Gene Expression: Sizing it all up

Authors: WOODY, JENNA - Iowa State University; Shoemaker, Randy

Submitted to: Frontiers in Plant Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/29/2011
Publication Date: 10/17/2011
Citation: Woody, J.L., Shoemaker, R.C. 2011. Gene Expression: Sizing it all up. Frontiers in Plant Genetics and Genomics. 2:70.

Interpretive Summary: An organism is the product of the expression of all the genes in its genome, in interaction with the environment. Understanding the subtleties of gene regulation has been a puzzle to scientists for decades. Only recently have geneticists begun to understand that physical attributes of the genome are correlated with levels and breadth of expression of genes. As a rule, genes expressed at a high level were thought to be smaller, and genes expressed in specific tissues were thought to be more complex. However, the literature is replete with inconsistencies. In this analysis the authors examined the literature as well as their own published data and review the applicability of some proposed models. They offer insight into complex interactions of gene and genome size and gene expression and evolution. This analysis provides important insight into gene and genome evolution.

Technical Abstract: Genomic architecture appears to be a largely unexplored component of gene expression. Although surely not the end of the story, we are learning that when it comes to gene expression, size is important. We have been surprised to find that certain patterns of expression, tissue-specific versus constitutive, or high expression versus low expression, are often associated with physical attributes of the gene and genome. Multiple studies have shown an inverse relationship between gene expression patterns and various physical parameters of the genome such as intron size, exon size, intron number and size of intergenic regions. An increase in expression level and breadth often correlates with a decrease in the size of physical attributes of the gene. Three models have been proposed to explain these relationships. However, contradictory results were found in several organisms when expression level and expression breadth were analyzed independently. However, when both factors were combined in a single study a novel relationship was revealed. At low levels of expression, an increase in expression breadth correlated with an increase in genic, intergenic and intragenic sizes. Contrastingly, at high levels of expression, an increase in expression breadth inversely correlated with the size of the gene. In this article we explore the several hypotheses regarding genome physical parameters and gene expression. We present some key findings and discuss contradictory results found in the literature.