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PAG Presenter Outlines Maize ENCODE Plans

SAN DIEGO (GenomeWeb) – Not to be outdone by humans and model organisms — which have had their regulatory elements and expression features profiled in the ENCODE and modENCODE projects, respectively — the maize plant is on its way to getting its own regulatory DNA encyclopedia.

At the Plant and Animal Genomes conference here yesterday, Cold Spring Harbor Laboratory investigator Rob Martienssen introduced the Maize EnCODE, or MaizeCODE project. It is being led by eight co-principal investigators and will involve researchers from  CSHL, the Dolan DNA Learning Center, New York University, Johns Hopkins University, and elsewhere.

A recently funded pilot effort for MaizeCODE is set to include histone modification analyses, RNA sequencing, DNA methylation profiling, and the like in half a dozen tissue types from plants in three inbred maize lines and one teosinte type, Martienssen told attendees at a plant epigenetics session.

Because plant biologists do not have access to the same sorts of cell lines used for human and animal studies, he explained, investigators working on the MaizeCODE project plan to rely on approaches such as tissue dissection and 3D fluorescence-activated cell sorting to analyze regulatory elements in various parts of the maize plant or protoplast.

For the maize transcriptome analyses, for example, the team plans to look at both long RNAs and small RNAs by sequencing. Specialized methods will be used, as well, such as "RNA annotation and mapping of promoters for analysis of gene expression" (Rampage), which offers a glimpse at potential promoter activity.

Likewise, the investigators will use chromatin immunoprecipitation, various sequencing-based methods, tagged transcription factor profiling, and other approaches to characterize histone acetylation marks, transcription factor networks, open chromatin regions, and DNA methylation patterns in maize.

Martienssen noted that members of the team are currently designing appropriate informatics to deal with MaizeCODE-related data, portals, and pipelines. Together, he said, an enhanced understanding of the regulatory elements at work in various maize tissues may help in interpreting potential associations in the plant.

From studies done so far, the team suspects that maize likely has some methylation features that are quite distinct from those found in other plants such as Arabidopsis thaliana.

In a study appearing in Genome Research in 2013, for example, Martienssen and his co-authors described cytosine methylation profiles and methylation heritability patterns gleaned from high-coverage bisulfite sequencing on maize plants from the B73 and Mo17 inbred maize lines. In particular, they reported that "methylation in different sequence contexts is guided differentially by small RNA and is correlated with transposon insertion and [messenger RNA] splicing."

That analysis also pointed to heritable, small RNA-mediated switches in methylation within some differentially methylated regions. Martienssen noted that these paramutation-like events are suspected of affecting thousands more maize genes.

The prevalence of potential paramutations, along with methylation-related effects on maize gene splicing, are among the many epigenetic features that are expected to become clearer once the team starts looking in detail across maize lines and tissues.

A maize reference genome, sequenced with Sanger technology, was reported in Science in 2009, accompanied by related papers in the journals PLOS Genetics, the Proceedings of the National Academy of Sciences, and Plant Physiology. And analyses of ancient corn DNA, including a 5,300-year-old corn genome published last year, are helping to untangle the population history of corn plants.

Meanwhile, a CSHL-led team published a Nature Communications paper in 2016 that highlighted some of the transcriptional complexity picked up in half a dozen corn tissues that were analyzed by single-molecule, long-read RNA sequencing.