Michael D. Nodine

This study maps DCP2-dependent 5' cap footprints in Arabidopsis thaliana using in vitro decapping and transcriptome sequencing, revealing 13,000 capped transcripts and their role in RNA stability and decay pathways.

The paper identifies premeiotic 24-nt phasiRNAs in maize and related species, showing they are distinct from meiotic 24-nt phasiRNAs in biogenesis and function.

Bookend improves transcript assembly by using 5' and 3' end information from RNA-seq data, achieving accurate transcriptome reconstruction in single cells and model organisms.

The paper identifies overlapping mRNA targets of ECT2 and ECT3 using HyperTRIBE and shows they regulate target mRNA abundance, not alternative polyadenylation.

The paper shows that chromatin states regulate siRNA production from transposable elements in Arabidopsis embryos, which helps re-establish DNA methylation and maintain epigenome homeostasis.

The paper analyzes gene expression and DNA methylation in Arabidopsis shoot stem cells, revealing transient transposon activation and epigenetic reprogramming during their transition to reproductive lineage.

This study shows that zygotic genome activation occurs soon after fertilization in Arabidopsis and is required before the first cell division.

The paper profiles miRNAs and their targets during Arabidopsis embryogenesis, showing their role in regulating transcription factors and embryo morphogenesis.

The paper develops a low-input mRNA-seq method to profile Arabidopsis embryos across developmental stages, revealing unique transcriptomes and four distinct transcriptional phases.