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Retrotransposon

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https://www.readbyqxmd.com/read/29155231/rtfadb-a-database-of-computationally-predicted-associations-between-retrotransposons-and-transcription-factors-in-the-human-and-mouse-genomes
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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 2, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29126199/evolutionary-epigenomics-of-retrotransposon-mediated-methylation-spreading-in-rice-by
#10
Jae Young Choi, Michael D Purugganan
Plant genomes contain numerous transposable elements (TEs), and many hypotheses on the evolutionary drivers that restrict TE activity have been postulated. Few models, however, have focused on the evolutionary epigenomic interaction between the plant host and its TE. The host genome recruits epigenetic factors, such as methylation, to silence TEs but methylation can spread beyond the TE sequence and influence the expression of nearby host genes. In this study, we investigated this epigenetic trade-off between TE and proximal host gene silencing by studying the epigenomic regulation of repressing long terminal repeat (LTR) retrotransposons (RTs) in Oryza sativa...
November 6, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29120263/trna-derived-small-rnas-new-players-in-genome-protection-against-retrotransposons
#11
German Martinez
Previously believed to be mere random degradation products, tRNA-derived small RNAs have been lately connected to a series of functions that include, surprisingly, genome protection against retrotransposons. tRNAs have been known for a long time to be involved in the replication cycle of retroviruses, pararetroviruses and retrotransposons as primers of their reverse transcription. tRNA-derived small RNAs, as functional small RNAs or as mere tRNA degradation products, have emerged as important players in the regulation of genic transcription...
November 9, 2017: RNA Biology
https://www.readbyqxmd.com/read/29118929/cestrum-strigilatum-ruiz-pav%C3%A3-n-1799-b-chromosome-shares-repetitive-dna-sequences-with-a-chromosomes-of-different-cestrum-linnaeus-1753-species
#12
André Luís Laforga Vanzela, Adriano Alves de Paula, Carolina Cristina Quintas, Thiago Fernandes, Joana Neres da Cruz Baldissera, Thaíssa Boldieri de Souza
Species of Cestrum (Linnaeus, 1753) have shown large diversity in the accumulation and distribution of repetitive DNA families, and B chromosomes have been described in seven species. Some types of repetitive DNA were identified in A and B chromosomes in species of this plant group, such as AT-rich SSR, 35S and 5S rDNA, C-Giemsa and C-CMA/DAPI bands and retrotransposons. To increase our understanding of the relationships of A and B chromosomes, the B of C. strigilatum Ruiz & Pavón, 1799 was microdissected, amplified and hybridized in situ against chromosomes of this species, and in six other species of this genus...
2017: Comparative Cytogenetics
https://www.readbyqxmd.com/read/29116069/-participation-of-the-pirna-pathway-in-recruiting-a-component-of-rna-polymerase-i-transcription-initiation-complex-to-germline-cell-nucleoli
#13
E A Fefelova, A D Stolyarenko, E Y Yakushev, V A Gvozdev, M S Klenov
Proteins of the Piwi family and short Piwi-interacting RNAs (piRNAs) ensure the protection of the genome from transposable elements. We have previously shown that nuclear Piwi protein tends to concentrate in the nucleoli of the cells of Drosophila melanogaster ovaries. It could be hypothesized that the function of Piwi in the nucleolus is associated with the repression of R1 and R2 retrotransposons inserted into the rDNA cluster. Here, we show that Piwi participates in recruiting Udd protein to nucleoli. Udd is a component of the conserved Selectivity Factor I-like (SL1-like) complex, which is required for transcription initiation by RNA polymerase I...
September 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/29110195/a-transposition-active-phyllostachys-edulis-long-terminal-repeat-ltr-retrotransposon
#14
Mingbing Zhou, Linlin Liang, Heikki Hänninen
Due to infrequent sexual reproduction, moso bamboo breeding by hybridization is extremely technically difficult. Insertional mutagenesis based on endogenous active transposons may thus serve as an alternative method to create new germplasm of moso bamboo. In the present study, using LTR-STRUC, a full-length intact long terminal repeat (LTR) retrotransposon was identified in the moso bamboo genome and was named PHRE2 (Phyllostachys edulis retrotransposon 2). The 5' and 3' LTR sequences of PHRE2 were highly (98...
November 6, 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/29109544/mapping-and-phasing-of-structural-variation-in-patient-genomes-using-nanopore-sequencing
#15
Mircea Cretu Stancu, Markus J van Roosmalen, Ivo Renkens, Marleen M Nieboer, Sjors Middelkamp, Joep de Ligt, Giulia Pregno, Daniela Giachino, Giorgia Mandrile, Jose Espejo Valle-Inclan, Jerome Korzelius, Ewart de Bruijn, Edwin Cuppen, Michael E Talkowski, Tobias Marschall, Jeroen de Ridder, Wigard P Kloosterman
Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, particularly for complex variation. Here we analyse the genomes of two patients with congenital abnormalities using the MinION nanopore sequencer and a novel computational pipeline-NanoSV. We demonstrate that nanopore long reads are superior to short reads with regard to detection of de novo chromothripsis rearrangements. The long reads also enable efficient phasing of genetic variations, which we leveraged to determine the parental origin of all de novo chromothripsis breakpoints and to resolve the structure of these complex rearrangements...
November 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/29109480/detection-of-subclonal-l1-transductions-in-colorectal-cancer-by-long-distance-inverse-pcr-and-nanopore-sequencing
#16
Barun Pradhan, Tatiana Cajuso, Riku Katainen, Päivi Sulo, Tomas Tanskanen, Outi Kilpivaara, Esa Pitkänen, Lauri A Aaltonen, Liisa Kauppi, Kimmo Palin
Long interspersed nuclear elements-1 (L1s) are a large family of retrotransposons. Retrotransposons are repetitive sequences that are capable of autonomous mobility via a copy-and-paste mechanism. In most copy events, only the L1 sequence is inserted, however, they can also mobilize the flanking non-repetitive region by a process known as 3' transduction. L1 insertions can contribute to genome plasticity and cause potentially tumorigenic genomic instability. However, detecting the activity of a particular source L1 and identifying new insertions stemming from it is a challenging task with current methodological approaches...
November 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29109362/papolb-tpap-regulates-spermiogenesis-independently-of-chromatoid-body-associated-factors
#17
Shin-Ichi Kashiwabara, Satsuki Tsuruta, Yutaro Yamaoka, Kanako Oyama, Chieko Iwazaki, Tadashi Baba
Mutant mice lacking a testis-specific cytoplasmic poly(A) polymerase, PAPOLB/TPAP, exhibit spermiogenesis arrest and male infertility. However, the mechanism by which PAPOLB regulates spermiogenesis remains unclear. In this study, we examined the relationships between PAPOLB and other spermiogenesis regulators present in the chromatoid body (CB). The loss of PAPOLB had no impact either on the abundance of CB components such as PIWIL1, TDRD6, YBX2, and piRNAs, or on retrotransposon expression. In addition, localization of CB proteins and CB architecture were both normal in PAPOLB-null mice...
November 3, 2017: Journal of Reproduction and Development
https://www.readbyqxmd.com/read/29109157/an-ultra-processive-accurate-reverse-transcriptase-encoded-by-a-metazoan-group-ii-intron
#18
Chen Zhao, Fei Liu, Anna Marie Pyle
Group II introns and non-LTR retrotransposons encode a phylogenetically-related family of highly processive reverse transcriptases (RTs) that are essential for mobility and persistence of these retroelements. Recent crystallographic studies on members of this RT family have revealed that they are structurally distinct from the retroviral RTs that are typically used in biotechnology. However, quantitative, structure-guided analysis of processivity, efficiency and accuracy of this alternate RT family has been lacking...
November 6, 2017: RNA
https://www.readbyqxmd.com/read/29104828/genome-size-and-identification-of-abundant-repetitive-sequences-in-vallisneria-spinulosa
#19
RuiJuan Feng, Xin Wang, Min Tao, Guanchao Du, Qishuo Wang
Vallisneria spinulosa is a freshwater aquatic plant of ecological and economic importance. However, there is limited cytogenetic and genomics information on Vallisneria. In this study, we measured the nuclear DNA content of Vallisneria spinulosa by flow cytometry, performed a de novo assembly, and annotated repetitive sequences by using a combination of next-generation sequencing (NGS) and bioinformatics tools. The genome size of Vallisneria spinulosa is approximately 3,595 Mbp, in which nearly 60% of the genome consists of repetitive sequences...
2017: PeerJ
https://www.readbyqxmd.com/read/29101267/identification-and-verification-of-potential-pirnas-from-domesticated-yak-testis
#20
Jishang Gong, Quanwei Zhang, Qi Wang, Youji Ma, Jiaxiang Du, Yong Zhang, Xingxu Zhao
PIWI-interacting RNAs (piRNA) are small non-coding RNA molecules expressed in animal germ cells that interact with PIWI family proteins to form RNA- protein complexes involved in epigenetic and post- transcriptional gene silencing of retrotransposons and other genetic elements in germ line cells, including reproductive stem cell self- sustainment, differentiation, meiosis and spermatogenesis. In the present study, weperformed high- throughput sequencing of piRNAs in testis samples from yaks in different stages of sexual maturity...
November 3, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
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