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https://www.readbyqxmd.com/read/28448516/natural-variation-of-pirna-expression-affects-immunity-to-transposable-elements
#1
Sergei Ryazansky, Elizaveta Radion, Anastasia Mironova, Natalia Akulenko, Yuri Abramov, Valeriya Morgunova, Maria Y Kordyukova, Ivan Olovnikov, Alla Kalmykova
In the Drosophila germline, transposable elements (TEs) are silenced by PIWI-interacting RNA (piRNA) that originate from distinct genomic regions termed piRNA clusters and are processed by PIWI-subfamily Argonaute proteins. Here, we explore the variation in the ability to restrain an alien TE in different Drosophila strains. The I-element is a retrotransposon involved in the phenomenon of I-R hybrid dysgenesis in Drosophila melanogaster. Genomes of R strains do not contain active I-elements, but harbour remnants of ancestral I-related elements...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28446146/flow-cytometry-sorting-of-nuclei-enables-the-first-global-characterization-of-paramecium-germline-dna-and-transposable-elements
#2
Frédéric Guérin, Olivier Arnaiz, Nicole Boggetto, Cyril Denby Wilkes, Eric Meyer, Linda Sperling, Sandra Duharcourt
BACKGROUND: DNA elimination is developmentally programmed in a wide variety of eukaryotes, including unicellular ciliates, and leads to the generation of distinct germline and somatic genomes. The ciliate Paramecium tetraurelia harbors two types of nuclei with different functions and genome structures. The transcriptionally inactive micronucleus contains the complete germline genome, while the somatic macronucleus contains a reduced genome streamlined for gene expression. During development of the somatic macronucleus, the germline genome undergoes massive and reproducible DNA elimination events...
April 26, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28445427/small-rna-pathways-that-protect-the-somatic-genome
#3
REVIEW
Seogang Hyun
Transposable elements (TEs) are DNA elements that can change their position within the genome, with the potential to create mutations and destabilize the genome. As such, special molecular systems have been adopted in animals to control TE activity in order to protect the genome. PIWI proteins, in collaboration with PIWI-interacting RNAs (piRNAs), are well known to play a critical role in silencing germline TEs. Although initially thought to be germline-specific, the role of PIWI-piRNA pathways in controlling TEs in somatic cells has recently begun to be explored in various organisms, together with the role of endogenous small interfering RNAs (endo-siRNAs)...
April 26, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28441441/a-novel-multiplexed-probe-based-quantitative-pcr-assay-for-the-soybean-root-and-stem-rot-pathogen-phytophthora-sojae-utilizes-its-transposable-element
#4
James S Haudenshield, Jeong Y Song, Glen L Hartman
Phytophthora root rot of soybean [Glycine max (L.) Merr.] is caused by the oomycete Phytophthora sojae (Kaufm. & Gerd.). P. sojae has a narrow host range, consisting primarily of soybean, and it is a serious pathogen worldwide. It exists in root and stem tissues as mycelium, wherein it can form oospores which subsequently germinate to release motile, infectious zoospores. Molecular assays detecting DNA of P. sojae are useful in disease diagnostics, and for determining the presence of the organism in host tissues, soils, and runoff or ponded water from potentially infested fields...
2017: PloS One
https://www.readbyqxmd.com/read/28440405/copy-number-variation-analysis-in-familial-nonsyndromic-congenital-anomalies-of-the-kidney-and-urinary-tract-evidence-for-the-causative-role-of-a-transposable-element-associated-genomic-rearrangement
#5
Ekaterini Siomou, Artemis G Mitsioni, Vasileios Giapros, Ioanna Bouba, Dimitrios Noutsopoulos, Ioannis Georgiou
Most congenital anomalies of the kidney and urinary tract (CAKUT) are sporadic, but familial occurrence has been described, suggesting a genetic contribution. Copy‑number variations (CNVs) were detected in patients with CAKUT to identify possible novel genomic regions associated with CAKUT. CNVs were investigated in 7 children with CAKUT from three unrelated families using array comparative genomic hybridization: female monozygotic twins with bilateral duplex collecting system/vesicoureteral reflux (VUR)/unilateral renal hypodyspasia (URHD); two male siblings with VUR/URHD; 3 male second cousins, one with bilateral VUR/URHD, one with bilateral VUR and one with ureterovesical junction obstruction (UVJO)...
April 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28438577/genomic-cg-dinucleotide-deficiencies-associated-with-transposable-element-hypermutation-in-basidiomycetes-some-lower-fungi-a-moss-and-a-clubmoss
#6
A John Clutterbuck
Many Basidiomycete genomes include substantial fractions that are deficient in CG dinucleotides, in extreme cases amounting to 70% of the genome. CG deficiency is variable and correlates with genome size and, more closely, with transposable element (TE) content. Many species have limited CG deficiency; it is therefore likely that there are other mechanisms that can control TE proliferation. Examination of TEs confirms that C-to-T transition mutations in CG dinucleotides may comprise a conspicuous proportion of differences between paired elements, however transition/transversion ratios are never as high as those due to RIP in some Ascomycetes, suggesting that repeat-associated CG mutation is not totally pervasive...
April 21, 2017: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/28432195/n-terminal-proteomics-assisted-profiling-of-the-unexplored-translation-initiation-landscape-in-arabidopsis-thaliana
#7
Patrick Willems, Elvis Ndah, Veronique Jonckheere, Simon Stael, Adriaan Sticker, Lennart Martens, Frank Van Breusegem, Kris Gevaert, Petra Van Damme
Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N-termini encoded in the Arabidopsis thaliana genome...
April 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28431120/solution-structure-of-a-reverse-transcriptase-recognition-site-of-a-line-rna-from-zebrafish
#8
Maina Otsu, Masaki Kajikawa, Norihiro Okada, Gota Kawai
Long interspersed nuclear element (LINE) is known to be transposed by reverse transcription using its RNA transcript. Recognition of the 3' stem-loop of LINE RNA by its reverse transcriptase (RT) is an important step of the retrotransposition. Our previous study revealed that the second G residue (G8) in the GGAUA loop of a 17mer LINE RNA from eel, UnaL2-17, is recognized by its RT and the U residue (U10) in the same loop is required to maintain the loop structure (Baba et al., 2004). ZfL2-2, a LINE from zebrafish, has the same 3' stem-loop with UnaL2 and ZfL2-1 has similar but distinct 3' stem-loop with an insertion which can form an additional stem-loop...
April 18, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28431016/somatic-transposition-and-meiotically-driven-elimination-of-an-active-helitron-family-in-pleurotus-ostreatus
#9
Alessandra Borgognone, Raúl Castanera, Elaia Muguerza, Antonio G Pisabarro, Lucía Ramírez
Helitrons constitute a superfamily of DNA transposons that were discovered in silico and are widespread in most eukaryotic genomes. They are postulated to mobilize through a "rolling-circle" mechanism, but the experimental evidence of their transposition has been described only recently. Here, we present the inheritance patterns of HELPO1 and HELPO2 helitron families in meiotically derived progeny of the basidiomycete Pleurotus ostreatus. We found distorted segregation patterns of HELPO2 helitrons that led to a strong under-representation of these elements in the progeny...
April 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28424974/transposable-elements-in-the-anopheles-funestus-transcriptome
#10
Rita D Fernández-Medina, Claudia M A Carareto, Cláudio J Struchiner, José M C Ribeiro
Transposable elements (TEs) are present in most of the eukaryotic genomes and their impact on genome evolution is increasingly recognized. Although there is extensive information on the TEs present in several eukaryotic genomes, less is known about the expression of these elements at the transcriptome level. Here we present a detailed analysis regarding the expression of TEs in Anopheles funestus, the second most important vector of human malaria in Africa. Several transcriptionally active TE families belonging both to Class I and II were identified and characterized...
April 19, 2017: Genetica
https://www.readbyqxmd.com/read/28420675/integrative-analysis-unveils-new-functions-for-the-drosophila-cutoff-protein-in-non-coding-rna-biogenesis-and-gene-regulation
#11
Yuri Pritykin, Tarcisio Brito, Trudi Schupbach, Mona Singh, Attilio Pane
Piwi-Interacting RNAs (piRNAs) are central components of the piRNA pathway, which directs transposon silencing and guarantees genome integrity in the germ cells of several metazoans. In Drosophila, piRNAs are produced from discrete regions of the genome termed piRNA clusters, whose expression relies on the RDC complex comprised of the core proteins Rhino, Deadlock and Cutoff. To date, the RDC complex has been exclusively implicated in the regulation of the piRNA loci. Here we further elucidate the function of Cutoff and the RDC complex by performing genome-wide ChIP-seq and RNA-seq assays in the Drosophila germline and analyzing these data together with other publicly available data sets...
April 18, 2017: RNA
https://www.readbyqxmd.com/read/28416702/massive-horizontal-transfer-of-transposable-elements-in-insects
#12
Jean Peccoud, Vincent Loiseau, Richard Cordaux, Clément Gilbert
Horizontal transfer (HT) of genetic material is central to the architecture and evolution of prokaryote genomes. Within eukaryotes, the majority of HTs reported so far are transfers of transposable elements (TEs). These reports essentially come from studies focusing on specific lineages or types of TEs. Because of the lack of large-scale survey, the amount and impact of HT of TEs (HTT) in eukaryote evolution, as well as the trends and factors shaping these transfers, are poorly known. Here, we report a comprehensive analysis of HTT in 195 insect genomes, representing 123 genera and 13 of the 28 insect orders...
April 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28407717/the-impact-of-insertion-sequences-on-bacterial-genome-plasticity-and-adaptability
#13
Joachim Vandecraen, Michael Chandler, Abram Aertsen, Rob Van Houdt
Transposable elements (TE), small mobile genetic elements unable to exist independently of the host genome, were initially believed to be exclusively deleterious genomic parasites. However, it is now clear that they play an important role as bacterial mutagenic agents, enabling the host to adapt to new environmental challenges and to colonize new niches. This review focuses on the impact of insertion sequences (IS), arguably the smallest TE, on bacterial genome plasticity and concomitant adaptability of phenotypic traits, including resistance to antibacterial agents, virulence, pathogenicity and catabolism...
April 13, 2017: Critical Reviews in Microbiology
https://www.readbyqxmd.com/read/28406751/repetitive-dna-loci-and-their-modulation-by-the-non-canonical-nucleic-acid-structures-r-loops-and-g-quadruplexes
#14
REVIEW
Amanda C Hall, Lauren A Ostrowski, Violena Pietrobon, Karim Mekhail
Cells have evolved intricate mechanisms to maintain genome stability despite allowing mutational changes to drive evolutionary adaptation. Repetitive DNA sequences, which represent the bulk of most genomes, are a major threat to genome stability often driving chromosome rearrangements and disease. The major source of repetitive DNA sequences and thus the most vulnerable constituents of the genome are the rDNA (rDNA) repeats, telomeres, and transposable elements. Maintaining the stability of these loci is critical to overall cellular fitness and lifespan...
March 4, 2017: Nucleus
https://www.readbyqxmd.com/read/28406439/protein-coding-genes-retrocopies-and-their-functions
#15
REVIEW
Magdalena Regina Kubiak, Izabela Makałowska
Transposable elements, often considered to be not important for survival, significantly contribute to the evolution of transcriptomes, promoters, and proteomes. Reverse transcriptase, encoded by some transposable elements, can be used in trans to produce a DNA copy of any RNA molecule in the cell. The retrotransposition of protein-coding genes requires the presence of reverse transcriptase, which could be delivered by either non-long terminal repeat (non-LTR) or LTR transposons. The majority of these copies are in a state of "relaxed" selection and remain "dormant" because they are lacking regulatory regions; however, many become functional...
April 13, 2017: Viruses
https://www.readbyqxmd.com/read/28405230/lorte-detecting-transposon-induced-genomic-variants-using-low-coverage-pacbio-long-read-sequences
#16
Eric Disdero, Jonathan Filée
BACKGROUND: Population genomic analysis of transposable elements has greatly benefited from recent advances of sequencing technologies. However, the short size of the reads and the propensity of transposable elements to nest in highly repeated regions of genomes limits the efficiency of bioinformatic tools when Illumina or 454 technologies are used. Fortunately, long read sequencing technologies generating read length that may span the entire length of full transposons are now available...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28401606/transcriptional-polymorphism-of-pirna-regulatory-genes-underlies-the-mariner-activity-in-d-simulans-testes
#17
Bastien Saint-Leandre, Isabelle Clavereau, Aurelie Hua-Van, Pierre Capy
During colonization of new areas, natural populations have to deal with changing environments, and transposable elements (TEs) can be useful "tools" in the adaptation process since they are major contributor to the structural and functional evolution of genomes. In this general context, the activity (copy number, transcriptional and excision rate) of the mariner mos1 element was estimated in 19 natural populations of D. simulans. It is shown (1) that mos1 expression is always higher and more variable in testes than in ovaries; (2) that mos1 activity is higher in colonizing populations compared to the sub-Saharan African ones (ancestral populations); (3) that mos1 variations in transcript levels and copy number are negatively correlated to transcriptional variations of piRNA genes, aubergine and argonaute3...
April 12, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28394353/genomic-analyses-of-primitive-wild-and-cultivated-citrus-provide-insights-into-asexual-reproduction
#18
Xia Wang, Yuantao Xu, Siqi Zhang, Li Cao, Yue Huang, Junfeng Cheng, Guizhi Wu, Shilin Tian, Chunli Chen, Yan Liu, Huiwen Yu, Xiaoming Yang, Hong Lan, Nan Wang, Lun Wang, Jidi Xu, Xiaolin Jiang, Zongzhou Xie, Meilian Tan, Robert M Larkin, Ling-Ling Chen, Bin-Guang Ma, Yijun Ruan, Xiuxin Deng, Qiang Xu
The emergence of apomixis-the transition from sexual to asexual reproduction-is a prominent feature of modern citrus. Here we de novo sequenced and comprehensively studied the genomes of four representative citrus species. Additionally, we sequenced 100 accessions of primitive, wild and cultivated citrus. Comparative population analysis suggested that genomic regions harboring energy- and reproduction-associated genes are probably under selection in cultivated citrus. We also narrowed the genetic locus responsible for citrus polyembryony, a form of apomixis, to an 80-kb region containing 11 candidate genes...
May 2017: Nature Genetics
https://www.readbyqxmd.com/read/28390096/copy-number-increases-of-transposable-elements-and-protein-coding-genes-in-an-invasive-fish-of-hybrid-origin
#19
Stefan Dennenmoser, Fritz J Sedlazeck, Elzbieta Iwaszkiewicz, Xiang-Yi Li, Janine Altmüller, Arne W Nolte
Evolutionary dynamics of structural genetic variation in lineages of hybrid origin is not well explored, although structural mutations may increase in controlled hybrid crosses. We therefore tested whether structural variants accumulate in a fish of recent hybrid origin, invasive Cottus, relative to both parental species Cottus rhenanus and Cottus perifretum. Copy number variation in exons of 10,979 genes was assessed using comparative genome hybridization arrays. Twelve genes showed significantly higher copy numbers in invasive Cottus compared to both parents...
April 8, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28389524/de-novo-rna-sequence-assembly-during-in-vivo-inflammatory-stress-reveals-hundreds-of-unannotated-lincrnas-in-human-blood-cd14-monocytes-and-in-adipose-tissue
#20
Chenyi Xue, Xuan Zhang, Hanrui Zhang, Jane F Ferguson, Ying Wang, Christine Hinkle, Mingyao Li, Muredach P Reilly
Long intergenic noncoding RNAs (lincRNAs) have emerged as key regulators of cellular functions and physiology. Yet functional lincRNAs often have low, context-specific and tissue-specific expression. We hypothesized that many human monocyte and adipose lincRNAs would be absent in current public annotations due to lincRNA tissue specificity, modest sequencing depth in public data, limitations of transcriptome assembly algorithms and lack of dynamic physiological contexts. Deep RNA-seq was performed in peripheral blood CD14+ monocytes (monocytes; average ~247 million reads per sample) and adipose tissue (average ~378 million reads per sample) collected before and after human experimental endotoxemia, an in vivo inflammatory stress, to identify tissue-specific and clinically relevant lincRNAs...
April 7, 2017: Physiological Genomics
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