Biology subjects

Higgins, K. M.

Publications and source records attributed to Higgins, K. M..

3 recordsLinked to original sources

bioRxiv2024

Conservation of imprinted expression across genotypes is correlated with consistency of imprinting across endosperm development in maize

Imprinted expression is an essential process for seed viability affecting hundreds of genes in Zea mays endosperm, however most studies have examined just one time point for analysis. The focus on single time points can limit our ability to identify imprinted genes, and our ability to draw conclusions for the role of imprinting in endosperm. In this study we examine imprinted expression across four time points ranging from the transition to endoreduplication from mitotic division through the beginning of programmed cell death. Additionally, we assessed imprinting variation across eight diverse maize lines, six of which have never before been assessed for imprinting. Through this analysis we identify over 700 imprinted genes with varying consistency across time points including 258 genes imprinted at every time point and 104 genes displaying transient imprinting. We find a correlation between high consistency of imprinting across time and high conservation of parental bias across eight diverse maize lines reciprocally crossed with B73. Additionally, we identify evidence of imprinting for three zein genes that are critical for nutrient accumulation in the endosperm, suggesting that imprinting may play a more important role in seed composition than previously thought. Taken together, this study provides a more holistic view of imprinting variation across time and across genotypes in maize and enables us to more thoroughly investigate the complex imprinting landscape. SummaryThough genomic imprinting is essential for seed development, changes in imprinted expression through endosperm development remain unclear. Here, the authors present a time series analysis of genomic imprinting in maize endosperm identifying over 1000 imprinted genes displaying consistent and transient imprinting. Additionally, the authors utilize imprinting data from B73 reciprocally crossed with eight diverse genotypes, and identify a correlation between consistency and conservation of imprinted expression. Together these results offer a more holistic view of imprinted expression in maize endosperm.

plant biology↗

bioRxiv2024

MDR1 DNA glycosylase regulates the expression of genomically imprinted genes and helitrons

Targeted demethylation by DNA glycosylases (DNGs) results in differential methylation between parental alleles in the endosperm, which drives imprinted expression. Here, we performed RNA sequencing on endosperm derived from DNG mutant mdr1 and wild-type endosperm. Consistent with the role of DNA methylation in gene silencing, we find 96 gene and 86 TE differentially expressed (DE) transcripts that lost expression in the hypermethylated mdr1 mutant. Compared with other endosperm transcripts, the mdr1 targets are enriched for TEs (particularly Helitrons), and DE genes are depleted for both core genes and GO term assignments, suggesting that the majority of DE transcripts are TEs and pseudo-genes. By comparing DE genes to imprinting calls from prior studies, we find that the majority of DE genes have maternally biased expression, and approximately half of all maternally expressed genes (MEGs) are DE in this study. In contrast, no paternally expressed genes (PEGs) are DE. DNG-dependent imprinted genes are distinguished by maternal demethylation and expression primarily in the endosperm, so we also performed EM-seq on hybrids to identify maternal demethylation and utilized a W22 gene expression atlas to identify genes expressed primarily in the endosperm. Overall, approximately [2/3] of all MEGs show evidence of regulation by DNA glycosylases. Taken together, this study solidifies the role of MDR1 in the regulation of maternally expressed, imprinted genes and TEs and identifies subsets of genes with DNG-independent imprinting regulation. Significance StatementThis work investigates the transcriptome changes resulting from the loss of function of DNA glycosylase MDR1, revealing that, in wild-type endosperm, targets of MDR1 are expressed predominantly from the maternal allele and this expression is suppressed in mutants. Furthermore, by combining expression data, DNA methylation data, and developmental expression data, we are able to categorize all maternally expressed, imprinted genes based on DNA glycosylase dependent or independent regulatory methods.

plant biology↗

bioRxiv2021

The maize gene maternal depression of r1 (mdr1) encodes a DNA glycosylase with maternal and paternal fertility functions

Demethylation of transposons can activate expression of nearby genes and cause imprinted gene expression in endosperm, and it is hypothesized to lead to expression of transposon siRNAs that reinforce silencing in the next generation through transfer either into egg or embryo. Here we describe maternal derepression of r1 (mdr1), which encodes a DNA glycosylase with homology to Arabidopsis DEMETER and which is partially responsible for demethylation of thousands of regions in endosperm. Instead of promoting siRNA expression in endosperm, MDR1 activity inhibits it. Methylation of most repetitive DNA elements in endosperm is not significantly affected by MDR1, with an exception of Helitrons. While maternally-expressed imprinted genes preferentially overlap with MDR1 demethylated regions, the majority of genes that overlap demethylated regions are not imprinted. Double mutant megagametophytes lacking both MDR1 and its close homolog DNG102 result in early seed failure, and double mutant microgametophytes fail pre-fertilization. These data establish DNA demethylation by glycosylases as essential in maize endosperm and pollen and suggest that neither transposon repression nor genomic imprinting are its main function in endosperm.

genetics↗