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https://www.readbyqxmd.com/read/29211718/pirna-mediated-regulation-of-transposon-alternative-splicing-in-the-soma-and-germ-line
#1
Felipe Karam Teixeira, Martyna Okuniewska, Colin D Malone, Rémi-Xavier Coux, Donald C Rio, Ruth Lehmann
Transposable elements can drive genome evolution, but their enhanced activity is detrimental to the host and therefore must be tightly regulated. The Piwi-interacting small RNA (piRNA) pathway is vital for the regulation of transposable elements, by inducing transcriptional silencing or post-transcriptional decay of mRNAs. Here we show that piRNAs and piRNA biogenesis components regulate precursor mRNA splicing of P-transposable element transcripts in vivo, leading to the production of the non-transposase-encoding mature mRNA isoform in Drosophila germ cells...
December 6, 2017: Nature
https://www.readbyqxmd.com/read/29209349/regulation-of-fig-ficus-carica-l-fruit-color-metabolomic-and-transcriptomic-analyses-of-the-flavonoid-biosynthetic-pathway
#2
Ziran Wang, Yuanyuan Cui, Alexander Vainstein, Shangwu Chen, Huiqin Ma
Combined metabolomic and transcriptomic analyses were carried out with fig cultivar Green Peel and its color mutant "Purple Peel." Five and twenty-two metabolites were identified as having significantly different contents between fruit peels of the two cultivars at young and mature stages, respectively. Cyanidin O-malonylhexoside demonstrated a 3,992-fold increase in the mature purple peel, the first identification of a major cyanidin in fig fruit; cyanidin 3-O-glucoside, cyanidin O-malonylhexoside O-hexoside and cyanidin-3,5-O-diglucoside were upregulated 100-fold, revealing the anthocyanins underlying the purple mutation...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29201533/trnas-as-primers-and-inhibitors-of-retrotransposons
#3
REVIEW
German Martinez
The functional relationship between tRNAs and retrotransposons have been known for more than 35 years. tRNAs are used as primer molecules to guide the reverse transcription of retrotransposons. Recently, tRNAs have also emerge as important players in the postranscriptional regulation of retrotransposons by means of tRNA-derived small RNAs. This surprisingly new layer of regulation indicates that tRNAs are used both in the promotion and the suppression of the reverse transcription of retrotransposons indicating their primary role in the life cycle of LTR retrotransposons...
2017: Mobile Genetic Elements
https://www.readbyqxmd.com/read/29201157/detection-of-the-line-1-retrotransposon-rna-binding-protein-orf1p-in-different-anatomical-regions-of-the-human-brain
#4
Debpali Sur, Raj Kishor Kustwar, Savita Budania, Anita Mahadevan, Dustin C Hancks, Vijay Yadav, S K Shankar, Prabhat K Mandal
Background: Recent reports indicate that retrotransposons - a type of mobile DNA - can contribute to neuronal genetic diversity in mammals. Retrotransposons are genetic elements that mobilize via an RNA intermediate by a "copy-and-paste" mechanism termed retrotransposition. Long Interspersed Element-1 (LINE-1 or L1) is the only active autonomous retrotransposon in humans and its activity is responsible for ~ 30% of genomic mass. Historically, L1 retrotransposition was thought to be restricted to the germline; however, new data indicate L1 s are active in somatic tissue with certain regions of the brain being highly permissive...
2017: Mobile DNA
https://www.readbyqxmd.com/read/29197696/small-rna-differential-expression-and-regulation-in-tuxpe%C3%A3-o-maize-embryogenic-callus-induction-and-establishment
#5
Naholi D Alejandri-Ramírez, Elva C Chávez-Hernández, Jose L Contreras-Guerra, Jose L Reyes, Tzvetanka D Dinkova
Somatic embryogenesis represents an alternative developmental process used to achieve genetic transformation and to approach key questions in maize development. It is known that embryogenic callus induction and plant regeneration are accompanied by microRNA expression changes. However, small RNA (sRNA) populations have not been explored during the proliferative callus subculture establishment and their impact on maintaining the dedifferentiated status and embryogenic potential is far from being completely understood...
November 30, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29196678/resolving-kangaroo-phylogeny-and-overcoming-retrotransposon-ascertainment-bias
#6
William G Dodt, Susanne Gallus, Matthew J Phillips, Maria A Nilsson
Reconstructing phylogeny from retrotransposon insertions is often limited by access to only a single reference genome, whereby support for clades that do not include the reference taxon cannot be directly observed. Here we have developed a new statistical framework that accounts for this ascertainment bias, allowing us to employ phylogenetically powerful retrotransposon markers to explore the radiation of the largest living marsupials, the kangaroos and wallabies of the genera Macropus and Wallabia. An exhaustive in silico screening of the tammar wallaby (Macropus eugenii) reference genome followed by experimental screening revealed 29 phylogenetically informative retrotransposon markers belonging to a family of endogenous retroviruses...
December 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29177514/transcriptome-analysis-of-pinus-halepensis-under-drought-stress-and-during-recovery
#7
Hagar Fox, Adi Doron-Faigenboim, Gilor Kelly, Ronny Bourstein, Ziv Attia, Jing Zhou, Yosef Moshe, Menachem Moshelion, Rakefet David-Schwartz
Forest trees use various strategies to cope with drought stress and these strategies involve complex molecular mechanisms. Pinus halepensis Miller (Aleppo pine) is found throughout the Mediterranean basin and is one of the most drought-tolerant pine species. In order to decipher the molecular mechanisms that P. halepensis uses to withstand drought, we performed large-scale physiological and transcriptome analyses. We selected a mature tree from a semi-arid area with suboptimal growth conditions for clonal propagation through cuttings...
November 21, 2017: Tree Physiology
https://www.readbyqxmd.com/read/29177456/multiple-innovations-in-genetic-and-epigenetic-mechanisms-cooperate-to-underpin-human-brain-evolution
#8
Mainá Bitar, Guy Barry
Our knowledge of how the human brain differs from those of other species in terms of evolutionary adaptations and functionality is limited. Comparative genomics reveal valuable insight, especially the expansion of human-specific non-coding regulatory and repeat-containing regions. Recent studies add to our knowledge of evolving brain function by investigating cellular mechanisms such as protein emergence, extensive sequence editing, retrotransposon activity, dynamic epigenetic modifications and multiple non-coding RNA functions...
November 21, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29171119/abundant-recent-activity-of-retrovirus-like-retrotransposons-within-and-among-flycatcher-species-implies-a-rich-source-of-structural-variation-in-songbird-genomes
#9
Alexander Suh, Linnéa Smeds, Hans Ellegren
Transposable elements (TEs) are genomic parasites capable of inserting virtually anywhere in the host genome, with manifold consequences for gene expression, DNA methylation, and genomic stability. Notably, they can contribute to phenotypic variation and hence be associated with, for example, local adaptation and speciation. However, some organisms such as birds have been widely noted for the low densities of TEs in their genomes and this has been attributed to a potential dearth in transposition during their evolution...
November 24, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29164313/genome-wide-analysis-of-a-recently-active-retrotransposon-au-sine-in-wheat-content-distribution-within-subgenomes-and-chromosomes-and-gene-associations
#10
Danielle Keidar, Chen Doron, Khalil Kashkush
Here, we show that Au SINE elements have strong associations with protein-coding genes in wheat. Most importantly Au SINE insertion within introns causes allelic variation and might induce intron retention. The impact of transposable elements (TEs) on genome structure and function is intensively studied in eukaryotes, especially in plants where TEs can reach up to 90% of the genome in some cases, such as in wheat. Here, we have performed a genome-wide in-silico analysis using the updated publicly available genome draft of bread wheat (T...
November 21, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/29163555/ttt-and-pikk-complex-genes-reverted-to-single-copy-following-polyploidization-and-retain-function-despite-massive-retrotransposition-in-maize
#11
Nelson Garcia, Joachim Messing
The TEL2, TTI1, and TTI2 proteins are co-chaperones for heat shock protein 90 (HSP90) to regulate the protein folding and maturation of phosphatidylinositol 3-kinase-related kinases (PIKKs). Referred to as the TTT complex, the genes that encode them are highly conserved from man to maize. TTT complex and PIKK genes exist mostly as single copy genes in organisms where they have been characterized. Members of this interacting protein network in maize were identified and synteny analyses were performed to study their evolution...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29155231/rtfadb-a-database-of-computationally-predicted-associations-between-retrotransposons-and-transcription-factors-in-the-human-and-mouse-genomes
#12
Gökhan Karakülah
In recent years, retrotransposons have gained increasing attention as a source of binding motifs for transcription factors (TFs). Despite the substantial roles of these mobile genetic elements in the regulation of gene expression, a comprehensive resource enabling the investigation of retrotransposon species that are bound by TFs is still lacking. Herein, I introduce for the first time a novel database called RTFAdb, which allows exploring computationally predicted associations between retrotransposons and TFs in diverse cell lines and tissues of human and mouse...
November 16, 2017: Genomics
https://www.readbyqxmd.com/read/29153391/structure-of-a-thermostable-group-ii-intron-reverse-transcriptase-with-template-primer-and-its-functional-and-evolutionary-implications
#13
Jennifer L Stamos, Alfred M Lentzsch, Alan M Lambowitz
Bacterial group II intron reverse transcriptases (RTs) function in both intron mobility and RNA splicing and are evolutionary predecessors of retrotransposon, telomerase, and retroviral RTs as well as the spliceosomal protein Prp8 in eukaryotes. Here we determined a crystal structure of a full-length thermostable group II intron RT in complex with an RNA template-DNA primer duplex and incoming deoxynucleotide triphosphate (dNTP) at 3.0-Å resolution. We find that the binding of template-primer and key aspects of the RT active site are surprisingly different from retroviral RTs but remarkably similar to viral RNA-dependent RNA polymerases...
November 9, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29145801/comparative-genomics-of-coniophora-olivacea-reveals-different-patterns-of-genome-expansion-in-boletales
#14
Raúl Castanera, Gúmer Pérez, Leticia López-Varas, Joëlle Amselem, Kurt LaButti, Vasanth Singan, Anna Lipzen, Sajeet Haridas, Kerrie Barry, Igor V Grigoriev, Antonio G Pisabarro, Lucía Ramírez
BACKGROUND: Coniophora olivacea is a basidiomycete fungus belonging to the order Boletales that produces brown-rot decay on dead wood of conifers. The Boletales order comprises a diverse group of species including saprotrophs and ectomycorrhizal fungi that show important differences in genome size. RESULTS: In this study we report the 39.07-megabase (Mb) draft genome assembly and annotation of C. olivacea. A total of 14,928 genes were annotated, including 470 putatively secreted proteins enriched in functions involved in lignocellulose degradation...
November 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29139111/a-retrotransposon-in-an-hkt1-family-sodium-transporter-causes-variation-of-leaf-na-exclusion-and-salt-tolerance-in-maize
#15
Ming Zhang, Yibo Cao, Zhiping Wang, Zhi-Qiang Wang, Junpeng Shi, Xiaoyan Liang, Weibin Song, Qijun Chen, Jinsheng Lai, Caifu Jiang
Soil salinity is one of several major abiotic stresses that constrain maize productivity worldwide. An improved understanding of salt-tolerance mechanisms will thus enhance the breeding of salt-tolerant maize and boost productivity. Previous studies have indicated that the maintenance of leaf Na(+) concentration is essential for maize salt tolerance, and the difference in leaf Na(+) exclusion has previously been associated with variation in salt tolerance between maize varieties. Here, we report the identification and functional characterization of a maize salt-tolerance quantitative trait locus (QTL), Zea mays Na(+) Content1 (ZmNC1), which encodes an HKT-type transporter (designated as ZmHKT1)...
November 15, 2017: New Phytologist
https://www.readbyqxmd.com/read/29134273/o-cdc7-kinase-where-art-thou
#16
Robert A Sclafani, Jay R Hesselberth
Although Cdc7 protein kinase is important for regulating DNA replication in all eukaryotes and is a target for cancer therapy, it has never been localized in cells. Recently, a novel molecular genomic method used by our laboratory to localize Cdc7 to regions of chromosomes. Originally, mutations in the CDC7 gene were found in the classic cdc mutant collection of Hartwell et al. (Genetics 74:267-286, 1973). The CDC7 gene was found to encode a protein kinase called DDK that has been studied for many years, establishing its precise role in the initiation of DNA replication at origins...
November 13, 2017: Current Genetics
https://www.readbyqxmd.com/read/29131321/ty1-fused-protein-body-formation-for-spatial-organization-of-metabolic-pathways-in-saccharomyces-cerevisiae
#17
Jong Yun Han, Jae Myeong Song, Sung Hwa Seo, Chonglong Wang, Seung-Goo Lee, Hongweon Lee, Seon-Won Kim, Eui-Sung Choi
Metabolite production through a multistep metabolic pathway can often be increased by efficient substrate channeling created by spatial sequestration of the metabolic reactions. Here, Tya, a structural component in the Ty1 retrotransposon element that forms virus-like particles (VLPs) in Saccharomyces cerevisiae, was used to spatially organize enzymes involved in a metabolic pathway into a multi-enzyme protein body in yeast. As a proof of principle, Tya fusion to three key enzymes involved in biosynthesis of the isoprenoids farnesene and farnesol was tested to assess its potential to improve productivity...
November 13, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29130960/piwi-proteins-and-piwi-interacting-rna-emerging-roles-in-cancer
#18
Yi-Neng Han, Yuan Li, Sheng-Qiang Xia, Yuan-Yuan Zhang, Jun-Hua Zheng, Wei Li
P-Element induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are a type of noncoding RNAs (ncRNAs) and interact with PIWI proteins. piRNAs were primarily described in the germline, but emerging evidence revealed that piRNAs are expressed in a tissue-specific manner among multiple human somatic tissue types as well and play important roles in transposon silencing, epigenetic regulation, gene and protein regulation, genome rearrangement, spermatogenesis and germ stem-cell maintenance. PIWI proteins were first discovered in Drosophila and they play roles in spermatogenesis, germline stem-cell maintenance, self-renewal, retrotransposons silencing and the male germline mobility control...
November 3, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29130603/proteogenomic-re-annotation-of-coccidioides-posadasii-strain-silveira
#19
Natalie M Mitchell, Andrew L Sherrard, Surendra Dasari, D Mitchell Magee, Thomas E Grys, Douglas F Lake
The aims of this study were to provide protein-based evidence upon which to re-annotate of the genome of C. posadasii, one of two closely related species of Coccidioides, a dimorphic fungal pathogen that causes coccidioidomycosis, also called Valley Fever. Proteins present in lysates and filtrates of in vitro grown mycelia and parasitic phase spherules from C. posadasii strain Silveira were analyzed using a GeLC-MS/MS method. Acquired spectra were processed with a proteogenomics workflow comprising a Silveira proteome database, a 6-frame translation of the Silveira genome and an ab initio gene prediction tool prior to validation against published ESTs...
November 12, 2017: Proteomics
https://www.readbyqxmd.com/read/29129531/the-diversity-structure-and-function-of-heritable-adaptive-immunity-sequences-in-the-aedes-aegypti-genome
#20
Zachary J Whitfield, Patrick T Dolan, Mark Kunitomi, Michel Tassetto, Matthew G Seetin, Steve Oh, Cheryl Heiner, Ellen Paxinos, Raul Andino
The Aedes aegypti mosquito transmits arboviruses, including dengue, chikungunya, and Zika virus. Understanding the mechanisms underlying mosquito immunity could provide new tools to control arbovirus spread. Insects exploit two different RNAi pathways to combat viral and transposon infection: short interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs) [1, 2]. Endogenous viral elements (EVEs) are sequences from non-retroviral viruses that are inserted into the mosquito genome and can act as templates for the production of piRNAs [3, 4]...
November 20, 2017: Current Biology: CB
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