Quantifying the major mechanisms of recent gene duplications in the human and mouse genomes: a novel strategy to estimate gene duplication rates

By studying two mechanisms of gene duplication, unequal crossover and retrotranspostion, and looking at both small gene families and the entire genome, a new estimate for the rate of gene duplication is made which is more accurate for both small and large gene families

Tandemly Arrayed Genes in Vertebrate Genomes

Tandemly arrayed genes (TAGs) are duplicated genes that are linked as neighbors on a chromosome, many of which have important physiological and biochemical functions. Here we performed a survey of these genes in 11 available vertebrate genomes. TAGs account for an average of about 14% of all genes in these vertebrate genomes, and about 25% of all duplications. The majority of TAGs (72–94%) have parallel transcription orientation (i.e., they are encoded on the same strand) in contrast to the genome, which has about 50% of its genes in parallel transcription orientation. The majority of tandem arrays have only two members. In all species, the proportion of genes that belong to TAGs tends to be higher in large gene families than in small ones; together with our recent finding that tandem duplication played a more important role than retroposition in large families, this fact suggests that among all types of duplication mechanisms, tandem duplication is the predominant mechanism of duplication, especially in large families. Finally, several species have a higher proportion of large tandem arrays that are species-specific than random expectation

An atlas of the speed of copy number changes in animal gene families and its implications

The notion that gene duplications generating new genes and functions is commonly accepted in evolutionary biology. However, this assumption is more speculative from theory rather than well proven in genome-wide studies. Here, we generated an atlas of the rate of copy number changes (CNCs) in all the gene families of ten animal genomes. We grouped the gene families with similar CNC dynamics into rate pattern groups (RPGs) and annotated their function using a novel bottom-up approach. By comparing CNC rate patterns, we showed that most of the species-specific CNC rates groups are formed by gene duplication rather than gene loss, and most of the changes in rates of CNCs may be the result of adaptive evolution. We also found that the functions of many RPGs match their biological significance well. Our work confirmed the role of gene duplication in generating novel phenotypes, and the results can serve as a guide for researchers to connect the phenotypic features to certain gene duplications

Loss of Abhd5 Promotes Colorectal Tumor Development and Progression by Inducing Aerobic Glycolysis and Epithelial-Mesenchymal Transition

How cancer cells shift metabolism to aerobic glycolysis is largely unknown. Here, we show that deficiency of a/b-hydrolase domain-containing 5 (Abhd5), an intracellular lipolytic activator that is also known as comparative gene identification 58 (CGI-58), promotes this metabolic shift and enhances malignancies of colorectal carcinomas (CRCs). Silencing of Abhd5 in normal fibroblasts induces malignant transformation. Intestine-specific knockout of Abhd5 in ApcMin/+ mice robustly increases tumorigenesis and malignant transformation of adenomatous polyps. In colon cancer cells, Abhd5 deficiency induces epithelial-mesenchymal transition by suppressing the AMPKa-p53 pathway, which is attributable to increased aerobic glycolysis. In human CRCs, Abhd5 expression falls substantially and correlates negatively with malignant features. Our findings link Abhd5 to CRC pathogenesis and suggest that cancer cells develop aerobic glycolysis by suppressin

Mixing state and particle hygroscopicity of organic-dominated aerosols over the Pearl River Delta region in China

Simultaneous measurements of aerosol hygroscopicity and particle-phase chemical composition were performed at a suburban site over the Pearl River Delta region in the late summer of 2016 using a self-assembled hygroscopic tandem differential mobility analyzer (HTDMA) and an Aerodyne quadruple aerosol chemical speciation monitor (ACSM), respectively. The hygroscopic growth factor (HGF) of the Aitken mode (30 nm, 60 nm) and accumulation mode (100 nm, 145 nm) particles were obtained under 90% relative humidity (RH). An external mixture was observed for particles of every size during this study, with a dominant mode of more-hygroscopic (MH) particles, as aged aerosols dominated due to the anthropogenic influence. The HGF of lesshygroscopic (LH) mode particles increased, while their number fractions decreased during the daytime due to a reduced degree of external mixing that probably resulted from the condensation of gaseous species. These LH mode particles in the early morning or late afternoon could be possibly dominated by carbonaceous material emitted from local automobile exhaust during rush hours. During polluted days with air masses flowing mainly from the coastal areas, the chemical composition of aerosols had a clear diurnal variation and a strong correlation with the mean HGF. Closure analysis was carried out between the HTDMA-measured HGF and the ACSM-derived hygroscopicity using various approximations for the hygroscopic growth factor of organic compounds (HGF(org)). Considering the assumptions regarding the differences in the mass fraction of each component between PM1 and 145 nm particles, the hygroscopicity-composition closure was achieved using an HGF(org) of 1.26 for the organic material in the 145 nm particles and a simple linear relationship between the HGForg and the oxidation level inferred from the O : C ratio of the organic material was suggested. Compared with the results from other environments, HGF(org) obtained from our measurements appeared to be less sensitive to the variation of its oxidation level, which is, however, similar to the observations in the urban atmosphere of other megacities in China. This finding suggests that the anthropogenic precursors or the photooxidation mechanisms might differ significantly between the suburban and urban atmosphere in China and those in other background environments. This may lead to different characteristics of the oxidation products in secondary organic aerosols (SOA) and therefore to a different relationship between the HGF(org) and its O : C ratio.Peer reviewe

An Atlas of the Speed of Copy Number Changes in Animal Gene Families and Its Implications

The notion that gene duplications generating new genes and functions is commonly accepted in evolutionary biology. However, this assumption is more speculative from theory rather than well proven in genome-wide studies. Here, we generated an atlas of the rate of copy number changes (CNCs) in all the gene families of ten animal genomes. We grouped the gene families with similar CNC dynamics into rate pattern groups (RPGs) and annotated their function using a novel bottom-up approach. By comparing CNC rate patterns, we showed that most of the species-specific CNC rates groups are formed by gene duplication rather than gene loss, and most of the changes in rates of CNCs may be the result of adaptive evolution. We also found that the functions of many RPGs match their biological significance well. Our work confirmed the role of gene duplication in generating novel phenotypes, and the results can serve as a guide for researchers to connect the phenotypic features to certain gene duplications

Burst of Young Retrogenes and Independent Retrogene Formation in Mammals

Retroposition and retrogenes gain increasing attention as recent studies show that they play an important role in human new gene formation. Here we examined the patterns of retrogene distribution in 8 mammalian genomes using 4 non-mammalian genomes as a contrast. There has been a burst of young retrogenes not only in primate lineages as suggested in a recent study, but also in other mammalian lineages. In mammals, most of the retrofamilies (the gene families that have retrogenes) are shared between species. In these shared retrofamilies, 14%–18% of functional retrogenes may have originated independently in multiple mammalian species. Notably, in the independently originated retrogenes, there is an enrichment of ribosome related gene function. In sharp contrast, none of these patterns hold in non-mammals. Our results suggest that the recruitment of the specific L1 retrotransposons in mammals might have been an important evolutionary event for the split of mammals and non-mammals and retroposition continues to be an important active process in shaping the dynamics of mammalian genomes, as compared to being rather inert in non-mammals