Biology subjects

Woolfenden, H. C.

Publications and source records attributed to Woolfenden, H. C..

4 recordsLinked to original sources

bioRxiv2026

The degree of subgenome expression bias in B. napus changes between cultivars, tissues and across time

Most extant plants show evidence of past polyploidization events in their genomes. Allopolyploids arise from hybridisation, resulting in the polyploid genome comprising subgenomes from different ancestors. Subsequent adaptation to their environment or selection pressure for specific traits has led to several allopolyploids exhibiting an unequal contribution from their subgenomes to their phenotype. Given the diversity of cultivars grown for different environments, it is possible that the associated regulatory changes may have given rise to different subgenome expression biases. Likewise, different tissues and developmental stages have distinct expression profiles that may correspond more strongly to one subgenome over the other(s). Here, we investigate different metrics for quantifying the contribution of each subgenome in space (tissue) and time (development) in cultivars of Brassica napus. Brassica napus has two subgenomes, A and C, from its ancestors Brassica rapa (A) and Brassica oleracea (C). We find that the C genome has higher overall expression than the A genome, whereas the average expression per gene is higher for the A genome. Direct comparison of homoeologous pairs reveals higher expression of genes on the C genome. We find that the degree of expression bias can change between cultivars, tissues and across time with bias quantification being strongly dependent on the metric. These findings help explain contradictory reports on expression bias and genome dominance. Significance statementWe demonstrate how different metrics of expression bias between subgenomes in polyploids can lead to conflicting inferences. We show that expression can be viewed as either A or C-biased, yet the differences are small, calling into question the relevance of subgenome dominance and expression bias in B. napus.

plant biology↗

bioRxiv2026

A Bayesian approach for identifying similar transcript dynamics using curve registration

Changes in gene expression over time can provide valuable insights into developmental processes and responses to the environment. Differences in expression may be indicative of potential differences in regulation. Comparing transcript dynamics may help identify correspondences between developmental stages within and between species, differences in the timing of key events during development, and transcriptional response to treatments or perturbations. A straightforward comparison between the dynamics is, however, hindered by measurements that were taken at different time points and over different timescales. To address this, we developed a statistical approach that seeks the optimal alignment between two time series as a function of a temporal shift and stretch. We validated our approach using simulated data and applied it to several transcriptome datasets, including comparisons between different plant species. Our development facilitates knowledge transfer from model systems to less studied species, the identification of modules of co-regulated genes, and the discovery of condition-specific, temporally differentially-expressed genes. The method is provided freely available as an R package.

bioinformatics↗

bioRxiv2023

Integrated Phenomics and Genomics reveals genetic loci associated with inflorescence growth in Brassica napus

A fundamental challenge to the production of climate-resilient crops is how to measure dynamic yield-relevant responses to the environment, such as growth rate, at a scale which informs mechanistic understanding and accelerates breeding. The timing, duration and architectural characteristics of inflorescence growth are crucial for optimising crop productivity and have been targets of selection during domestication. We report a robust and versatile procedure for computationally assessing environmentally-responsive flowering dynamics. In the oilseed crop, Brassica napus, there is wide variation in flowering response to winter cold (vernalization). We subjected a diverse set of B. napus accessions to different vernalization temperatures and monitored shoot responses using automated image acquisition. We developed methods to computationally infer multiple aspects of flowering from this dynamic data, enabling characterisation of speed, duration and peaks of inflorescence development across different crop types. We input these multiple traits to genome- and transcriptome-wide association studies, and identified potentially causative variation in a priori phenology genes (including EARLY FLOWERING3) for known traits and in uncharacterised genes for computed traits. These results could be used in marker assisted breeding to design new ideotypes for improved yield and better adaptation to changing climatic conditions.

plant biology↗

bioRxiv2019

In vivo mRNA structure regulates miRNA cleavage in Arabidopsis

MicroRNA (miRNA)-mediated cleavage is involved in numerous essential cellular pathways. miRNAs recognize target RNAs via sequence complementarity. In addition to complementarity, in vitro and in silico studies have suggested that RNA structure may influence the accessibility of mRNAs to miRNA-Induced Silencing Complexes (miRISCs), thereby affecting RNA silencing. However, the regulatory mechanism of mRNA structure in miRNA cleavage remains elusive. Here, we investigated the role of in vivo RNA secondary structure in miRNA cleavage by developing the new CAP-STRUCTURE-seq method to capture the intact mRNA structurome in Arabidopsis thaliana. This approach revealed that miRNA target sites were not structurally accessible for miRISC binding prior to cleavage in vivo. Instead, the unfolding of the target site structure is the primary determinant for miRISC activity in vivo. Notably, we found that the single-strandedness of the two nucleotides immediately downstream of the target site, named Target Adjacent structure Motif (TAM), can promote miRNA cleavage but not miRNA binding, thus decoupling target site binding from cleavage. Our findings demonstrate that mRNA structure in vivo can regulate miRNA cleavage, providing evidence of mRNA structure-dependent regulation of biological processes.

molecular biology↗