Jonathan Isaiah Gent

Maternal repression of imprinted genes in endosperm by gene body demethylation

The paper shows that maternal removal of gene body methylation drives imprinting of PEGs in maize, with implications for gene regulation in rice but not Arabidopsis.

A switch from TE-like heterochromatin to euchromatin underlies activation of protein storage genes in maize endosperm

The paper identifies TE-like methylated genes in maize endosperm that are demethylated and highly expressed, revealing a switch from heterochromatin to euchromatin that activates protein storage genes.

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

This study shows that MDR1 DNA glycosylase regulates maternally expressed imprinted genes and TEs in endosperm by demethylation, with two-thirds of MEGs showing DNG-dependent regulation.

Increased maize chromosome number by engineered chromosome fission

This paper describes the engineering of chromosome fission in maize using synthetic centromeres, resulting in stable, functional chromosome pairs that increase the diploid chromosome number from 20 to 22.

Two CENH3 paralogs in the green alga Chlamydomonas reinhardtii have a redundantly essential function and associate with ZeppL-LINE1 elements

The paper characterizes two CENH3 paralogs in Chlamydomonas reinhardtii, showing their essential function and association with ZeppL-LINE1 elements in centromeres.

Antagonistic kinesin-14s within a single chromosomal drive haplotype

The paper investigates the role of TRKIN in maize meiotic drive, finding it to be deleterious when paired with normal chromosomes and suggesting it is being purged from populations.

Potent pollen gene regulation by DNA glycosylases in maize

The paper identifies 58 DNG target genes in maize pollen that are silenced in plant body tissues but expressed in pollen, revealing their role in pollen viability and function.

Differences in activity and stability drive transposable element variation in tropical and temperate maize.

The paper develops a pan-TE annotation tool to analyze TE variation in maize, finding that tropical maize has more TE sequences due to active and less methylated LTR retrotransposons.

The maize striate leaves2 (sr2) gene encodes a conserved DUF3732 domain homologous to the rice yss1 gene

The paper identifies the sr2 gene in maize, which encodes a DUF3732 protein homologous to the rice yss1 gene, and shows it is involved in plastid gene expression.

Synthetic maize centromeres transmit chromosomes across generations

The paper demonstrates the feasibility of using synthetic centromeres in maize to transmit chromosomes across generations through a LexA-CENH3 tethering approach.

The maize gene maternal derepression of r1 (mdr1) encodes a DNA glycosylase that demethylates DNA and reduces siRNA expression in endosperm

This paper identifies MDR1 as a DNA glycosylase in maize that demethylates DNA and reduces siRNA expression in endosperm, challenging the role of demethylation in transposon repression and genomic imprinting.

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

A multi-genome analysis of maize reveals previously unknown variation in gene content, genome structure, and methylation.

Maize centromeric chromatin scales with changes in genome size

The paper shows that centromere size in maize scales with genome size, independent of CentC satellite DNA, and involves multiple limiting factors.

Gapless assembly of maize chromosomes using long read technologies

The paper presents a gapless maize genome assembly using long read technologies and optical maps, achieving telomere-to-telomere assemblies for chromosomes 3 and 9.

Reprogramming of 24nt siRNAs in rice gametes

The paper characterizes 24nt siRNA distributions in rice gametes, revealing distinct patterns compared to vegetative tissues and suggesting reprogramming of small RNA pathways in gametes.

Loss of mCHH islands in maize chromomethylase and DDM1-type nucleosome remodeler mutants

The paper examines DNA methylation and small RNA expression in maize mutants lacking chromomethylases and DDM1-type nucleosome remodelers, revealing a role for chromomethylation and DDM1 in RdDM at mCHH islands.

Improved maize reference genome with single molecule technologies

The paper improves the maize reference genome using single molecule technologies, resulting in longer contigs and better annotation of repetitive elements and genes.