Biology subjects

Briffa, A.

Publications and source records attributed to Briffa, A..

3 recordsLinked to original sources

bioRxiv2024

A curve fitting method for analysing starch granule size distributions in cereals

Background and ObjectivesThe size distribution of starch granules is an important factor determining functional and nutritional properties of starch. However, a simple, standardised method for their analysis is lacking. Here, we developed an approach for estimating granule size parameters using a Python script that fits curves to volumetric granule size distributions generated using a Coulter counter. FindingsThe bimodal size distribution of starch from most wheat and barley cultivars could be best described with a mixed distribution curve. A log-normal distribution was fitted to the small B-type granules, and a normal distribution was fitted to the large A-type granules, allowing estimation of their relative abundance and size parameters, despite their overlapping size distributions. However, the optimal fitting is altered in wheat mutants with large perturbations in B-type granule content. In maize and rice, which have unimodal granule size distributions, size parameters were calculated by fitting a single normal distribution. ConclusionsCurve fitting is an effective approach for estimating starch granule size parameters in diverse cereals, particularly the Triticeae with A- and B-type granules. Significance and noveltyWe provide new tools and guidelines for the quantitative analysis of granule size in cereals.

plant biology↗

bioRxiv2022

Unified establishment and epigenetic inheritance of DNA methylation through cooperative MET1 activity

Methylation of CG dinucleotides (mCG), which regulates eukaryotic genome functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How mCG is established and transmitted across generations despite imperfect enzyme fidelity remains mysterious. Here we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted by active demethylation and suppressed by histone variant H2A.Z. Based on these observations, we develop a mathematical model that precisely recapitulates mCG inheritance dynamics and predicts intragenic mCG patterns and their population-scale variation given only CG site spacing as input. The model reveals that intragenic mCG undergoes large, millennia-long epigenetic fluctuations, and can therefore mediate evolution on this timescale. Our results demonstrate how genic methylation patterns are created, reconcile imperfect mCG maintenance with long-term stability, and establish a quantitative model that unifies the establishment and epigenetic inheritance of mCG. HighlightsO_LIMET1 mediates a unified process of mCG establishment and maintenance within genes C_LIO_LIROS1 and H2A.Z regulate the epigenetic dynamics of genic mCG C_LIO_LIA mathematical model predicts genic mCG patterns and their population variance C_LIO_LIGenic mCG undergoes large epigenetic fluctuations that can last thousands of years C_LI

genetics↗

bioRxiv2022

Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons

Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited over many generations. Such inheritance is thought to be mediated by a semiconservative mechanism that produces binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is stably inherited across many generations and is quantitatively associated with transposon expression. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamic balance of these activities. We find that DRM2 - the core methyltransferase of the RNA-directed DNA methylation pathway - catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation.

genetics↗