No abstract

The transcriptome provides the database from which a cell assembles its collection of proteins. Translation of individual mRNA species into their encoded proteins is regulated, producing discrepancies between mRNA and protein levels. Using a new modeling approach to data analysis, a striking diversity is revealed in association of the transcriptome with the translational machinery. Each mRNA has its own pattern of ribosome loading, a circumstance that provides an extraordinary dynamic range of regulation, above and beyond actual transcript levels. Using this approach together with quantitative proteomics, we explored the immediate changes in gene expression in response to activation of a mitogen-activated protein kinase pathway in yeast by mating pheromone. Interestingly, in 26% of those transcripts where the predicted protein synthesis rate changed by at least 3-fold, more than half of these changes resulted from altered translational efficiencies. These observations underscore that analysis of transcript level, albeit extremely important, is insufficient by itself to describe completely the phenotypes of cells under different conditions. Molecular & Cellular Proteomics 3:478 -489, 2004.

The homeobox gene knottedl (knl) was first isolated by transposon tagging a dominant leaf mutant in maize. Related maize genes, isolated by virtue of sequence conservation within the homeobox, fall into two classes based on sequence similarity and expression patterns. Here, we report the characterization of two genes, KNATl and KNAT2 (forbotted-like from Arabidopsis thaliana) that were cloned from Arabidopsis using the k n l homeobox as a heterologous probe. The homeodomains of KNATl and KNAT2 are very similar to the homeodomains of proteins encoded by ClaSS 1 maize genes, ranging from 78 to 95% amino acid identity. Overall, the deduced KNATl and KNAT2 proteins sham dmino acid identities of 53 and 4096, respectively, with the KN1 protein. lntron positions are also fairly well conserved among KNAT7, KNAT2, and knl. Based on in situ hybridization analysis, the expression pattern of KNATl during vegetative development is similar to that of class 1 maize genes. In the shoot apex, KNAT7 transcript is localized primarily to the shoot apical meristem; down-regulation of expression occurs as leaf primordia are initiated. In contrast to the expression of class 1 maize genes in floral and inflorescence meristems, the expression of KNATl in the shoot meristem decreases during the floral transition and is restricted to the cortex of the inflorescence stem. Transgenic Arabidopsis plants carrying the KNAT7 cDNA and the kn7 cDNA fused to the cauliflower mosaic virus 35s promoter were generated. Misexpression of KNATl and k n l resulted in highly abnormal leaf morphology that included severely lobed leaves. The expression pattern of KNATl in the shoot meristem combined with the results of transgenic overexpression experiments supports the hypothesis that class 1 knl-like genes play a role in morphogenesis.

SUMMARY Genome-wide transcriptional profiling was used to characterize the molecular underpinnings of neocortical organization in rhesus macaque, including cortical areal specialization and laminar cell type diversity. Microarray analysis of individual cortical layers across sensorimotor and association cortices identified robust and specific molecular signatures for individual cortical layers and areas, prominently involving genes associated with specialized neuronal function. Overall, transcriptome-based relationships were related to spatial proximity, being strongest between neighboring cortical areas and between proximal layers. Primary visual cortex (V1) displayed the most distinctive gene expression compared to other cortical regions in rhesus and human, both in the specialized layer 4 as well as other layers. Laminar patterns were more similar between macaque and human compared to mouse, as was the unique V1 profile that was not observed in mouse. These data provide a unique resource detailing neocortical transcription patterns in a non-human primate with great similarity in gene expression to human.

No abstract