scholarly journals Epigenetic Requirements for Triggering Heterochromatinization and Piwi-Interacting RNA Production from Transgenes in the Drosophila Germline

Cells ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 922
Author(s):  
Pavel A. Komarov ◽  
Olesya Sokolova ◽  
Natalia Akulenko ◽  
Emilie Brasset ◽  
Silke Jensen ◽  
...  
Keyword(s):  
De Novo ◽  
Threshold Level ◽  
Selective Advantage ◽  
Minimal Amount ◽  
Genomic Context ◽  
Transcription Profiles ◽  
Convergent Transcription ◽  
Pirna Cluster ◽  
In The Wild ◽  
Pirna Pathway

Transgenes containing a fragment of the I retrotransposon represent a powerful model of piRNA cluster de novo formation in the Drosophila germline. We revealed that the same transgenes located at different genomic loci form piRNA clusters with various capacity of small RNA production. Transgenic piRNA clusters are not established in piRNA pathway mutants. However, in the wild-type context, the endogenous ancestral I-related piRNAs heterochromatinize and convert the I-containing transgenes into piRNA-producing loci. Here, we address how the quantitative level of piRNAs influences the heterochromatinization and piRNA production. We show that a minimal amount of maternal piRNAs from ancestral I-elements is sufficient to form the transgenic piRNA clusters. Supplemental piRNAs stemming from active I-element copies do not stimulate additional chromatin changes or piRNA production from transgenes. Therefore, chromatin changes and piRNA production are initiated by a minimum threshold level of complementary piRNAs, suggesting a selective advantage of prompt cell response to the lowest level of piRNAs. It is noteworthy that the weak piRNA clusters do not transform into strong ones after being targeted by abundant I-specific piRNAs, indicating the importance of the genomic context for piRNA cluster establishment. Analysis of ovarian transcription profiles suggests that regions facilitating convergent transcription favor the formation of transgenic piRNA clusters.

scholarly journals De Novo Development of mtDNA Deletion Due to Decreased POLG and SSBP1 Expression in Humans

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 284
Author(s):  
Yeonmi Lee ◽  
Taeho Kim ◽  
Miju Lee ◽  
Seongjun So ◽  
Mustafa Zafer Karagozlu ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
De Novo ◽  
Wild Type Allele ◽  
Wild Type ◽  
Factors Associated ◽  
Mtdna Deletions ◽  
Nuclear Factors ◽  
Mtdna Deletion ◽  
In The Wild ◽  
Mtdna Replication

Defects in the mitochondrial genome (mitochondrial DNA (mtDNA)) are associated with both congenital and acquired disorders in humans. Nuclear-encoded DNA polymerase subunit gamma (POLG) plays an important role in mtDNA replication, and proofreading and mutations in POLG have been linked with increased mtDNA deletions. SSBP1 is also a crucial gene for mtDNA replication. Here, we describe a patient diagnosed with Pearson syndrome with large mtDNA deletions that were not detected in the somatic cells of the mother. Exome sequencing was used to evaluate the nuclear factors associated with the patient and his family, which revealed a paternal POLG mutation (c.868C > T) and a maternal SSBP1 mutation (c.320G > A). The patient showed lower POLG and SSBP1 expression than his healthy brothers and the general population of a similar age. Notably, c.868C in the wild-type allele was highly methylated in the patient compared to the same site in both his healthy brothers. These results suggest that the co- deficient expression of POLG and SSBP1 genes could contribute to the development of mtDNA deletion.

scholarly journals Extending the Coding Potential of Viral Genomes with Overlapping Antisense ORFs: A Case for the De Novo Creation of the Gene Encoding the Antisense Protein ASP of HIV-1

Viruses ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 146
Author(s):  
Angelo Pavesi ◽  
Fabio Romerio
Keyword(s):  
De Novo ◽  
Point Mutations ◽  
Selective Advantage ◽  
Genomic Region ◽  
Fine Tuning ◽  
Sequence Evolution ◽  
Viral Genomes ◽  
Stop Codons ◽  
Hiv 1

Gene overprinting occurs when point mutations within a genomic region with an existing coding sequence create a new one in another reading frame. This process is quite frequent in viral genomes either to maximize the amount of information that they encode or in response to strong selective pressure. The most frequent scenario involves two different reading frames in the same DNA strand (sense overlap). Much less frequent are cases of overlapping genes that are encoded on opposite DNA strands (antisense overlap). One such example is the antisense ORF, asp in the minus strand of the HIV-1 genome overlapping the env gene. The asp gene is highly conserved in pandemic HIV-1 strains of group M, and it is absent in non-pandemic HIV-1 groups, HIV-2, and lentiviruses infecting non-human primates, suggesting that the ~190-amino acid protein that is expressed from this gene (ASP) may play a role in virus spread. While the function of ASP in the virus life cycle remains to be elucidated, mounting evidence from several research groups indicates that ASP is expressed in vivo. There are two alternative hypotheses that could be envisioned to explain the origin of the asp ORF. On one hand, asp may have originally been present in the ancestor of contemporary lentiviruses, and subsequently lost in all descendants except for most HIV-1 strains of group M due to selective advantage. Alternatively, the asp ORF may have originated very recently with the emergence of group M HIV-1 strains from SIVcpz. Here, we used a combination of computational and statistical approaches to study the genomic region of env in primate lentiviruses to shed light on the origin, structure, and sequence evolution of the asp ORF. The results emerging from our studies support the hypothesis of a recent de novo addition of the antisense ORF to the HIV-1 genome through a process that entailed progressive removal of existing internal stop codons from SIV strains to HIV-1 strains of group M, and fine tuning of the codon sequence in env that reduced the chances of new stop codons occurring in asp. Altogether, the study supports the notion that the HIV-1 asp gene encodes an accessory protein, providing a selective advantage to the virus.

scholarly journals De Novo Genome Assembly of the Meadow Brown Butterfly, Maniola jurtina

2020 ◽  
Vol 10 (5) ◽  
pp. 1477-1484
Author(s):  
Kumar Saurabh Singh ◽  
David J. Hosken ◽  
Nina Wedell ◽  
Richard ffrench-Constant ◽  
Chris Bass ◽  
...  
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Single Copy ◽  
De Novo Genome Assembly ◽  
Modern Biology ◽  
Final Assembly ◽  
Gene Sets ◽  
Gene Count ◽  
In The Wild ◽  
Maniola Jurtina

Meadow brown butterflies (Maniola jurtina) on the Isles of Scilly represent an ideal model in which to dissect the links between genotype, phenotype and long-term patterns of selection in the wild - a largely unfulfilled but fundamental aim of modern biology. To meet this aim, a clear description of genotype is required. Here we present the draft genome sequence of M. jurtina to serve as a founding genetic resource for this species. Seven libraries were constructed using pooled DNA from five wild caught spotted females and sequenced using Illumina, PacBio RSII and MinION technology. A novel hybrid assembly approach was employed to generate a final assembly with an N50 of 214 kb (longest scaffold 2.9 Mb). The sequence assembly described here predicts a gene count of 36,294 and includes variants and gene duplicates from five genotypes. Core BUSCO (Benchmarking Universal Single-Copy Orthologs) gene sets of Arthropoda and Insecta recovered 90.5% and 88.7% complete and single-copy genes respectively. Comparisons with 17 other Lepidopteran species placed 86.5% of the assembled genes in orthogroups. Our results provide the first high-quality draft genome and annotation of the butterfly M. jurtina.

scholarly journals piRNA and Transposon Dynamics in Drosophila: A Female Story

2020 ◽  
Vol 12 (6) ◽  
pp. 931-947 ◽  
Author(s):  
Bastien Saint-Leandre ◽  
Pierre Capy ◽  
Aurelie Hua-Van ◽  
Jonathan Filée
Keyword(s):  
Small Rna ◽  
Drosophila Simulans ◽  
Genomic Context ◽  
Genome Sequences ◽  
Genomic Features ◽  
Male Germline ◽  
Recent Activity ◽  
Pirna Pathway ◽  
Female Germline ◽  
The Relationship

Abstract The germlines of metazoans contain transposable elements (TEs) causing genetic instability and affecting fitness. To protect the germline from TE activity, gonads of metazoans produce TE-derived PIWI-interacting RNAs (piRNAs) that silence TE expression. In Drosophila, our understanding of piRNA biogenesis is mainly based on studies of the Drosophila melanogaster female germline. However, it is not known whether piRNA functions are also important in the male germline or whether and how piRNAs are affected by the global genomic context. To address these questions, we compared genome sequences, transcriptomes, and small RNA libraries extracted from entire testes and ovaries of two sister species: D. melanogaster and Drosophila simulans. We found that most TE-derived piRNAs were produced in ovaries and that piRNA pathway genes were strongly overexpressed in ovaries compared with testes, indicating that the silencing of TEs by the piRNA pathway mainly took place in the female germline. To study the relationship between host piRNAs and TE landscape, we analyzed TE genomic features and how they correlate with piRNA production in the two species. In D. melanogaster, we found that TE-derived piRNAs target recently active TEs. In contrast, although Drosophila simulans TEs do not display any features of recent activity, the host still intensively produced silencing piRNAs targeting old TE relics. Together, our results show that the piRNA silencing response mainly takes place in Drosophila ovaries and indicate that the host piRNA response is implemented following a burst of TE activity and could persist long after the extinction of active TE families.

scholarly journals SPO71 Encodes a Developmental Stage-Specific Partner for Vps13 in Saccharomyces cerevisiae

2013 ◽  
Vol 12 (11) ◽  
pp. 1530-1537 ◽  
Author(s):  
Jae-Sook Park ◽  
Yuuya Okumura ◽  
Hiroyuki Tachikawa ◽  
Aaron M. Neiman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
De Novo ◽  
Ectopic Expression ◽  
Membrane Vesicles ◽  
Specific Gene ◽  
Wild Type ◽  
Protein Mutation ◽  
Prospore Membrane ◽  
In The Wild ◽  
Membrane Morphogenesis

ABSTRACT The creation of haploid gametes in yeast, termed spores, requires the de novo formation of membranes within the cytoplasm. These membranes, called prospore membranes, enclose the daughter nuclei generated by meiosis. Proper growth and closure of prospore membranes require the highly conserved Vps13 protein. Mutation of SPO71 , a meiosis-specific gene first identified as defective in spore formation, was found to display defects in membrane morphogenesis very similar to those seen in vps13 Δ cells. Specifically, prospore membranes are smaller than in the wild type, they fail to close, and membrane vesicles are present within the prospore membrane lumen. As in vps13 Δ cells, the levels of phophatidylinositol-4-phosphate are reduced in the prospore membranes of spo71 Δ cells. SPO71 is required for the translocation of Vps13 from the endosome to the prospore membrane, and ectopic expression of SPO71 in vegetative cells results in mislocalization of Vps13. Finally, the two proteins can be coprecipitated from sporulating cells. We propose that Spo71 is a sporulation-specific partner for Vps13 and that they act in concert to regulate prospore membrane morphogenesis.

scholarly journals A piRNA Pathway Primed by Individual Transposons Is Linked to De Novo DNA Methylation in Mice

2008 ◽  
Vol 31 (6) ◽  
pp. 785-799 ◽  
Author(s):  
Alexei A. Aravin ◽  
Ravi Sachidanandam ◽  
Deborah Bourc'his ◽  
Christopher Schaefer ◽  
Dubravka Pezic ◽  
...  
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Pirna Pathway

scholarly journals Gammaherpesvirus Lytic Gene Expression as Characterized by DNA Array

2002 ◽  
Vol 76 (12) ◽  
pp. 6244-6256 ◽  
Author(s):  
Joo Wook Ahn ◽  
Kenneth L. Powell ◽  
Paul Kellam ◽  
Dagmar G. Alber
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Expression Profiles ◽  
Cdna Array ◽  
Gene Expression Profiles ◽  
Hierarchical Cluster ◽  
Murine Gammaherpesvirus ◽  
Transcription Profiles ◽  
A Genome

ABSTRACT Gammaherpesviruses are associated with a number of diseases including lymphomas and other malignancies. Murine gammaherpesvirus 68 (MHV-68) constitutes the most amenable animal model for this family of pathogens. However experimental characterization of gammaherpesvirus gene expression, at either the protein or RNA level, lags behind that of other, better-studied alpha- and beta-herpesviruses. We have developed a cDNA array to globally characterize MHV-68 gene expression profiles, thus providing an experimental supplement to a genome that is chiefly annotated by homology. Viral genes started to be transcribed as early as 3 h postinfection (p.i.), and this was followed by a rapid escalation of gene expression that could be seen at 5 h p.i. Individual genes showed their own transcription profiles, and most genes were still being expressed at 18 h p.i. Open reading frames (ORFs) M3 (chemokine-binding protein), 52, and M9 (capsid protein) were particularly noticeable due to their very high levels of expression. Hierarchical cluster analysis of transcription profiles revealed four main groups of genes and allowed functional predictions to be made by comparing expression profiles of uncharacterized genes to those of genes of known function. Each gene was also categorized according to kinetic class by blocking de novo protein synthesis and viral DNA replication in vitro. One gene, ORF 73, was found to be expressed with α-kinetics, 30 genes were found to be expressed with β-kinetics, and 42 genes were found to be expressed with γ-kinetics. This fundamental characterization furthers the development of this model and provides an experimental basis for continued investigation of gammaherpesvirus pathology.

scholarly journals Recruitment of cdk9 to the Immediate-Early Viral Transcriptosomes during Human Cytomegalovirus Infection Requires Efficient Binding to Cyclin T1, a Threshold Level of IE2 86, and Active Transcription

2009 ◽  
Vol 83 (11) ◽  
pp. 5904-5917 ◽  
Author(s):  
Anokhi J. Kapasi ◽  
Charles L. Clark ◽  
Karen Tran ◽  
Deborah H. Spector
Keyword(s):  
Human Cytomegalovirus ◽  
De Novo ◽  
Threshold Level ◽  
Immediate Early ◽  
Cyclin T1 ◽  
Cellular Factors ◽  
Active Transcription ◽  
Exogenous Expression ◽  
Kinetics Of ◽  
De Novo Protein Synthesis

ABSTRACT Human cytomegalovirus (HCMV) infection results in the formation of nuclear viral transcriptosomes, which are sites dedicated to viral immediate-early (IE) transcription. At IE times of the infection, viral and cellular factors, including several components of transcription such as cyclin-dependent kinase 9 (cdk9), localize at these sites. To determine the mechanism and requirements of specific recruitment of cdk9 to the viral transcriptosomes, infection in the presence of inhibitor drugs and infection of cell lines expressing exogenous mutant cdk9 were performed. We found that cdk9 localization to the viral transcriptosomes requires de novo protein synthesis. In addition, active transcription is required for recruitment and maintenance of cdk9 at the viral transcriptosomes. In cells infected with a recombinant IE2 HCMV (IE2 86 ΔSX virus) in which IE2 gene expression is greatly reduced, cdk9 localization at the transcriptosome is delayed and corresponds to the kinetics of accumulation of the IE2 protein at these sites. Infection in the presence of the cdk9 inhibitors Flavopiridol and DRB (5,6-dichloro-1-β-d-ribofuranosylbenzimidazole) allowed cdk9 localization to the viral transcriptosomes. A kinase-inactive cdk9 (D167N) expressed during the infection also localizes to the viral transcriptosomes, indicating that kinase activity of cdk9 is not a requirement for its localization to the sites of IE transcription. Exogenous expression of additional cdk9 mutants indicates that binding of Brd4 to the cdk9 complex is not required but that efficient binding to cyclin T1 is essential.

scholarly journals Transcriptomic analysis of juvenile wood formation during the growing season in Pinus canariensis

Holzforschung ◽  
2017 ◽  
Vol 71 (12) ◽  
pp. 919-937 ◽  
Author(s):  
Víctor Chano ◽  
Unai López de Heredia ◽  
Carmen Collada ◽  
Álvaro Soto
Keyword(s):  
De Novo ◽  
Juvenile Wood ◽  
Growing Season ◽  
Cell Types ◽  
Wood Formation ◽  
Wound Response ◽  
Pinus Canariensis ◽  
Developmental Issues ◽  
Transcription Profiles ◽  
Cambial Zone

AbstractA noticeable proportion of low transcribed genes involved in wood formation in conifers may have been missed in previous transcriptomic studies. This could be the case for genes related to less abundant cell types, such as axial parenchyma and resin ducts, and genes related to juvenile wood. In this study, two normalized libraries have been obtained from the cambial zone of young individuals ofPinus canariensisC. Sm. ex DC, a species in which such cells are comparatively abundant. These two libraries cover earlywood (EW) and latewood (LW) differentiation, and reads have beende novometa-assembled into one transcriptome. A high number of previously undescribed genes have been found. The transcriptional profiles during the growing season have been analyzed and several noticeable differences with respect to previous studies have been found. This work contributes to a more complete picture of wood formation in conifers. The genes and their transcription profiles described here provide a useful molecular tool for further studies focused on relevant developmental issues, such as wound response and the formation of traumatic wood, re-sprouting, etc., presumably related to those cells.

scholarly journals Identification and characterization of zebrafish Tlr4 co-receptor Md-2

2019 ◽  
Author(s):  
Andrea N. Loes ◽  
Melissa N. Hinman ◽  
Dylan R. Farnsworth ◽  
Adam C. Miller ◽  
Karen Guillemin ◽  
...  
Keyword(s):  
Immune Cells ◽  
De Novo ◽  
Model Organism ◽  
Innate Immune ◽  
Functional Assay ◽  
Innate Immune Cells ◽  
Apparent Difference ◽  
Loss Of Function ◽  
Genomic Context ◽  
Specific Subset

ABSTRACTThe zebrafish (Danio rerio) is a powerful model organism for studies of the innate immune system. One apparent difference between human and zebrafish innate immunity is the cellular machinery for LPS-sensing. In amniotes, the protein complex formed by Toll-like receptor 4 and myeloid differentiation factor 2 (Tlr4/Md-2) recognizes the bacterial molecule lipopolysaccharide (LPS) and triggers an inflammatory response. It is believed that zebrafish have neither Md-2 nor Tlr4: Md-2 has not been identified outside of amniotes, while the zebrafish tlr4 genes appear to be paralogs, not orthologs, of amniote TLR4s. We revisited these conclusions. We identified a zebrafish gene encoding Md-2, ly96. Using single-cell RNA-Seq, we found that ly96 is transcribed in cells that also transcribe genes diagnostic for innate immune cells, including the zebrafish tlr4-like genes. Unlike amniote LY96, zebrafish ly96 expression is restricted to a small number of macrophage-like cells. In a functional assay, zebrafish Md-2 and Tlr4a form a complex that activates NF-κB signaling in response to LPS, but ly96 loss-of-function mutations gave little protection against LPS-toxicity in larval zebrafish. Finally, by analyzing the genomic context of tlr4 genes in eleven jawed vertebrates, we found that tlr4 arose prior to the divergence of teleosts and tetrapods. Thus, an LPS-sensitive Tlr4/Md-2 complex is likely an ancestral feature shared by mammals and zebrafish, rather than a de novo invention on the tetrapod lineage. We hypothesize that zebrafish retain an ancestral, low-sensitivity Tlr4/Md-2 complex that confers LPS-responsiveness to a specific subset of innate immune cells.

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