Impact of transposable elements on the human genome

Methylation guide RNA evolution in archaea: structure, function and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species

Archaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2′-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene annotation because reliable, fully automated detection methods are not available. We expanded and curated a comprehensive gene set across six species of the crenarchaeal genus Pyrobaculum, particularly rich in C/D box sRNA genes. Using high-throughput small RNA sequencing, specialized computational searches and comparative genomics, we analyzed 526 Pyrobaculum C/D box sRNAs, organizing them into 110 families based on synteny and conservation of guide sequences which determine methylation targets. We examined gene duplications and rearrangements, including one family that has expanded in a pattern similar to retrotransposed repetitive elements in eukaryotes. New training data and inclusion of kink-turn secondary structural features enabled creation of an improved search model. Our analyses provide the most comprehensive, dynamic view of C/D box sRNA evolutionary history within a genus, in terms of modification function, feature plasticity, and gene mobility.

Evolutionary Story of the Low/Medium-Affinity IgG Fc Receptor Gene Cluster

Low/intermediate affinity Fc-gamma receptors (FcγR) are crucial for the recognition of immune complexes and IgG-sensitized microorganisms by phagocytic and cytotoxic effector cells. In all mammalian species studied so far, their genes are clustered in a single locus. However, this locus differs between humans and mice, both in the number of genes and the structure/function of the encoded receptors. We show that murine fcgr3 evolved through several steps into FCGR2A, its ortholog, which is specific to primates. One of these steps was the insertion of a retroviral element bringing a new intracellular exon comprising a non-canonical ITAM motif. We also show that the fcgr3-hspa6-fcgr4-fcgr2b module in mammals that has evolved in a FCGR2A-HSPA6-FCGR4-FCGR2B module in primates, was subsequently duplicated in apes through a Non-Allelic Homologous Recombination (NAHR), giving birth to FCGR2C, a hybrid gene between FCGR2B and FCGR2A. The FCGR4 duplication, which occurred simultaneously, eventually resulted in the emergence of FCGR3B, while FCGR3A remained the true FCGR4 ortholog. FCGR2C and FCGR3B, markers of this NAHR, are present in gorillas and chimpanzees, whereas they are absent in orangutans and more distant primates, such as gibbons and macaques. These data need to be taken into account when testing IgG-based therapies in animal species.

Low coverage sequencing for repetitive DNA analysis in Passiflora edulis Sims: citogenomic characterization of transposable elements and satellite DNA

BACKGROUND

The cytogenomic study of repetitive regions is fundamental for the understanding of morphofunctional mechanisms and genome evolution. Passiflora edulis a species of relevant agronomic value, this work had its genome sequenced by next generation sequencing and bioinformatics analysis performed by RepeatExplorer pipeline. The clusters allowed the identification and characterization of repetitive elements (predominant contributors to most plant genomes). The aim of this study was to identify, characterize and map the repetitive DNA of P. edulis, providing important cytogenomic markers, especially sequences associated with the centromere.

RESULTS

Three clusters of satellite DNAs (69, 118 and 207) and seven clusters of Long Terminal Repeat (LTR) retrotransposons of the superfamilies Ty1/Copy and Ty3/Gypsy and families Angela, Athila, Chromovirus and Maximus-Sire (6, 11, 36, 43, 86, 94 and 135) were characterized and analyzed. The chromosome mapping of satellite DNAs showed two hybridization sites co-located in the 5S rDNA region (PeSat_1), subterminal hybridizations (PeSat_3) and hybridization in four sites, co-located in the 45S rDNA region (PeSat_2). Most of the retroelements hybridizations showed signals scattered in the chromosomes, diverging in abundance, and only the cluster 6 presented pericentromeric regions marking. No satellite DNAs and retroelement associated with centromere was observed.

CONCLUSION

P. edulis has a highly repetitive genome, with the predominance of Ty3/Gypsy LTR retrotransposon. The satellite DNAs and LTR retrotransposon characterized are promising markers for investigation of the evolutionary patterns and genetic distinction of species and hybrids of Passiflora.

Whats, hows and whys of programmed DNA elimination in Tetrahymena

Programmed genome rearrangements in ciliates provide fascinating examples of flexible epigenetic genome regulations and important insights into the interaction between transposable elements (TEs) and host genomes. DNA elimination in Tetrahymena thermophila removes approximately 12 000 internal eliminated sequences (IESs), which correspond to one-third of the genome, when the somatic macronucleus (MAC) differentiates from the germline micronucleus (MIC). More than half of the IESs, many of which show high similarity to TEs, are targeted for elimination in cis by the small RNA-mediated genome comparison of the MIC to the MAC. Other IESs are targeted for elimination in trans by the same small RNAs through repetitive sequences. Furthermore, the small RNA–heterochromatin feedback loop ensures robust DNA elimination. Here, we review an updated picture of the DNA elimination mechanism, discuss the physiological and evolutionary roles of DNA elimination, and outline the key questions that remain unanswered.

A piece of the pi(e): The diverse roles of animal piRNAs and their PIWI partners

Small non-coding RNAs are indispensable to many biological processes. A class of endogenous small RNAs, termed PIWI-interacting RNAs (piRNAs) because of their association with PIWI proteins, has known roles in safeguarding the genome against inordinate transposon mobilization, embryonic development, and stem cell regulation, among others. This review discusses the biogenesis of animal piRNAs and their diverse functions together with their PIWI protein partners, both in the germline and in somatic cells, and highlights the evolutionarily conserved aspects of these molecular players in animal biology.

Stress cycles in stem cells/iPSCs development: implications for tissue repair

Stem cells have become a major topic, both publicly and scientifically, owing to their potential to cure diseases and repair damaged tissues. Particular attention has been given to the so-called "induced pluripotent stem cells" (iPSCs) in which somatic cells are induced by the expression of transcription factor encoding transgenes-a methodology first established by Takahashi and Yamanaka (Cell 126:663-676, 2006)-to acquire pluripotent state. This methodology has captured researchers' imagination as a potential procedure to obtain patient-specific therapies while also solving both the problem of transplant rejection and the ethical concerns often raised regarding the use of embryonic stem cells in regenerative medicine. The study of the biology of stem cells/iPSCs, in recent years, has uncovered some fundamental weaknesses that undermine their potential use in transplantation therapies.

From Reductionism to Holism: Systems-oriented Approaches in Cancer Research

Somatic mutation theory of cancer has directed cancer research during the last century. A deluge of information on cellular, molecular, and genetic behavior was uncovered, but so was a mind-numbing complexity that still challenges research and concepts, and expectations in the war on cancer have by and large not been fulfilled. A change of paradigm beyond reductionism has been called for, especially as research ubiquitously points at the importance of tissue, microenvironment, extracellular matrix, embryonic and morphogenetic fields, and fields of tissue maintenance and organization in the processes of carcinogenesis, cancer control, and cancer progression, as well as in the control of cellular and genetic behavior. Holistic, organismic systems concepts open new perspectives for cancer research and treatment, as well as general biological understanding.

Characterization and functional annotation of nested transposable elements in eukaryotic genomes

The movement of transposable elements (TE) in eukaryotic genomes can often result in the occurrence of nested TEs (the insertion of TEs into pre-existing TEs). We performed a general TE assessment using available databases to detect nested TEs and analyze their characteristics and putative functions in eukaryote genomes. A total of 802 TEs were found to be inserted into 690 host TEs from a total number of 11,329 TEs. We reveal that repetitive sequences are associated with an increased occurrence of nested TEs and sequence biased of TE insertion. A high proportion of the genes which were associated with nested TEs are predicted to localize to organelles and participate in nucleic acid and protein binding. Many of these function in metabolic processes, and encode important enzymes for transposition and integration. Therefore, nested TEs in eukaryotic genomes may negatively influence genome expansion, and enrich the diversity of gene expression or regulation.

Diversity and evolution of Ty1-copia and Ty3-gypsy retroelements in the non-photosynthetic flowering plants Orobanche and Phelipanche (Orobanchaceae)

We present the first study on the diversity and evolution of Ty1-copia and Ty3-gypsy retroelements in a group of non-photosynthetic flowering plants. To this end partial sequences of the reverse transcriptase (rt) gene were obtained from 20 clones for each retroelement type from seven and six accessions of Orobanche and Phelipanche (Orobanchaceae), respectively. Overall sequence similarity is higher in Ty3-gypsy elements than in Ty1-copia elements in agreement with the results from other angiosperm groups. Higher sequence diversity and stronger phylogenetic structure, especially of Ty1-copia sequences, in Orobanche species compared to Phelipanche species support the previously suggested hypothesis (based on karyological and cytological data) that genomes of Orobanche species are more dynamic than those of Phelipanche species. No evidence was found for intraspecific differences of retroelement diversity nor for differences between pest taxa and their putative wild relatives, e.g., O. crenata and O. owerini. The occurrence of a few sequences from Phelipanche species in clades otherwise comprising sequences from Orobanche species might be due to horizontal gene transfer, but the alternative of vertical transmission cannot be rejected unambiguously.

A movable feast: diverse retrotransposons and their contribution to barley genome dynamics

Cellular genes comprise at most 5% of the barley genome; the rest is occupied primarily by retrotransposons. Retrotransposons move intracellularly by a replicative mechanism similar to that of retroviruses. We describe the major classes of retrotransposons in barley, including the two nonautonomous groups that were recently identified, and detail the evidence supporting our current understanding of their life cycle. Data from analyses of long contiguous segments of the barley genome, as well as surveys of the prevalence of full-length retrotransposons and their solo LTR derivatives in the genus Hordeum, indicate that integration and recombinational loss of retrotransposons are major factors shaping the genome. The sequence conservation and integrative capacity of barley retrotransposons have made them excellent sources for development of molecular marker systems.

Tempo and mode of evolution of a primate-specific retrotransposon belonging to the LINE 1 family

L1P_MA2 is a primate-specific subfamily of L1 retrotransposons. The consensus sequence of this element differs from the canonical L1 consensus by the presence of a 3800-bp region in 5' (L1M1_5). Part of this region has been proposed to be involved in a dystrophin mutation affecting the correct splicing of the gene and causing an X-linked dilated cardiomyopathy. In consideration of the potential involvement in splicing regulation of this element and also because of its atypical structure, we investigated its evolutionary history by analyzing the inter- and intraspecific divergence of L1P_MA2 sequences in various species of primates. The resulting phylogenetic trees show long terminal branches and short basal internodes, as expected for a rapid event of diversification that occurred in the past. The phylogenetic analysis and the intraspecific divergence estimates revealed a pattern of evolution for this element similar in all primates with the exception of lemurs, thus suggesting that the major wave of expansion of L1P_MA2 in primate genomes occurred after the divergence between Prosimiae and Anthropoidea. These results clearly indicate that a phylogenetic approach is more appropriate than methods based on sequence data from a single species, when investigating time and mode of evolution of retro-elements.

The diversity of retroelements in diploid and allotetraploid Brassica species

Using universal PCR primers, some 80 fragments of retroelement reverse transcriptase genes were isolated from 16 accessions of the three diploid and three derived allotetraploid species of Brassica in the triangle of U. Sequence analysis showed that the Ty1/copia and LINE-like elements were distinct, while a third clade could be sub-divided into Ty3/gypsy, Athila and virus-like branches, providing evidence that there are multiple sub-lineages within this group normally considered to be gypsy-like elements in plants. The parsimony trees showed no branches correlating with the known genome relationships for the six diploid and allotetraploid Brassica species, probably because members of the element families were present in the common ancestor of the Brassica and, unlike other repetitive sequences, there is no evidence for genome-wide homogenization, although convergent evolution or horizontal transfer cannot be ruled out. Southern hybridization suggested some sub-families were amplified in individual species. The data show that retroelement sequence data do not allow inference of phylogeny, but knowledge of evolution of such abundant sequences assists in exploitation and interpretation of data from other species including models with much smaller genomes and may provide markers.

The role of somatic and germline mutations in aging and a mutation interaction model of aging

Mutations with a deleterious effect that is expressed after the average reproductive period are not effectively selected against and can accumulate in the germline. A conservative estimate is that at least 1-2% of new deleterious mutations affect some aspect of DNA replication, repair, or chromosome segregation. Since deleterious mutations can have an effect even as heterozygotes, this mutation accumulation can create an inherited background of late-acting mutations that themselves enhance mutation rate. This can have an interactive effect, in that it may increase the rate of somatic mutation during an individual's lifetime. The aging individual therefore becomes increasingly mosaic for somatic mutations, which in turn could potentially contribute to the gradual deterioration of biological processes and influence what we experience as senescence. Interventions that reduce somatic and germ cell mutations should, therefore, reduce the aging process in present and future generations.

Cytosine methylation mediates sexual conflict

Transposons are infectious agents in sexual populations and can go to fixation even if they reduce the fitness of the host. Sexual hosts are therefore under selective pressure to evolve defensive functions that relieve the fitness penalty imposed by transposons. In mammals, this defensive function depends on transcriptional silencing through targeted cytosine methylation of transposon promoters in both germ-line and somatic tissues (with the probable involvement of some post-transcriptional gene silencing by pathways related to RNA interference). New families of transposons evolve in response to selective pressures imposed by host silencing mechanisms, with the result that the mammalian genome has suffered waves of transposon bombardment that have contributed the majority of the total sequence. Cytosine methylation defends the sexual genome against transposon damage even as it enforces a requirement for sexual reproduction through the phenomenon of genomic imprinting.

Structural determinants of BRCA1 translational regulation

The BRCA1 gene is involved in sporadic breast and ovarian cancer mainly through reduced expression. BRCA1 mRNAs containing different leader sequences show different patterns of expression. In a normal mammary gland mRNA with a shorter leader sequence, 5'-UTRa is expressed only, whereas in breast cancer tissue mRNA with a longer leader, 5'-UTRb is expressed also. We show that the translation efficiency of transcripts containing 5'-UTRb is 10 times lower than those containing 5'-UTRa. The structures of 5'-UTRa and 5'-UTRb were determined by chemical and enzymatic probing aided by a new method developed for monitoring the number of co-existing stable conformers. Specific factors responsible for reduced translation of mRNA containing 5'-UTRb were determined using a variety of transcripts with mutations in the leader sequence. These factors include a stable secondary structure formed by truncated Alu element and upstream AUG codons. The novel mechanism by which BRCA1 may be involved in sporadic breast and ovarian cancer is proposed. It is based on the expression patterns of BRCA1 mRNAs and differences in their translatability. According to this mechanism the deregulation of the BRCA1 transcription in cancer, resulting in a higher proportion of translationally inhibited transcripts containing 5'-UTRb, contributes to the decrease in the BRCA1 protein observed in sporadic breast and ovarian cancers.

The evolutionary origin and genomic organization of SINEs in Arabidopsis thaliana

We have characterized the two families of SINE retroposons present in Arabidopsis thaliana. The origin, distribution, organization, and evolutionary history of RAthE1 and RAthE2 elements were studied and compared to the well-characterized SINE S1 element from Brassica. Our studies show that RAthE1, RAthE2, and S1 retroposons were generated independently from three different tRNAs. The RAthE1 and RAthE2 families are older than the S1 family and are present in all tested Cruciferae species. The evolutionary history of the RAthE1 family is unusual for SINEs. The 144 RAthE1 elements of the Arabidopsis genome cannot be classified in distinct subfamilies of different evolutionary ages as is the case for S1, RAthE2, and mammalian SINEs. Instead, most RAthE1 elements were probably derived steadily from a single source gene that was maintained intact and active for at least 12-20 Myr, a result suggesting that the RAthE1 source gene was under selection. The distribution of RAthE1 and RAthE2 elements on the Arabidopsis physical map was studied. We observed that, in contrast to other Arabidopsis transposable elements, SINEs are not concentrated in the heterochromatic regions. Instead, SINEs are grouped in the euchromatic chromosome territories several hundred kilobase pairs long. In these territories, SINE elements are closely associated with genes. A retroposition partnership between Arabidopsis SINEs and LINEs is proposed.

Origin of the mutations in the parkin gene in Europe: exon rearrangements are independent recurrent events, whereas point mutations may result from Founder effects

A wide variety of mutations in the parkin gene, including exon deletions and duplications, as well as point mutations, result in autosomal recessive early-onset parkinsonism. Interestingly, several of these anomalies were found repeatedly in unrelated patients and may therefore result from recurrent, de novo mutational events or from founder effects. In the present study, haplotype analysis, using 10 microsatellite markers covering a 4.7-cM region known to contain the parkin gene, was performed in 48 families, mostly from European countries, with early-onset autosomal recessive parkinsonism. The patients carried 14 distinct mutations in the parkin gene, and each mutation was detected in more than one family. Our results support the hypothesis that exon rearrangements occurred independently, whereas some point mutations, found in families from different geographic origins, may have been transmitted by a common founder.