Entries by Nancy Hofmann

Designer PPR Proteins as Tools to Explore RNA Binding in vivo

Techniques to isolate the RNA molecules bound to a specific protein, via co-immunoprecipitation, for instance, have been available for years. The converse—methods to identify the proteins bound to a specific RNA—have been harder to come by, in part because of difficulty in elucidating the determinants of RNA binding specificity (reviewed in Helder et al., 2016). […]

The Dynamic Transcriptome: Using Clustered Time Points to Tease Apart Rice Tiller Angle Control

Given the importance of branch angle in determining overall plant form, we know surprisingly little about how those angles are controlled. Branch angle clearly has genetic underpinnings but also responds strongly to light and gravity, as well as to water availability and other stimuli (reviewed in Roychoudhry and Kepinski, 2015). Analysis of tiller angle in […]

Ethylene Represses Gene Transcription via Histone Deacetylases

Approximately half of all ethylene-responsive genes are downregulated in the presence in ethylene (Chang et al, 2013), but this repression has received relatively little attention compared to the ethylene-mediated activation of expression. The known positive regulators of ethylene signaling include ETHYLENE INSENSITIVE 2 (EIN2) and the transcription factor EIN3. Intriguingly, EIN3 binds to promoters of […]

Nanopore Sequencing Comes to Plant Genomes

The next generation of next-generation sequencing is upon us. Third-generation sequencing aims to provide long stretches of sequence – ultimately to the chromosome level – at bargain basement prices. Progress is being made toward those goals with the emergence of long-read sequencing techniques and new methods for scaffolding, as well as rapidly developing software for […]

Evidence for Two Distinct Stages in Secondary Cell Wall Formation of Xylem

A hallmark of xylem development is the deposition of secondary cell wall material in specific patterns (reviewed in Patrick et al, 2007). These cell wall deposits structurally reinforce the xylem to withstand negative pressure during water transport and differ in different xylem cell types. While it is not entirely clear how the patterns of deposition […]

So Much Data, So Little Time: ePlant Steps into the Breach for Plant Researchers

The ever-increasing amount of data available to researchers has come with similarly increasing cognitive loads in efforts to use these data. Even when data sets are stored in well-curated databases, it can be time-consuming to master the specific tools harbored at each site and cumbersome to move between data types. A new tool created by […]

A Genome-wide Approach to Understanding a Non-Canonical ARF

The canonical auxin-response pathway in plants begins with auxin sensing by F-box proteins, triggering degradation of AUX/IAA proteins that act as transcriptional repressors via their interaction with sequence-specific DNA-binding AUXIN RESPONSE FACTORS (ARFs; reviewed in Weijers and Wagner, 2016).  Recently, the unusual ARF protein ETTIN (ETT) was proposed to represent an even shorter pathway through […]

The Who, What, and Where of Plant Polyprenol Biosynthesis Point to Thylakoid Membranes and Photosynthetic Performance

Isoprenoids are a huge group of compounds that include primary metabolites such as carotenoids, chlorophylls, and hormones, as well as a plethora of specialized secondary metabolites. In addition to their importance in the physiology of plants (and of other kingdoms of life), isoprenoids have drawn attention in recent years for their applications in human health […]