RT Journal Article
SR Electronic
T1 Widespread imprinting of transposable elements and young genes in the maize endosperm
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.04.08.032573
DO 10.1101/2020.04.08.032573
A1 Sarah N Anderson
A1 Peng Zhou
A1 Kaitlin Higgins
A1 Yaniv Brandvain
A1 Nathan M Springer
YR 2020
UL http://biorxiv.org/content/early/2020/04/09/2020.04.08.032573.abstract
AB Fertilization and seed development is a critical time in the plant life cycle, and coordinated development of the embryo and endosperm are required to produce a viable seed. In the endosperm, some genes show imprinted expression where transcripts are derived primarily from one parental genome. Imprinted gene expression has been observed across many flowering plant species, though only a small proportion of genes are imprinted. Understanding the rate of turnover for gain or loss of imprinted expression has been complicated by the reliance on single nucleotide polymorphisms between alleles to enable testing for imprinting. Here, we develop a method to use whole genome assemblies of multiple genotypes to assess for imprinting of both shared and variable portions of the genome using data from reciprocal crosses. This reveals widespread maternal expression of genes and transposable elements with presence-absence variation within maize and across species. Most maternally expressed features are expressed primarily in the endosperm, suggesting that maternal de-repression in the central cell facilitates expression. Furthermore, maternally expressed TEs are enriched for maternal expression of the nearest gene. Read alignments over maternal TE-gene pairs indicate fused transcripts, suggesting that variable TEs contribute imprinted expression of nearby genes.