Genomic Selective Constraints in Murid Noncoding DNA

Abstract

Recent work has suggested that there are many more selectively constrained, functional noncoding than coding sites in mammalian genomes. However, little is known about how selective constraint varies amongst different classes of noncoding DNA. We estimated the magnitude of selective constraint on a large dataset of mouse-rat gene orthologs and their surrounding noncoding DNA. Our analysis indicates that there are more than three times as many selectively constrained, nonrepetitive sites within noncoding DNA as in coding DNA in murids. The majority of these constrained noncoding sites appear to be located within intergenic regions, at distances greater than 5 kilobases from known genes. Our study also shows that in murids, intron length and mean intronic selective constraint are negatively correlated with intron ordinal number. Our results therefore suggest that functional intronic sites tend to accumulate toward the 5′ end of murid genes. Our analysis also reveals that mean number of selectively constrained noncoding sites varies substantially with the function of the adjacent gene. We find that, among others, developmental and neuronal genes are associated with the greatest numbers of putatively functional noncoding sites compared with genes involved in electron transport and a variety of metabolic processes. Combining our estimates of the total number of constrained coding and noncoding bases we calculate that over twice as many deleterious mutations have occurred in intergenic regions as in known genic sequence and that the total genomic deleterious point mutation rate is 0.91 per diploid genome, per generation. This estimated rate is over twice as large as a previous estimate in murids. Most DNA can typically be divided into two categories: regions that encode the instructions for the assembly of a protein molecule (protein-coding genes) and those that do not (noncoding). Although mammalian genomes are primarily noncoding, relatively little is known about how much of this is functional, where such regions are found in the genome, and what functions they are likely to perform. In this study, the authors investigated the quantity and location of functional noncoding DNA in mice and rats. They estimate that functional noncoding DNA is at least three times as common as coding DNA in rodents, and the majority is located large distances from known protein-coding genes. Putatively functional intronic DNA tends to be clustered towards the gene 5′ end, suggesting that much intronic sequence is instrumental in regulating gene expression. This study also finds that genes involved in development and the nervous system are typically associated with much higher quantities of functional noncoding DNA, suggesting that these genes require more finely tuned control of their expression. One implication of this study is the finding that disease-causing mutations have occurred more frequently in noncoding regions and may have affected gene expression, rather than protein structure.