Weeding the Gems

Your UK Arabidopsis Research Round-up this week contains studies that aim to define a network of lateral root formation, elucidate modes of calcium signaling, determine mechanisms of epigenetic memory and also the influence of exon-edge evolution in determining the extent of selective pressure.

Liu J, Whalley HJ, Knight MR. Combining modelling and experimental approaches to explain how calcium signatures are decoded by calmodulin-binding transcription activators (CAMTAs) to produce specific gene expression responses. New Phytologist. 2015 Apr 27. doi: 10.1111/nph.13428.

Marc Knight’s group at the University of Durham have attempted to decode the complex mechanism by which calcium controls changes in gene expression. They have developed an experimentally parameterized model that reveals calcium signals are amplified by the binding of calmodulin and calmodulin-binding transcription activators (CAMTAs). Interestingly, the model suggests that gene expression change in response to a calcium signature is defined by the previous history of that signal.

Lavenus J, Goh T, Guyomarc’h S, Hill K, Lucas M, Voß U, Kenobi K, Wilson MH, Farcot E, Hagen G, Guilfoyle TJ, Fukaki H, Laplaze L, Bennett MJ. Inference of the Arabidopsis Lateral Root Gene Regulatory Network Suggests a Bifurcation Mechanism That Defines Primordia Flanking and Central Zones. Plant Cell. 2015 May 5. pii: tpc.114.132993.

The biology of lateral root (LR) formation has been well researched over the past decade although a full robust regulatory network that controls this process has remained elusive. CPIB at the University of Nottingham, together with European collaborators have used a series of transcriptomic datasets to develop a time-delay correlation algorithm (TDCor) to infer the gene expression network (GRN) controlling LR initiation. The GRNs associated with AUXIN RESPONSE FACTOR7 and ARF5 predict a mutual inhibition and a patterning mechanism that controls flanking and central zone specification of LR primordia.

Berry S, Hartley M, Olsson TS, Dean C, Howard M Local chromatin environment of a Polycomb target gene instructs its own epigenetic inheritance. Elife. 2015 May 8;4. doi: 10.7554/eLife.07205.

Epigenetic ‘memory’ allows plant cells to retain a memory of past environmental or development events. One key regulator of this process is the Polycomb Repressive Complex2 (PRC2). Histone proteins that are modified by the PRC2 can be inherited through cell division. The groups of Mark Howard and Caroline Dean at the JIC investigated whether this inheritance directs long term memory in a cis or trans manner. Two copies of the Arabidopsis FLC gene, which is a target for PRC2, were monitored in the same plant. Interestingly they reveal that one FLC copy could be silenced but the other remained active, providing evidence that epigenetic memory, at least of FLC, is stored in trans but not in cis.

Bush SJ, Kover PX, Urrutia AO. Lineage-specific sequence evolution and exon edge conservation partially explain the relationship of evolutionary rate and expression level in A. thaliana. Mol Ecol. 2015 Apr 30. doi: 10.1111/mec.13221.

Alongside genetic changes in response to phenotypic adaptation, the elements of a genes DNA structure can also affect evolutionary rates. In Arabidopsis the ‘edge’ of exons, which flank introns and contain splice enhancers are known to have a higher degree of evolutionary conservation compared to coding regions. Dr Arazi Urrutia and collaborators from the University of Bath assessed selective pressure (measured by dN/dS) and showed that exon edge conservation partially explains the relationship between rates of protein evolution and expression level. Without any consideration of exon-edge conservation can potentially increase the number of genes designated as being under adaptive selection. Therefore the authors conclude that exon-edge conversation should be an important consideration when assessing overall dN/dS ratios.