Evolutionary origin of regulatory regions of retrogenes in Drosophila

<p>Abstract</p> <p>Background</p> <p>Retrogenes are processed copies of other genes. This duplication mechanism produces a copy of the parental gene that should not contain introns, and usually does not contain cis-regulatory regions. Here, we computationally address the evolutionary origin of promoter and other cis-regulatory regions in retrogenes using a total of 94 <it>Drosophila </it>retroposition events we recently identified. Previous tissue expression data has revealed that a large fraction of these retrogenes are specifically and/or highly expressed in adult testes of <it>Drosophila</it>.</p> <p>Results</p> <p>In this work, we infer that retrogenes do not generally carry regulatory regions from aberrant upstream or normal transcripts of their parental genes, and that expression patterns of neighboring genes are not consistently shared by retrogenes. Additionally, transposable elements do not appear to substantially provide regulatory regions to retrogenes. Interestingly, we find that there is an excess of retrogenes in male testis neighborhoods that is not explained by insertional biases of the retroelement machinery used for retroposition.</p> <p>Conclusion</p> <p>We conclude that retrogenes' regulatory regions mostly do not represent a random set of existing regulatory regions. On the contrary, our conclusion is that selection is likely to have played an important role in the persistence of autosomal testis biased retrogenes. Selection in favor of retrogenes inserted in male testis neighborhoods and at the sequence level to produce testis expression is postulated to have occurred.</p

Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila

BACKGROUND: Processed copies of genes (retrogenes) are duplicate genes that originated through the reverse-transcription of a host transcript and insertion in the genome. This type of gene duplication, as any other, could be a source of new genes and functions. Using whole genome sequence data for 12 Drosophila species, we dated the origin of 94 retroposition events that gave rise to candidate functional genes in D. melanogaster. RESULTS: Based on this analysis, we infer that functional retrogenes have emerged at a fairly constant rate of 0.5 genes per million years per lineage over the last approximately 63 million years of Drosophila evolution. The number of functional retrogenes and the rate at which they are recruited in the D. melanogaster lineage are of the same order of magnitude as those estimated in the human lineage, despite the higher deletion bias in the Drosophila genome. However, unlike primates, the rate of retroposition in Drosophila seems to be fairly constant and no burst of retroposition can be inferred from our analyses. In addition, our data also support an important role for retrogenes as a source of lineage-specific male functions, in agreement with previous hypotheses. Finally, we identified three cases of functional retrogenes in D. melanogaster that have been independently retroposed and recruited in parallel as new genes in other Drosophila lineages. CONCLUSION: Together, these results indicate that retroposition is a persistent mechanism and a recurrent pathway for the emergence of new genes in Drosophila

Interactions of long-term grazing and woody encroachment can shift soil biogeochemistry and microbiomes in savanna ecosystems

Semi-arid grasslands and savannas in the southern Great Plains USA are extensively used for livestock grazing. Over the past century, Juniperus (juniper) and Quercus (oak) species abundance have increased due to intensive grazing and reduced fire frequency. We investigated the interactions between livestock grazing history (none, moderate, heavy) and vegetation cover (grassland, juniper, oak) using a ∼ 70-year grazing experiment in west-central Texas. We explored effects on soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), microbial community composition, and function. SOC and TN were 50–150 % higher under juniper and oak compared to grasslands, and 10–30 % lower in grazed vs. ungrazed areas. Vegetation × grazing interaction showed greater SOC and TN loss under oak than juniper or grasslands. Ungrazed controls had higher soil TP than grazed areas, with oak and juniper soils having more TP than grasslands. Bacterial and fungal communities differed between grassland and woody vegetation. Grazing affected only bacterial communities. SOC, TN, TP accounted for differences in community structure. Abundances of genes related to methane, nitrogen, sulfur metabolisms, and dominant fungal trophic modes were linked to soil C, N, P ratios. These findings highlight how long-term livestock grazing and woody plant encroachment influence soil C, N, P cycles, altering soil microbial community structure and function. This study provides insights for savanna ecosystem management and integrating land cover effects into biogeochemical models for global change scenarios

Paramyxovirus Infection Regulates T Cell Responses by BDCA-1 + and BDCA-3 + Myeloid Dendritic Cells

Abstract Respiratory syncytial virus (RSV) and human Metapneumovirus (hMPV), viruses belonging to the family Paramyxoviridae, are the most important causes of lower respiratory tract infection in young children. Infections with RSV and hMPV are clinically indistinguishable, and both RSV and hMPV infection have been associated with aberrant adaptive immune responses. Myeloid Dendritic cells (mDCs) play a pivotal role in shaping adaptive immune responses during infection; however, few studies have examined how interactions of RSV and hMPV with individual mDC subsets (BDCA-1 + and BDCA-3 + mDCs) affect the outcome of anti-viral responses. To determine whether RSV and hMPV induce virus-specific responses from each subset, we examined co-stimulatory molecules and cytokines expressed by BDCA-1 + and BDCA-3 + mDCs isolated from peripheral blood after infection with hMPV and RSV, and examined their ability to stimulate T cell proliferation and differentiation. Our data show that RSV and hMPV induce virus-specific and subset-specific patterns of co-stimulatory molecule and cytokine expression. RSV, but not hMPV, impaired the capacity of infected mDCs to stimulate T cell proliferation. Whereas hMPVinfected BDCA-1 + and BDCA-3 + mDCs induced expansion of Th17 cells, in response to RSV, BDCA-1 + mDCs induced expansion of Th1 cells and BDCA-3 + mDCs induced expansion of Th2 cells and Tregs. These results demonstrate a virusspecific and subset-specific effect of RSV and hMPV infection on mDC function, suggesting that these viruses may induce different adaptive immune responses

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms

A Spatially Resolved Dark- versus Light-Zone Microenvironment Signature Subdivides Germinal Center-Related Aggressive B Cell Lymphomas

We applied digital spatial profiling for 87 immune and stromal genes to lymph node germinal center (GC) dark- and light-zone (DZ/LZ) regions of interest to obtain a differential signature of these two distinct microenvironments. The spatially resolved 53-genes signature, comprising key genes of the DZmutational machinery and LZ immune and mesenchymal milieu, was applied to the transcriptomes of 543 GC-related diffuse large B cell lymphomas and double-hit ( DH) lymphomas. According to the DZ/LZ signature, the GC-related lymphomas were sub-classified into two clusters. The subgroups differed in the distribution of DH cases and survival, with most DH displaying a distinct DZ-like profile. The clustering analysis was also performed using a 25-genes signature composed of genes positively enriched in the non-B, stromal sub-compartments, for the first time achieving DZ/LZ discrimination based on stromal/immune features. The report offers new insight into the GC microenvironment, hinting at a DZ microenvironment of origin in DH lymphomas

The common marmoset genome provides insight into primate biology and evolution

We report the whole-genome sequence of the common marmoset (Callithrix jacchus). The 2.26-Gb genome of a female marmoset was assembled using Sanger read data (6×) and a whole-genome shotgun strategy. A first analysis has permitted comparison with the genomes of apes and Old World monkeys and the identification of specific features that might contribute to the unique biology of this diminutive primate, including genetic changes that may influence body size, frequent twinning and chimerism. We observed positive selection in growth hormone/insulin-like growth factor genes (growth pathways), respiratory complex I genes (metabolic pathways), and genes encoding immunobiological factors and proteases (reproductive and immunity pathways). In addition, both protein-coding and microRNA genes related to reproduction exhibited evidence of rapid sequence evolution. This genome sequence for a New World monkey enables increased power for comparative analyses among available primate genomes and facilitates biomedical research application. © 2014 Nature America, Inc

Germinal center dysregulation by histone methyltransferase EZH2 promotes lymphomagenesis

Protection against deadly pathogens requires the production of high-affinity antibodies by B cells, which are generated in germinal centers (GCs). Alteration of the GC developmental program is common in many B cell malignancies. Identification of regulators of the GC response is crucial to develop targeted therapies for GC B cell dysfunctions, including lymphomas. The histone H3 lysine 27 methyltransferase enhancer of zeste homolog 2 (EZH2) is highly expressed in GC B cells and is often constitutively activated in GC-derived non-Hodgkin lymphomas (NHLs). The function of EZH2 in GC B cells remains largely unknown. Herein, we show that Ezh2 inactivation in mouse GC B cells caused profound impairment of GC responses, memory B cell formation, and humoral immunity. EZH2 protected GC B cells against activation-induced cytidine deaminase (AID) mutagenesis, facilitated cell cycle progression, and silenced plasma cell determinant and tumor suppressor B-lymphocyte–induced maturation protein 1 (BLIMP1). EZH2 inhibition in NHL cells induced BLIMP1, which impaired tumor growth. In conclusion, EZH2 sustains AID function and prevents terminal differentiation of GC B cells, which allows antibody diversification and affinity maturation. Dysregulation of the GC reaction by constitutively active EZH2 facilitates lymphomagenesis and identifies EZH2 as a possible therapeutic target in NHL and other GC-derived B cell diseases.Published versio

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics

Culex quinquefasciatus (the southern house mosquito) is an important mosquito vector of viruses such as West Nile virus and St. Louis encephalitis virus, as well as of nematodes that cause lymphatic filariasis. C. quinquefasciatus is one species within the Culex pipiens species complex and can be found throughout tropical and temperate climates of the world. The ability of C. quinquefasciatus to take blood meals from birds, livestock, and humans contributes to its ability to vector pathogens between species. Here, we describe the genomic sequence of C. quinquefasciatus: Its repertoire of 18,883 protein-coding genes is 22% larger than that of Aedes aegypti and 52% larger than that of Anopheles gambiae with multiple gene-family expansions, including olfactory and gustatory receptors, salivary gland genes, and genes associated with xenobiotic detoxification

Molecular analysis of gametogenesis in amphibian anurans belonging to the ‘Rana esculenta complex’

In metazoan species, sexual reproduction occur through the fusion of male and female gametes. Mature haploid gametes generate by the differentiation of the germ cells via meiotic cell division, the gametogenesis process. Both germline cells development than gametes formation from germ cells represent evolutionary controlled crucial steps in the maintenance of species identity. The study of germline development and gametogenesis have been greatly improved after the analysis of the genetic network involved in these processes in model animal organisms. Several genes are presently known to retain a conserved role in groups like amphibian anurans, insects and nematodes, which germline cells are specified by the inheritance of maternal determinants, than taxa such as mammals and amphibian urodeles, which germ cells arise after interactions between tissues during gastrulation. Although limited by important evolutionary constrains, gametogenesis can undergo complex changes in some cases, for example after the crossbreeding of related but distinct species. Whenever pre-meiotic isolation mechanisms fail to avoid interspecific crosses, the consequent hybrids are usually non-fertile if not viable due to post-meiotic isolation processes. Among the few exceptions of this rule in vertebrates, the western Palaearctic group of water frogs, also know as ‘Rana esculenta complex’, offer a unique example. This complex is formed by several pure species and at least three different interspecific hybrid lineages characterized by the extremely rare reproductive mode named hybridogenesis. During the larval development of hybridogenetic forms, one parental genome is eliminated and the second chromosome set is duplicated only in the germline, before the beginning of the first meiosis division, and adult hybrids produce haploid gametes containing one unrecombined genome of the second parental species. The hybrids constitution is recovered by their backcrossing with the parental species whose genome has been eliminated. Rana esculenta, the first green frog species classified by Linneus, represents instead the hybridogenetic hybrids of the two species Rana lessonae and Rana ridibunda, but it usually forms mixed populations only with R. lessonae in the most widespread and best characterized system belonging to the ‘Rana esculenta complex’, named L-E. Several investigations carried out on the L-E system demonstrated that in the vast majority of cases the R. lessonae genome is eliminated, whereas the R. ridibunda chromosomes are duplicated before the first meiosis in R. esculenta germ cells. However, a molecular approach to the study of the modified gametogenesis of these anuran hybrids have not been performed yet. In this perspective, several genes known to be conservatively involved in the germline determination and maintenance, as well as in gametogenesis, have been isolated in R. lessonae, and their expression pattern has been determined in R. esculenta, R. lessonae, R. ridibunda, in the present work, in order to improve our knowledge of the gametogenesis in hybridogenetic forms. Selected genes belong to the three different gene families of the DEAD box ATP-dependent RNA helicases, Pumilio and Y-box, which members encode translational regulators of messenger RNA. Full-length cDNAs of the five genes RlVlg and RlPl10 (DEAD box ATP-dependent RNA helicases family), Rlpum1, Rlpum2 (Pumilio family) and Rlybox2 (Y-box family) were cloned from R. lessonae testis and ovary cDNA libraries, and both RT-PCR on adult tissues than in situ hybridization experiments on testis and ovary showed that these genes are expressed during early stages of both oogenesis and gametogenesis in adult gonads. RlVlg represents the homologue of Drosophila vasa gene, a specific marker of germ line in metazoans, and is active only in germ cells. RlPl10 is homologue to the DEAD box genes An3 in Xenopus and Pl10 in mouse and is expressed in both somatic than germline tissues, as well as the two pumilio genes Rlpum1 and Rlpum2. Rlybox2 instead constitutes the germline specifically-expressed member of the Y-box family in vertebrates and, as expected, its transcript has been detected only in testis and ovary of adult frogs. During oogenesis of R. lessonae, R. ridibunda and R. esculenta, the five genes showed a decreasing expression in the early stages I-III (RlPl10, Rlpum1, Rlpum2 and Rlybox2), or I-IV (RlVlg), whereas no activity was observed in the late stages V-VI. On the basis of in situ hybridization experiments on testis sections, the genes RlVlg, RlPl10 and Rlpum1 showed a differential expression in spermatogenesis stages. RlVlg mRNA was detected in spermatogonia and primary spermatocytes, whereas RlPl10 is expressed in spermatogonia and all the meiotic stages. Immunohistochemical analysis of the expression of the specific G2 and M cell phases marker histone H3 phosphorylated at Serine ten (Ser-10-P-H3) allowed to determine that RlVlg expression in male germ cells occurred before and after the mitotic and first meiotic divisions, respectively. On the contrary, RlPl10 activity is extended to the whole cell cycle. Finally, Rlpum1 transcript was found in both interphase and dividing spermatogonia, and in primary spermatocytes before and after the first meiotic division