Links between core promoter and basic gene features influence gene expression

<p>Abstract</p> <p>Background</p> <p>Diversity in rates of gene expression is essential for basic cell functions and is controlled by a variety of intricate mechanisms. Revealing general mechanisms that control gene expression is important for understanding normal and pathological cell functions and for improving the design of expression systems. Here we analyzed the relationship between general features of genes and their contribution to expression levels.</p> <p>Results</p> <p>Genes were divided into four groups according to their core promoter type and their characteristics analyzed statistically. Surprisingly we found that small variations in the TATA box are linked to large differences in gene length. Genes containing canonical TATA are generally short whereas long genes are associated with either non-canonical TATA or TATA-less promoters. These differences in gene length are primarily determined by the size and number of introns. Generally, gene expression was found to be tightly correlated with the strength of the TATA-box. However significant reduction in gene expression levels were linked with long TATA-containing genes (canonical and non-canonical) whereas intron length hardly affected the expression of TATA-less genes. Interestingly, features associated with high translation are prevalent in TATA-containing genes suggesting that their protein production is also more efficient.</p> <p>Conclusion</p> <p>Our results suggest that interplay between core promoter type and gene size can generate significant diversity in gene expression.</p

Using expression profiles of Caenorhabditis elegans neurons to identify genes that mediate synaptic connectivity.

Synaptic wiring of neurons in Caenorhabditis elegans is largely invariable between animals. It has been suggested that this feature stems from genetically encoded molecular markers that guide the neurons in the final stage of synaptic formation. Identifying these markers and unraveling the logic by which they direct synapse formation is a key challenge. Here, we address this task by constructing a probabilistic model that attempts to explain the neuronal connectivity diagram of C. elegans as a function of the expression patterns of its neurons. By only considering neuron pairs that are known to be connected by chemical or electrical synapses, we focus on the final stage of synapse formation, in which neurons identify their designated partners. Our results show that for many neurons the neuronal expression map of C. elegans can be used to accurately predict the subset of adjacent neurons that will be chosen as its postsynaptic partners. Notably, these predictions can be achieved using the expression patterns of only a small number of specific genes that interact in a combinatorial fashion

The median, 25% and 75% quartiles of tissue average expression for each gene sets

The gene sets were divided into short (intron 8000 nt, grey box), and the median, 25% and 75% quartile of the avarage expression for each gene set is shown. The p-values of the differences in the median value between each two gene sets as indicated. NS is non-significant difference (p > 0.05).<p><b>Copyright information:</b></p><p>Taken from "Links between core promoter and basic gene features influence gene expression"</p><p>http://www.biomedcentral.com/1471-2164/9/92</p><p>BMC Genomics 2008;9():92-92.</p><p>Published online 25 Feb 2008</p><p>PMCID:PMC2279122.</p><p></p

Gene sets which differ in their core promoter, as described in the text, were analyzed for the length of their genes (A), mRNA (B) and introns (C)

The boxplots present the median, 25% and 75% quartile values that were calculated from 527 TATA, 694 TATA-1, 3916 TATA-2 and 9491 TATA-less genes. The p-values of the differences in the median value between each two gene sets as indicated. NS is non-significant difference (p > 0.05).<p><b>Copyright information:</b></p><p>Taken from "Links between core promoter and basic gene features influence gene expression"</p><p>http://www.biomedcentral.com/1471-2164/9/92</p><p>BMC Genomics 2008;9():92-92.</p><p>Published online 25 Feb 2008</p><p>PMCID:PMC2279122.</p><p></p

Proteomic profiling of distinct clonal populations of bone marrow mesenchymal stem cells

Mesenchymal stem cells (MSCs) have attracted immense research interest in the field of regenerative medicine due to their ability to be cultured for successive passages and multi-lineage differentiation. The molecular mechanisms governing MSC self-renewal and differentiation remain largely unknown. The development of sophisticated techniques, in particular clinical proteomics, has enabled researchers in various fields to identify and characterize cell specific biomarkers for therapeutic purposes. This study seeks to understand the cellular and sub-cellular processes responsible for the existence of stem cell populations in bone marrow samples by revealing the whole cell proteome of the clonal cultures of bone marrow-derived MSCs (BMSCs). Protein profiling of the MSC clonal populations was conducted by Two-Dimensional Liquid Chromatography/Matrix-Assisted Laser Desorption/Ionisation (MALDI) Mass Spectrometry (MS). A total of 83 proteins were identified with high confidence of which 11 showed differential expression between subpopulations, which included cytoskeletal and structural proteins, calcium binding proteins, cytokinetic proteins, and members of the intermediate filament family. This study generated a proteome reference map of BMSCs from the clonal populations, which will be valuable to better understand the underlying mechanism of BMSC self-renewal and differentiation

Israeli Academy of Science. Correspondence author:

Running title: Large gene screening of vasculogenesis from human embryonic stem cells Key words: human embryonic stem cells; differentiation; development; vascular; endothelial cells; smooth muscle cells; vasculogenesis; angiogenesi