The secondary structure of nucleic acids containing quartets of guanines, termed G-quadruplexes, is known to regulate the transcription of many genes. Several G-quadruplexes can be formed in the HIV-1 long terminal repeat promoter region and their stabilization results in the inhibition of HIV-1 replication. Here, we identified helquat-based compounds as a new class of anti-HIV-1 inhibitors that inhibit HIV-1 replication at the stage of reverse transcription and provirus expression. Using Taq polymerase stop and FRET melting assays, we have demonstrated their ability to stabilize G-quadruplexes in the HIV-1 long-terminal repeat sequence. Moreover, these compounds were not binding to the general G-rich region, but rather to G-quadruplex-forming regions. Finally, docking and molecular dynamics calculations indicate that the structure of the helquat core greatly affects the binding mode to the individual G-quadruplexes. Our findings can provide useful information for the further rational design of inhibitors targeting G-quadruplexes in HIV-1.
Endogenous retroviruses (ERVs) constitute a significant part of vertebrate genomes. They originated from past retroviral infections and some of them retain transcriptional activity. The key mechanism avoiding uncontrolled ERV transcription is DNA methylation-mediated epigenetic silencing. Despite numerous studies describing the involvement of ERV activity in cellular processes, epigenetic regulation of ERVs is still poorly understood. We previously described a cervid endogenous retrovirus (CrERV) in the mule deer genome. This virus exhibits massive insertional polymorphism, suggesting recent activity. Here we employed NGS-based strategy to determine the methylation pattern of CrERV integrations in four mule deer. Besides the vast majority of methylated integrations, we identified a tiny fraction of demethylated proviral copies. These copies represent evolutionary older integrations located near gene promoters. In general, our work is a first attempt to characterize the epigenetic landscape of insertionally polymorphic ERV on a whole-genome scale and offers insight into its interactions with a host.
Retrotransposable elements are widely distributed and diverse in eukaryotes. Their copy number increases through reverse-transcription-mediated propagation, while they can be lost through recombinational processes, generating genomic rearrangements. We previously identified extensive structurally uniform retrotransposon groups in which no member contains the gag, pol, or env internal domains. Because of the lack of protein-coding capacity, these groups are non-autonomous in replication, even if transcriptionally active. The Cassandra element belongs to the non-autonomous group called terminal-repeat retrotransposons in miniature (TRIM). It carries 5S RNA sequences with conserved RNA polymerase (pol) III promoters and terminators in its long terminal repeats (LTRs). Here, we identified multiple extended tandem arrays of Cassandra retrotransposons within different plant species, including ferns. At least 12 copies of repeated LTRs (as the tandem unit) and internal domain (as a spacer), giving a pattern that resembles the cellular 5S rRNA genes, were identified. A cytogenetic analysis revealed the specific chromosomal pattern of the Cassandra retrotransposon with prominent clustering at and around 5S rDNA loci. The secondary structure of the Cassandra retroelement RNA is predicted to form super-loops, in which the two LTRs are complementary to each other and can initiate local recombination, leading to the tandem arrays of Cassandra elements. The array structures are conserved for Cassandra retroelements of different species. We speculate that recombination events similar to those of 5S rRNA genes may explain the wide variation in Cassandra copy number. Likewise, the organization of 5S rRNA gene sequences is very variable in flowering plants; part of what is taken for 5S gene copy variation may be variation in Cassandra number. The role of the Cassandra 5S sequences remains to be established.
- MeSH
- chromozomy hmyzu MeSH
- fylogeneze MeSH
- genom rostlinný MeSH
- genomika metody MeSH
- interakce hostitele a parazita genetika MeSH
- koncové repetice * MeSH
- konformace nukleové kyseliny MeSH
- molekulární evoluce MeSH
- můry genetika MeSH
- rekombinace genetická MeSH
- retroelementy * MeSH
- RNA ribozomální 5S genetika MeSH
- rostliny genetika parazitologie MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: Genomic imprinting is an epigenetic phenomenon that allows a subset of genes to be expressed mono-allelically based on the parent of origin and is typically regulated by differential DNA methylation inherited from gametes. Imprinting is pervasive in murine extra-embryonic lineages, and uniquely, the imprinting of several genes has been found to be conferred non-canonically through maternally inherited repressive histone modification H3K27me3. However, the underlying regulatory mechanisms of non-canonical imprinting in post-implantation development remain unexplored. RESULTS: We identify imprinted regions in post-implantation epiblast and extra-embryonic ectoderm (ExE) by assaying allelic histone modifications (H3K4me3, H3K36me3, H3K27me3), gene expression, and DNA methylation in reciprocal C57BL/6 and CAST hybrid embryos. We distinguish loci with DNA methylation-dependent (canonical) and independent (non-canonical) imprinting by assaying hybrid embryos with ablated maternally inherited DNA methylation. We find that non-canonical imprints are localized to endogenous retrovirus-K (ERVK) long terminal repeats (LTRs), which act as imprinted promoters specifically in extra-embryonic lineages. Transcribed ERVK LTRs are CpG-rich and located in close proximity to gene promoters, and imprinting status is determined by their epigenetic patterning in the oocyte. Finally, we show that oocyte-derived H3K27me3 associated with non-canonical imprints is not maintained beyond pre-implantation development at these elements and is replaced by secondary imprinted DNA methylation on the maternal allele in post-implantation ExE, while being completely silenced by bi-allelic DNA methylation in the epiblast. CONCLUSIONS: This study reveals distinct epigenetic mechanisms regulating non-canonical imprinted gene expression between embryonic and extra-embryonic development and identifies an integral role for ERVK LTR repetitive elements.
- MeSH
- genomový imprinting * MeSH
- histonový kód * MeSH
- koncové repetice MeSH
- maternální dědičnost * MeSH
- metylace DNA MeSH
- myši MeSH
- Retroviridae fyziologie MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- myši MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Bovine leukemia virus (BLV) is a member of the genus Deltaretrovirus of the family Retroviridae and cause a chronic lymphosarcoma, which is extensive in cattle. In yaks (Bos grunniens), the distribution, strains and genetic characteristics of BLV have rarely been studied. The aim of our study was to investigate BLV infections in domestic yaks and determine the genetic variability of BLV circulating in a region of the Qinghai Tibet Plateau, China. Blood samples were collected from 798 yaks, which were from different farms from Gansu, Qinghai and Sichuan provinces surrounding the Qinghai-Tibet Plateau. Nested PCR targeting BLV long terminal repeats was used to detect the BLV provirus. The highest prevalence of BLV infection was in Gansu province, where it was 18.93% (39/206) in white yaks from Tianzhu City and 19.14% (31/162) in black yaks from Gannan City. In Qinghai and Sichuan provinces, the prevalence of BLV in black yaks was 14.83% (35/236) and 14.94% (29/194), respectively. The prevalence of BLV was not significantly different in yaks up to one year old than in older animals. Phylogenetic analysis was performed using 16 different env-gp51 (497-bp) gene sequences from the three provinces and 71 known BLV strains, which revealed that in both Gansu and Qinghai provinces, genotypes 6 and 10 of the BLV strains were at high levels, whereas only genotype 10 was prevalent in Sichuan Province. Phylogenetic analysis and sequence comparisons revealed 95.7-99.8% sequence identity among the full-length env genes of 16 strains, nearly full-length genome sequences of six BLV strains, and those of the known genotypes 6 and 10 of BLV. This study provides comprehensive information is regarding the widespread infection of domestic yaks with BLV on the Qinghai-Tibet Plateau of China, and shows that at least two BLV genotypes (genotypes 6 and 10) are circulating in this population.
- MeSH
- enzootická bovinní leukóza epidemiologie přenos virologie MeSH
- exprese genu MeSH
- fylogeneze * MeSH
- genotyp * MeSH
- geny env * MeSH
- koncové repetice MeSH
- molekulární epidemiologie MeSH
- prevalence MeSH
- sekvence nukleotidů MeSH
- sekvenční homologie nukleových kyselin MeSH
- sekvenční seřazení MeSH
- skot MeSH
- virus bovinní leukemie klasifikace genetika izolace a purifikace MeSH
- zvířata MeSH
- Check Tag
- skot MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Tibet epidemiologie MeSH
Endogenous retrovirus (ERV) sequences provide a rich source of information about the long-term interactions between retroviruses and their hosts. However, most ERVs are derived from a subset of retrovirus groups, while ERVs derived from certain other groups remain extremely rare. In particular, only a single ERV sequence has been identified that shows evidence of being related to an ancient Deltaretrovirus, despite the large number of vertebrate genome sequences now available. In this report, we identify a second example of an ERV sequence putatively derived from a past deltaretroviral infection, in the genomes of several species of horseshoe bats (Rhinolophidae). This sequence represents a fragment of viral genome derived from a single integration. The time of the integration was estimated to be 11-19 million years ago. This finding, together with the previously identified endogenous Deltaretrovirus in long-fingered bats (Miniopteridae), suggest a close association of bats with ancient deltaretroviruses.
- MeSH
- Chiroptera klasifikace virologie MeSH
- Deltaretrovirus klasifikace genetika MeSH
- endogenní retroviry klasifikace genetika MeSH
- fylogeneze MeSH
- genom genetika MeSH
- genomika MeSH
- koncové repetice genetika MeSH
- molekulární evoluce MeSH
- rekombinace genetická MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: Many studies have shown that guanine-rich DNA sequences form quadruplex structures (G4) in vitro but there is scarce evidence of guanine quadruplexes in vivo. The majority of potential quadruplex-forming sequences (PQS) are located in transposable elements (TEs), especially close to promoters within long terminal repeats of plant LTR retrotransposons. RESULTS: In order to test the potential effect of G4s on retrotransposon expression, we cloned the long terminal repeats of selected maize LTR retrotransposons upstream of the lacZ reporter gene and measured its transcription and translation in yeast. We found that G4s had an inhibitory effect on translation in vivo since "mutants" (where guanines were replaced by adenines in PQS) showed higher expression levels than wild-types. In parallel, we confirmed by circular dichroism measurements that the selected sequences can indeed adopt G4 conformation in vitro. Analysis of RNA-Seq of polyA RNA in maize seedlings grown in the presence of a G4-stabilizing ligand (NMM) showed both inhibitory as well as stimulatory effects on the transcription of LTR retrotransposons. CONCLUSIONS: Our results demonstrate that quadruplex DNA located within long terminal repeats of LTR retrotransposons can be formed in vivo and that it plays a regulatory role in the LTR retrotransposon life-cycle, thus also affecting genome dynamics.
- MeSH
- G-kvadruplexy * MeSH
- genetická transkripce MeSH
- genom rostlinný * MeSH
- koncové repetice * MeSH
- kukuřice setá genetika růst a vývoj metabolismus MeSH
- reportérové geny * MeSH
- retroelementy * MeSH
- Saccharomyces cerevisiae genetika růst a vývoj MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: The rise and fall of the Y chromosome was demonstrated in animals but plants often possess the large evolutionarily young Y chromosome that is thought has expanded recently. Break-even points dividing expansion and shrinkage phase of plant Y chromosome evolution are still to be determined. To assess the size dynamics of the Y chromosome, we studied intraspecific genome size variation and genome composition of male and female individuals in a dioecious plant Silene latifolia, a well-established model for sex-chromosomes evolution. RESULTS: Our genome size data are the first to demonstrate that regardless of intraspecific genome size variation, Y chromosome has retained its size in S. latifolia. Bioinformatics study of genome composition showed that constancy of Y chromosome size was caused by Y chromosome DNA loss and the female-specific proliferation of recently active dominant retrotransposons. We show that several families of retrotransposons have contributed to genome size variation but not to Y chromosome size change. CONCLUSIONS: Our results suggest that the large Y chromosome of S. latifolia has slowed down or stopped its expansion. Female-specific proliferation of retrotransposons, enlarging the genome with exception of the Y chromosome, was probably caused by silencing of highly active retrotransposons in males and represents an adaptive mechanism to suppress degenerative processes in the haploid stage. Sex specific silencing of transposons might be widespread in plants but hidden in traditional hermaphroditic model plants.
- MeSH
- chromozomy rostlin * MeSH
- délka genomu MeSH
- DNA rostlinná * MeSH
- genom rostlinný MeSH
- hybridizace in situ fluorescenční MeSH
- koncové repetice MeSH
- mapování chromozomů MeSH
- molekulární evoluce * MeSH
- repetitivní sekvence nukleových kyselin MeSH
- retroelementy * MeSH
- sekvenční delece * MeSH
- Silene klasifikace genetika MeSH
- umlčování genů * MeSH
- variabilita počtu kopií segmentů DNA MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Retrotransposons are "copy-and-paste" insertional mutagens that substantially contribute to mammalian genome content. Retrotransposons often carry long terminal repeats (LTRs) for retrovirus-like reverse transcription and integration into the genome. We report an extraordinary impact of a group of LTRs from the mammalian endogenous retrovirus-related ERVL retrotransposon class on gene expression in the germline and beyond. In mouse, we identified more than 800 LTRs from ORR1, MT, MT2, and MLT families, which resemble mobile gene-remodeling platforms that supply promoters and first exons. The LTR-mediated gene remodeling also extends to hamster, human, and bovine oocytes. The LTRs function in a stage-specific manner during the oocyte-to-embryo transition by activating transcription, altering protein-coding sequences, producing noncoding RNAs, and even supporting evolution of new protein-coding genes. These functions result, for example, in recycling processed pseudogenes into mRNAs or lncRNAs with regulatory roles. The functional potential of the studied LTRs is even higher, because we show that dormant LTR promoter activity can rescue loss of an essential upstream promoter. We also report a novel protein-coding gene evolution-D6Ertd527e-in which an MT LTR provided a promoter and the 5' exon with a functional start codon while the bulk of the protein-coding sequence evolved through a CAG repeat expansion. Altogether, ERVL LTRs provide molecular mechanisms for stochastically scanning, rewiring, and recycling genetic information on an extraordinary scale. ERVL LTRs thus offer means for a comprehensive survey of the genome's expression potential, tightly intertwining with gene expression and evolution in the germline.
- MeSH
- endogenní retroviry MeSH
- genetická transkripce MeSH
- koncové repetice * MeSH
- křečci praví MeSH
- lidé MeSH
- molekulární evoluce * MeSH
- myši MeSH
- oocyty cytologie metabolismus MeSH
- promotorové oblasti (genetika) MeSH
- regulace genové exprese * MeSH
- retroelementy * MeSH
- skot MeSH
- zvířata MeSH
- zygota cytologie metabolismus MeSH
- Check Tag
- křečci praví MeSH
- lidé MeSH
- myši MeSH
- skot MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
Transposable elements (TEs) proliferate within the genome of their host, which responds by silencing them epigenetically. Much is known about the mechanisms of silencing in plants, particularly the role of siRNAs in guiding DNA methylation. In contrast, little is known about siRNA targeting patterns along the length of TEs, yet this information may provide crucial insights into the dynamics between hosts and TEs. By focusing on 6456 carefully annotated, full-length Sirevirus LTR retrotransposons in maize, we show that their silencing associates with underlying characteristics of the TE sequence and also uncover three features of the host-TE interaction. First, siRNA mapping varies among families and among elements, but particularly along the length of elements. Within the cis-regulatory portion of the LTRs, a complex palindrome-rich region acts as a hotspot of both siRNA matching and sequence evolution. These patterns are consistent across leaf, tassel, and immature ear libraries, but particularly emphasized for floral tissues and 21- to 22-nt siRNAs. Second, this region has the ability to form hairpins, making it a potential template for the production of miRNA-like, hairpin-derived small RNAs. Third, Sireviruses are targeted by siRNAs as a decreasing function of their age, but the oldest elements remain highly targeted, partially by siRNAs that cross-map to the youngest elements. We show that the targeting of older Sireviruses reflects their conserved palindromes. Altogether, we hypothesize that the palindromes aid the silencing of active elements and influence transposition potential, siRNA targeting levels, and ultimately the fate of an element within the genome.
- MeSH
- epigeneze genetická MeSH
- exprese genu MeSH
- koncové repetice MeSH
- konzervovaná sekvence MeSH
- kukuřice setá genetika metabolismus MeSH
- malá interferující RNA genetika MeSH
- metylace DNA MeSH
- molekulární evoluce MeSH
- obrácené repetice MeSH
- regulace genové exprese u rostlin MeSH
- rostlinné geny MeSH
- rostlinné viry genetika MeSH
- sekvence nukleotidů MeSH
- transpozibilní elementy DNA MeSH
- virové geny MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
