Mammalian Genome Evolution Research Articles

Frequent emergence and functional resurrection of processed pseudogenes in the human and mouse genomes

Despite the wide distribution of processed pseudogenes in mammalian genomes, such as those of human and mouse, relatively little is known about their roles in genomic evolution. While gene duplications are recognized as one of the major driving forces in genome evolution, processed pseudogenes, which are retrotransposed copies of mRNAs, have been regarded as junk or selfish DNA for a long time. In order to elucidate the quantitative and qualitative contribution of processed pseudogenes to the mammalian genome evolution, we attempted to detect processed pseudogenes by extensively mapping the mRNAs to both the human and mouse genomes, and then we estimated the rate of their emergence. As a result, we revealed that the rate of pseudogene emergence was about 1–2% per gene per million years, which was as high as the rate (0.9%) of gene duplication in the human genome, although the rate of pseudogene emergence was found to drastically decrease in the hominid lineage. Furthermore, 1% of the processed pseudogenes seemed to be reinvigorated by post-retrotransposition transcription, many of them preserving the intact coding regions. Since the expression patterns of transcribed pseudogenes in various tissues were quite different between human and mouse, their emergence might have led to species-specific evolution. Our results indicate that the generation of processed pseudogenes was not wholly futile but instead has been an indispensable resource, driving dynamic evolution of the mammalian genomes.

High-resolution comparative mapping among man, cattle and mouse suggests a role for repeat sequences in mammalian genome evolution

BackgroundComparative mapping provides new insights into the evolutionary history of genomes. In particular, recent studies in mammals have suggested a role for segmental duplication in genome evolution. In some species such as Drosophila or maize, transposable elements (TEs) have been shown to be involved in chromosomal rearrangements. In this work, we have explored the presence of interspersed repeats in regions of chromosomal rearrangements, using an updated high-resolution integrated comparative map among cattle, man and mouse.ResultsThe bovine, human and mouse comparative autosomal map has been constructed using data from bovine genetic and physical maps and from FISH-mapping studies. We confirm most previous results but also reveal some discrepancies. A total of 211 conserved segments have been identified between cattle and man, of which 33 are new segments and 72 correspond to extended, previously known segments. The resulting map covers 91% and 90% of the human and bovine genomes, respectively. Analysis of breakpoint regions revealed a high density of species-specific interspersed repeats in the human and mouse genomes.ConclusionAnalysis of the breakpoint regions has revealed specific repeat density patterns, suggesting that TEs may have played a significant role in chromosome evolution and genome plasticity. However, we cannot rule out that repeats and breakpoints accumulate independently in the few same regions where modifications are better tolerated. Likewise, we cannot ascertain whether increased TE density is the cause or the consequence of chromosome rearrangements. Nevertheless, the identification of high density repeat clusters combined with a well-documented repeat phylogeny should highlight probable breakpoints, and permit their precise dating. Combining new statistical models taking the present information into account should help reconstruct ancestral karyotypes.

Is mammalian chromosomal evolution driven by regions of genome fragility?

An analysis of the distribution of evolutionary breakpoints in eight species suggests that certain human chromosomal regions are repeatedly used during the evolutionary process, are associated with fragile sites, and show an enrichment of tandem repeats.

The dog has its day

Domestication and selective breeding have transformed wolves into the diversity of dogs we see today. The sequence of the genome of one breed adds to our understanding of mammalian biology and genome evolution.

Correlation Between Alterations in Nucleosomal Organization of LINEs in the Promoter of Cytochrome P450 2B1/2 Gene and Induction of CYP 2B1/2B2 mRNA Expression byb Phenobarbitone in Rat Liver

Mammalian genome contains a high proportion of repetitive DNA with a sizeable fraction of Long Interspersed Nuclear Elements (LINEs). LINEs have been functionally implicated in the organization and evolution of mammalian genome. However, functions of LINEs in the promoter region and gene expression are poorly understood. Here, we report two small, conserved LINE sequences (3P and 5P) that occur as multiple copies of inverted repeats in the rat Cytochrome P450 2B1/2B2 (CYP 2B1/2) gene promoter. Using 3P or 5P as a single primer, the CYP 2B1/2 promoter DNA was amplified by PCR from the rat genome. Phenobarbitone (PB), a prototype xenobiotic drug, strongly induced CYP 2B1/2 mRNA expression in the rat liver. 3P and 5P LINE sequences showed an alteration in the nucleosomal organization in the CYP 2B1/2 promoter after 2, 4, and 6 h of PB induction, and the promoter was mostly devoid of nucleosomes during the induction. Reorganization of nucleosomes associated with these LINE sequences were strongly correlated with induction of CYP 2B1/2 mRNA expression by PB in vivo. Our results strongly suggest that these LINE sequences in CYP 2B1/2 gene promoter(s) may facilitate transcriptional activation of the gene(s) by PB through retention and reorganization of nucleosomes. This might be a novel function of LINEs in the mammalian genome that correlates the chromatin structure with gene expression during drug metabolism.

A New Mechanism of Retrogene Formation in Mammalian Genomes: In Vivo Recombination during RNA Reverse Transcription

L1 LINE retrotransposons play an important role in the shaping and permanent evolution of mammalian genomes. In particular, occupying about 20% of genomic DNA, they transduce their 3' flanking sequences to new genomic loci and create pseudogenes by reverse transcribing different kinds of cellular RNAs. Recently we discovered in mammalian genomes several families of chimeric pseudogenes, consisting of fused copies of various cellular transcripts. The characteristic peculiarities of such chimeric inserts suggest the involvement of L1 enzymatic machinery in their formation. The detailed sequence analysis revealed that 5' terminal parts of the chimeras are copies of nuclear RNAs, while 3' terminal sequences were formed on the templates of transcripts having cytoplasmic orientation. These data enabled us to propose the mechanism for the chimeras formation, comprising the switch of templates during RNA reverse transcription by L1 reverse transcriptase. The further identification of not only "double", but also "triple" chimeric retrogenes evidences the possibility of the double template switches as well. Some of the found chimeras are transcriptionally active, thus allowing to consider the discovered phenomenon as the new mechanism of the gene formation by "shuffling" of pre-existing transcribed sequences. Being active in mammals now, the mechanism appeared at least 75 million years ago and is evolutionary conserved.

Shotgun sequence assembly and recent segmental duplications within the human genome

Complex eukaryotic genomes are now being sequenced at an accelerated pace primarily using whole-genome shotgun (WGS) sequence assembly approaches. WGS assembly was initially criticized because of its perceived inability to resolve repeat structures within genomes. Here, we quantify the effect of WGS sequence assembly on large, highly similar repeats by comparison of the segmental duplication content of two different human genome assemblies. Our analysis shows that large (> 15 kilobases) and highly identical (> 97%) duplications are not adequately resolved by WGS assembly. This leads to significant reduction in genome length and the loss of genes embedded within duplications. Comparable analyses of mouse genome assemblies confirm that strict WGS sequence assembly will oversimplify our understanding of mammalian genome structure and evolution; a hybrid strategy using a targeted clone-by-clone approach to resolve duplications is proposed.

Recombination, GC-content and the human pseudoautosomal boundary paradox

The pseudoautosomal boundary of mammalian sex chromosomes separates a low-recombination region (X- or Y-specific) from a high-recombination region (the pseudoautosomal region), providing a good opportunity to investigate the influence of recombination on molecular evolutionary processes. The mouse and human patterns of sequence variation, however, are discordant: a striking difference of GC-content and evolutionary rate was reported between the proximal and distal sides of the pseudoautosomal boundary in the mouse genome, whereas this difference was not found in the human genome. The paradox might be explained by the mirror histories of the pseudoautosomal boundary in the two species, and by the asymmetric nature of the forces driving GC-content evolution in mammalian genomes.

The rat comes clean

The rat genome sequence, the third mammalian genome sequence to be generated, was recently reported in Nature. The sequence provides new insights into mammalian genome evolution and the opportunity to translate decades of descriptive phenotyping to an understanding of the molecular mechanisms that underlie these phenotypes.

A natural allele of Nxf1 suppresses retrovirus insertional mutations.

Endogenous retroviruses have shaped the evolution of mammalian genomes. Host genes that control the effects of retrovirus insertions are therefore of great interest. The modifier-of-vibrator-1 locus (Mvb1) controls levels of correctly processed mRNA from genes mutated by endogenous retrovirus insertions into introns, including the Pitpn(vb) tremor mutation and the Eya1(BOR) model of human branchiootorenal syndrome. Positional complementation cloning identifies Mvb1 as the nuclear export factor Nxf1, providing an unexpected link between the mRNA export receptor and pre-mRNA processing. Population structure of the suppressive allele in wild Mus musculus castaneus suggests selective advantage. A congenic Mvb1(CAST) allele is a useful tool for modifying gene expression from existing mutations and could be used to manipulate engineered mutations containing retroviral elements.

An exhaustive search for tandem repeats and long duplicated chromosomal regions within the mouse genome.

Traces of ancient duplications of extensive chromosomal regions are being discovered within the human genome. For example, the MHC (major histocompatibility complex) gene region on chromosome 6 (6p21.3) encodes a cluster of genes that are homologous to those on chromosome 9 (9q33-q34) . These regions appear to have arisen from regional duplication around the time of vertebrate emergence. To elucidate the evolution of mammalian genomes, it is crucial to search for duplicated chromosomal regions in the mouse genome. In this study, we searched for long duplicated chromosomal regions in the mouse genome using the map information derived from the Mouse Genome Database and the numerous homologous gene pairs from GenBank. To identify the regions, we searched for homologous gene pairs among the genomic sequences extracted from GenBank (r.118) . We defined the candidates of duplicated regions as those having more than two homologous gene pairs located within 5cM on each chromosome. We conducted a statistical test considering the distribution of homologous gene pairs and tandem repeats in the mouse genome. Twenty-seven pairs of duplicated regions were found in this study. Seven procollagen genes, three Hox gene clusters, six integrin genes, three fibroblast growth factor receptor genes and three eye absent homolog genes were located in the duplicated regions.

Mapping of five genes from human chromosome 17 to chromosome hn of the common shrew Sorex araneus

Larkin D. M., Serov O. L. and Zhdanova N. S. 2000. Mapping of five genes from human chromosome 17 to chromosome hn of the common shrew Sorex araneus. [In: Evolution in the Sorex araneus group: Cytogenetic and molecular aspects. J. B. Searle and J. M. Wojcik, eds], Acta Theriologica 45, Suppl. 1: 143-146. Comparative mapping shows that the syntenic gene group which is located on human chromosome 17 (HSA17) is preserved in most mammalian species. Insectivores (including shrews) appear to be closer to the ancestral eutherians than other mammalian orders. That is why common shrews are of special interest for the study of mammalian genome evolution. A set of human, mouse and bovine PCR primers previously used for mapping the bovine homologue o f HSA17 was applied to the mapping effort in shrews. Three of 21 primer pairs tested yielded a single PCR product of expected size. Addi­ tionally, we have developed consensus PCR primers for GLUT4 based on human, mouse and porcine sequences, and for THRA1 using human and porcine sequences. As a result, genes for NF1, MYL4, THRA1, GLUT4 and MPO were assigned to shrew chromosome hn (SARhn) using a set of shrew-mouse somatic hybrids. PCR products of shrew THRA1 and MPO were partially sequenced and showed 95% homology to sheep THRA1 and 91% homology to human MPO sequences respectively with the NCBI BLAST program. The data obtained confirm the homology between HSA17 and SARhn revealed by zoo-FISH analysis. It is suggested this syntenic group was present in the ancestral mammalian founder karyotype.

The biological properties and evolutionary dynamics of mammalian LINE-1 retrotransposons

Mammalian LINE-1 (L1) elements belong to the superfamily of autonomously replicating retrotransposable elements that lack the long terminal repeated (LTR) sequences typical of retroviruses and retroviral-like retrotransposons. The non-LTR superfamily is very ancient and L1-like elements are ubiquitous in nature, having been found in plants, fungi, invertebrates, and various vertebrate classes from fish to mammals. L1 elements have been replicating and evolving in mammals for at least the past 100 million years and now constitute 20% or more of some mammalian genomes. Therefore, L1 elements presumably have had a profound, perhaps defining, effect on the evolution, structure, and function of mammalian genomes. L1 elements contain regulatory signals and encode two proteins: one is an RNA-binding protein and the second one presumably functions as an integrase-replicase, because it has both endonuclease and reverse transcriptase activities. This work reviews the structure and biological properties of L1 elements, including their regulation, replication, evolution, and interaction with their mammalian hosts. Although each of these processes is incompletely understood, what is known indicates that they represent challenging and fascinating biological phenomena, the resolution of which will be essential for fully understanding the biology of mammals.

Estimating the Number of Mouse Genes and the Duplicated Regions within the Mouse Genome

To elucidate the evolution of mammalian genomes, it is crucial to estimate the number of genes in thegenome and to measure the degree of redundancy in the genome in various species. The number ofhuman protein-coding genes was recently estimated as 35,000-40,000, though it is still controversial.Also, traces of ancient duplications of extensive chromosomal regions were being discovered withinthe human genome. In this study, we estimated the number of mouse genes using expressed sequencetags of full-length cDNA library and a set of genes obtained by clustering mRNA sequences fromDDBJ/EMBL/GenBank. We also estimated the duplicated chromosomal regions within the mousegenome using the map information derived from the Mouse Genome Database and the numeroushomologous gene pairs from DDBJ/EMBL/GenBank.

Exon shuffling mimicked in cell culture.

Undesired side products of DNA transfections are usually discarded. However, here, we show that such products may provide insight into mutational events that are also a major driving force in protein evolution. While studying the small heat-shock protein alphaA-crystallin, we transfected the hamster alphaA-crystallin gene into a mouse muscle cell line. One of the stable transfected cell lines expressed, in addition to the expected normal alphaA- and alternatively spliced alphaAins-crystallins, two slightly larger, immunologically cross-reacting proteins. These proteins were found to be encoded by a mutant alphaA-crystallin gene with a large intragenic duplication, arisen by illegitimate recombination at two CCCAT homologies, approximately 1.8 kilobases apart in the normal hamster alphaA-crystallin gene. As a consequence, a tandem-duplicated exon 3 sequence is present in the mature mRNA of this gene, resulting in a 41-residue repeat in the translated proteins. Cells expressing the elongated alphaA-crystallins have normal growth characteristics and the usual diffuse cytoplasmic distribution of immunoreactive alphaA-crystallin. Size-exclusion chromatography of cell extracts indicated that the mutant proteins are readily incorporated into the normal large water-soluble alphaA-crystallin complexes, showing that the insert does not disturb the integrity of these complexes. This viable alphaA-crystallin mutant thus mimics the origins and effects of exon duplication, which is a common consequence of exon shuffling in mammalian genome evolution.

The human COX10 gene is disrupted during homologous recombination between the 24 kb proximal and distal CMT1A-REPs.

The CMT1A-REPs are two large directly repeating DNA sequences located on chromosome 17p11.2-p12 flanking the region duplicated in patients with Charcot-Marie-Tooth disease type 1A (CMT1A) and deleted in patients with hereditary neuropathy with liability to pressure palsies (HNPP). We have sequenced two cosmids, c74F4 and c15H12, which contain the entire proximal and distal CMT1A-REPs and determined that these repeats are approximately 99% identical across a 24,011 bp region. In addition, both contain an exon of the human heme A:farnesyltransferase gene (COX10). Hybridization studies revealed that COX10 spans the distal CMT1A-REP, while the proximal CMT1A-REP contains an isolated COX10 'pseudo-exon'. There is also a COX10 hybridization signal on chromosome 10 which appears to represent a processed pseudogene. We propose that the distal CMT1A-REP represents the progenitor copy of COX10 exon VI which was duplicated with surrounding intronic sequences during mammalian genome evolution and that the HNPP deletion results in a COX10 null allele.

HIV genetic variation is directed and restricted by DNA precursor availability

The effects of deoxynucleoside triphosphate (dNTP) imbalances on the fidelity of human immunodeficiency virus type 1 (HIV-1) replication were investigated. Using detergent permeabilized virions and biased dNTP concentrations different types of hypermutants were readily produced. However, the mutant spectrum was different from naturally occurring hypermutants demonstrating that the host cell may restrict variation. Using a genetic screen based on the blue/white β-galactosidase complementation assay, G→A hypermutants were recovered from HIV-infected thymidine treated U937 cells. Furthermore, hypermutants were recovered from 1 to 2% of resting or activated peripheral blood mononuclear cells indicating that small proportions of primary cells had distorted intracellular [dTTP] and [dCTP]. Such imbalances may underlie a proportion of somatic and germline point mutations and shape to some extent the evolution of mammalian and viral genomes.

Localization of new genes and markers to the distal part of the human major histocompatibility complex (MHC) region and comparison with the mouse: new insights into the evolution of mammalian genomes

We have refined and extended the map of the distal half of the human major histocompatibility complex. The map is continuous from HLA-E to 1000 kb telomeric of HLA-F and includes six new markers and genes. In addition, the corresponding sequences that were not previously mapped in the mouse genome have been located. The human and the mouse organizations have therefore been compared. This comparison allows us to demonstrate that the structure of the distal part of the MHC is similar in the two species. In addition, this comparison shows the presence of a breakpoint of synteny telomeric of the distal part of the H-2 region. Indeed, the region telomeric of HLA in human is found on a chromosome different from that carrying H-2 in mouse. The mapping analysis of paralogous genes (structurally related genes) around the breakpoint shows that the human organization probably represents the putative human/mouse ancestral one. This evolutionary breakpoint was precisely mapped in human, and the surrounding region was cloned into yeast artificial chromosomes. Finally, we show that the region found around the breakpoint was involved several times in chromosome recombinations in the mouse lineage, as it seems to correspond also to the t-complex distal inversion point.

Comparative mapping reveals extensive linkage conservation—but with gene order rearrangements—between the pig and the human genomes

A porcine comparative map based on 83 coding loci was constructed. Comparisons to the human and mouse genetic maps revealed linkage conservation between humans and pigs more extensive than that between any of these and the mouse. The average lengths of conserved chromosome segments between pig and human and between pig and mouse were estimated at 37 and 21 cM, respectively. Rearrangements of gene orders within homologous chromosome segments were found to be common among these distantly related mammals. The development of a comparative map is an advance in pig genome analysis and contributes to the dissection of mammalian genome evolution.

A genetic linkage map of the mouse: current applications and future prospects.

Technological advances have made possible the development of high-resolution genetic linkage maps for the mouse. These maps in turn offer exciting prospects for understanding mammalian genome evolution through comparative mapping, for developing mouse models of human disease, and for identifying the function of all genes in the organism.