YeATSAM analysis of the walnut and chickpea transcriptome reveals key genes undetected by current annotation tools

Background: The transcriptome, a treasure trove of gene space information, remains severely under-used by current genome annotation methods. Methods: Here, we present an annotation method in the YeATS suite (YeATSAM), based on information encoded by the transcriptome, that demonstrates artifacts of the assembler, which must be addressed to achieve proper annotation. Results and Discussion: YeATSAM was applied to the transcriptome obtained from twenty walnut tissues and compared to MAKER-P annotation of the recently published walnut genome sequence (WGS). MAKER-P and YeATSAM both failed to annotate several hundred proteins found by the other. Although many of these unannotated proteins have repetitive sequences (possibly transposable elements), other crucial proteins were excluded by each method. An egg cell-secreted protein and a homer protein were undetected by YeATSAM, although these did not produce any transcripts. Importantly, MAKER-P failed to classify key photosynthesis-related proteins, which we show emanated from Trinity assembly artifacts potentially not handled by MAKER-P. Also, no proteins from the large berberine bridge enzyme (BBE) family were annotated by MAKER-P. BBE is implicated in biosynthesis of several alkaloids metabolites, like anti-microbial berberine. As further validation, YeATSAM identified ~1000 genes that are not annotated in the NCBI database by Gnomon. YeATSAM used a RNA-seq derived chickpea (Cicer arietinum L.) transcriptome assembled using Newbler v2.3. Conclusions: Since the current version of YeATSAM does not have an ab initio module, we suggest a combined annotation scheme using both MAKER-P and YeATSAM to comprehensively and accurately annotate the WGS.

Transition of Homer isoforms during skeletal muscle regeneration

Homer represents a new and diversified family of proteins that includes several isoforms, Homer 1, 2, and 3; some of these isoforms have been reported to be present in striated muscles. In this study, the presence of Homer isoforms 1a, 1b/c/d, 2b, and 3 was thoroughly investigated in rat skeletal muscles under resting conditions. Transition in Homer isoforms compositon was studied under experimental conditions of short-term and long-term adaptation, e.g., fatigue and regeneration, respectively. First, we show that Homer 1a was constitutively expressed and was transiently upregulated during regeneration. In C2C12 cell cultures, Homer 1a was also upregulated during formation of myotubes. No change of Homer 1a was observed in fatigue. Second, Homer 1b/c/d and Homer 2b were positively and linearly related to muscle mass change during regeneration, and third, Homer 3 was not detectable under resting conditions but was transiently expressed during regeneration although with a temporal pattern distinct from that of Homer 1a. Thus a switch in Homer isoforms is associated to muscle differentiation and regeneration. Homers may play a role not only in signal transduction of skeletal muscle, in particular regulation of Ca2+ release from sarcoplasmic reticulum (Ward CW, Feng W, Tu J, Pessah IN, Worley PF, and Schneider MF. Homer protein increases activation of Ca2+ sparks in permeabilized skeletal muscle. J Biol Chem 279: 5781–5787, 2004), but also in adaptation.

Effects of Vesl/Homer Proteins on Intracellular Signaling

The clustering of signaling molecules at specialized cellular sites allows cells to effectively convert extracellular signals into intracellular signals and to produce a concerted functional output with specific temporal and spatial patterns. A prime example for these molecules and their effects on cellular signaling are the postsynaptic density proteins of the central nervous system. Recently, one group of these proteins, the Vesl/Homer protein family has received increased attention because of its unique molecular properties that allow both the clustering end functional modulation of a plethora of different binding Proteins. Within multlprotein signaling complexes, Vesl/Homer Proteins influence proteins as diverse as metabotropic glutamate receptors; transient receptor potential channels; intracellular calcium channels; the scaffolding protein, Shank; small GTPases; transcription factors; and cytoskeletal proteins. Furthermore, interaction with such functionally relevant proteins also links Vesl/Homer proteins indirectly to an even larger group of cellular effector proteins, putting the Vesl/Homer Proteins at the crossroads of several critical intracellular signaling processes. In addition to the initial reports of Vesl/Homer protein expression in the central nervous system, members of this protein family have now been identified in other excitable cells in various muscle types and in a large number of nonexcitable cells. The widespread expression of Vesl/Homer proteins in different organs and their functional importance in cellular protein signaling complexes is further evidenced by their conservation in organisms from Drosoohila to humans.