also of key agricultural importance, as crops need to flower at the right time of year to allow efficient pollination and harvesting. Many genes are known to affect flowering time control in plants. Here, we use computational approaches to estimate how different genes interact in flowering time control in Arabidopsis, a small plant in the mustard family which is widely used for molecular studies. We use large-scale studies of how gene expression changes in different plant lines which have disrupted or adjusted flowering time to group the many genes involved in flowering into different interacting pathway, which we visualise as sets of coloured nodes controlling one another in a network. We show that two genes may have new rols in integrating information from different pathways, and discuss how their behaviour might help them to function as intregrators of biological information - including the daily oscaillations in their expression.

genetics↗

bioRxiv2019

Identification of candidate flowering and sex genes in white Guinea yam (D. rotundata Poir.) by SuperSAGE transcriptome profiling

Dioecy (distinct male and female individuals) combined with scarce to non-flowering are common features of cultivated yam (Dioscorea spp.). However, the molecular mechanisms underlying flowering and sex determination in Dioscorea are unknown. We conducted SuperSAGE transcriptome profiling of male, female and monoecious individuals to identify flowering and sex-related genes in white Guinea yam (D. rotundata). SuperSAGE analysis generated a total of 20,236 unique tags, of which 13,901 were represented by a minimum of 10 tags. Of these, 88 tags were significantly differentially expressed in male, female and monoecious plants. Of the 88 differentially expressed SuperSAGE tags, 18 corresponded to genes previously implicated in flower development and sex determination in multiple plant species. We validated the SuperSAGE data with quantitative real-time PCR (qRT-PCR)-based analysis of the expression of four candidate genes. Our findings suggest that mechanisms of flowering and sex determination are likely conserved in Dioscorea. We further investigated the flowering patterns of 1938 D. rotundata accessions representing diverse geographical origins over two years, revealing that over 85% of the accessions are either male or non-flowering, and that less than 15% are female, while monoecious plants are rare. Intensity of flowering appeared to be a function of sex, with male plants flowering more abundantly than female ones. Candidate genes identified in this study can be targeted with the aim to induce regular flowering in poor to non-flowering cultivars. Findings of the study provide important inputs for further studies aiming to overcome the challenge of flowering in yams and to improve the efficiency of yam breeding.

plant biology↗