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retrotransposons

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https://www.readbyqxmd.com/read/27899577/a-comprehensive-approach-to-expression-of-l1-loci
#1
Prescott Deininger, Maria E Morales, Travis B White, Melody Baddoo, Dale J Hedges, Geraldine Servant, Sudesh Srivastav, Madison E Smither, Monica Concha, Dawn L DeHaro, Erik K Flemington, Victoria P Belancio
L1 elements represent the only currently active, autonomous retrotransposon in the human genome, and they make major contributions to human genetic instability. The vast majority of the 500 000 L1 elements in the genome are defective, and only a relatively few can contribute to the retrotransposition process. However, there is currently no comprehensive approach to identify the specific loci that are actively transcribed separate from the excess of L1-related sequences that are co-transcribed within genes. We have developed RNA-Seq procedures, as well as a 1200 bp 5' RACE product coupled with PACBio sequencing that can identify the specific L1 loci that contribute most of the L1-related RNA reads...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898770/the-amaranth-genome-genome-transcriptome-and-physical-map-assembly
#2
J W Clouse, D Adhikary, J T Page, T Ramaraj, M K Deyholos, J A Udall, D J Fairbanks, E N Jellen, P J Maughan
Amaranth ( L.) is an emerging pseudocereal native to the New World that has garnered increased attention in recent years because of its nutritional quality, in particular its seed protein and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleopolyploid that shows disomic inheritance (2 = 32), and has an estimated genome size of 466 Mb. Here we present a high-quality draft genome sequence of the grain amaranth. The genome assembly consisted of 377 Mb in 3518 scaffolds with an N of 371 kb...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27894878/functionally-conserved-rna-binding-and-protein-protein-interaction-properties-of-line-orf1p-in-an-ancient-clade-of-non-ltr-retrotransposons-of-entamoeba-histolytica
#3
Amit Kumar Gaurav, Jitender Kumar, Mridula Agrahari, Alok Bhattacharya, Vijay Pal Yadav, Sudha Bhattacharya
Retrotransposons are mobile genetic elements found in most organisms. Their origin and evolution is not very well understood. Retrotransposons that lack long terminal repeats (non-LTR) have been classified based on their reverse transcriptase (RT) and endonuclease sequences into groups, of which R2 is the most ancient. Its members contain a single open reading frame (ORF) while there are two ORFs in the other groups, of which ORF2 contains the RT and endonuclease sequences. It is thought that ORF1 was added later to the single-ORF-containing elements, and codes for a protein with nucleic acid binding activity...
November 25, 2016: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/27874048/inverse-changes-in-l1-retrotransposons-between-blood-and-brain-in-major-depressive-disorder
#4
Shu Liu, Tingfu Du, Zeyue Liu, Yan Shen, Jianbo Xiu, Qi Xu
Long interspersed nuclear element-1 (LINE-1 or L1) is a type of retrotransposons comprising 17% of the human and mouse genome, and has been found to be associated with several types of neurological disorders. Previous post-mortem brain studies reveal increased L1 copy number in the prefrontal cortex from schizophrenia patients. However, whether L1 retrotransposition occurs similarly in major depressive disorder (MDD) is unknown. Here, L1 copy number was measured by quantitative PCR analysis in peripheral blood of MDD patients (n = 105) and healthy controls (n = 105)...
November 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27871309/draft-genome-of-the-living-fossil-ginkgo-biloba
#5
Rui Guan, Yunpeng Zhao, He Zhang, Guangyi Fan, Xin Liu, Wenbin Zhou, Chengcheng Shi, Jiahao Wang, Weiqing Liu, Xinming Liang, Yuanyuan Fu, Kailong Ma, Lijun Zhao, Fumin Zhang, Zuhong Lu, Simon Ming-Yuen Lee, Xun Xu, Jian Wang, Huanming Yang, Chengxin Fu, Song Ge, Wenbin Chen
BACKGROUND: Ginkgo biloba L. (Ginkgoaceae) is one of the most distinctive plants. It possesses a suite of fascinating characteristics including a large genome, outstanding resistance/tolerance to abiotic and biotic stresses, and dioecious reproduction, making it an ideal model species for biological studies. However, the lack of a high-quality genome sequence has been an impediment to our understanding of its biology and evolution. FINDINGS: The 10.61 Gb genome sequence containing 41,840 annotated genes was assembled in the present study...
November 21, 2016: GigaScience
https://www.readbyqxmd.com/read/27871234/a-genome-wide-bac-end-sequence-survey-provides-first-insights-into-sweetpotato-ipomoea-batatas-l-lam-genome-composition
#6
Zengzhi Si, Bing Du, Jinxi Huo, Shaozhen He, Qingchang Liu, Hong Zhai
BACKGROUND: Sweetpotato, Ipomoea batatas (L.) Lam., is an important food crop widely grown in the world. However, little is known about the genome of this species because it is a highly heterozygous hexaploid. Gaining a more in-depth knowledge of sweetpotato genome is therefore necessary and imperative. In this study, the first bacterial artificial chromosome (BAC) library of sweetpotato was constructed. Clones from the BAC library were end-sequenced and analyzed to provide genome-wide information about this species...
November 21, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27867147/evolution-of-krab-containing-zinc-finger-proteins-and-their-roles-in-species-evolution
#7
Wang Jinlong, Wang Jian, Tian Chunyan
The C2H2 zinc finger protein family, one of the largest families of transcription factor/transcriptional regulator in mammal, arose from a small ancestral group of eukaryotic zinc finger transcription factors through many repeated gene duplications accompanied by functional divergence. As the biggest subfamily of C2H2 zinc finger protein family, Kruppel-associated box-containing zinc finger proteins (KRAB-ZFPs) appeared at the period oftetrapod, expand rapidly along with species evolution, and take about 60% of the total C2H2 zinc finger proteins in human...
November 20, 2016: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/27861119/splicing-repression-allows-the-gradual-emergence-of-new-alu-exons-in-primate-evolution
#8
Jan Attig, Igor Ruiz de Los Mozos, Nejc Haberman, Zhen Wang, Warren Emmett, Kathi Zarnack, Julian König, Jernej Ule
Alu elements are retrotransposons that frequently form new exons during primate evolution. Here, we assess the interplay of splicing repression by hnRNPC and nonsense-mediated mRNA decay (NMD) in the quality control and evolution of new Alu-exons. We identify 3100 new Alu-exons and show that NMD more efficiently recognises transcripts with Alu-exons compared to other exons with premature termination codons. However, some Alu-exons escape NMD, especially when an adjacent intron is retained, highlighting the importance of concerted repression by splicing and NMD...
November 18, 2016: ELife
https://www.readbyqxmd.com/read/27858507/numerous-small-hammerhead-ribozyme-variants-associated-with-penelope-like-retrotransposons-cleave-rna-as-dimers
#9
Christina E Lünse, Zasha Weinberg, Ronald R Breaker
Hammerhead ribozymes represent the most common of the nine natural classes of self-cleaving RNAs. The hammerhead catalytic core includes 11 highly-conserved nucleotides located largely within the unpaired regions of a junction formed by stems I, II and III. The vast majority of previously reported examples carry an additional pseudoknot or other tertiary interactions between nucleotides that precede stem I and nucleotides in the loop of stem II. These extra contacts are critical for high-speed RNA catalysis...
November 18, 2016: RNA Biology
https://www.readbyqxmd.com/read/27856912/the-dna-methyltransferase-dnmt3c-protects-male-germ-cells-from-transposon-activity
#10
Joan Barau, Aurélie Teissandier, Natasha Zamudio, Stéphanie Roy, Valérie Nalesso, Yann Hérault, Florian Guillou, Déborah Bourc'his
DNA methylation is prevalent in mammalian genomes and plays a central role in the epigenetic control of development. The mammalian DNA methylation machinery is thought to be composed of three DNA methyltransferase enzymes (DNMT1, DNMT3A, and DNMT3B) and one cofactor (DNMT3L). Here, we describe the discovery of Dnmt3C, a de novo DNA methyltransferase gene that evolved via a duplication of Dnmt3B in rodent genomes and was previously annotated as a pseudogene. We show that DNMT3C is the enzyme responsible for methylating the promoters of evolutionarily young retrotransposons in the male germ line and that this specialized activity is required for mouse fertility...
November 18, 2016: Science
https://www.readbyqxmd.com/read/27853884/horizontal-transfer-of-a-novel-helentron-in-insects
#11
Hua-Hao Zhang, Guo-Yin Li, Xiao-Min Xiong, Min-Jin Han, Fang-Yin Dai
Helentrons represent a novel subtype of Helitrons. However, the evolutionary history of Helentrons in organisms is not clearly understood. In this study, we performed structure and autonomous partner analyses, which revealed that bm_455, a TE obtained from the Bombyx mori TE database, BmTEdb, was a member of Helentrons but not a long-terminal repeat (LTR) retrotransposon. Further analyses showed that bm_455 was also present in a wide range of insects including lepidopterans, coleopterans and hymenopterans using a homology-based search strategy...
November 16, 2016: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/27849219/genomic-and-phylogenetic-evidence-of-viper-retrotransposon-domestication-in-trypanosomatids
#12
Adriana Ludwig, Marco Aurelio Krieger
Transposable elements are important residents of eukaryotic genomes and eventually the host can domesticate them to serve cellular functions. We reported here a possible domestication event of the vestigial interposed retroelement (VIPER) in trypanosomatids. We found a large gene in a syntenic location in Leishmania braziliensis, L. panamensis, Leptomanas pyrrhocoris, and Crithidia fasciculata whose products share similarity in the C-terminal portion with the third protein of VIPER. No remnants of other VIPER regions surrounding the gene sequence were found...
November 16, 2016: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/27843500/somatic-retrotransposition-is-infrequent-in-glioblastomas
#13
Pragathi Achanta, Jared P Steranka, Zuojian Tang, Nemanja Rodić, Reema Sharma, Wan Rou Yang, Sisi Ma, Mark Grivainis, Cheng Ran Lisa Huang, Anna M Schneider, Gary L Gallia, Gregory J Riggins, Alfredo Quinones-Hinojosa, David Fenyö, Jef D Boeke, Kathleen H Burns
BACKGROUND: Gliomas are the most common primary brain tumors in adults. We sought to understand the roles of endogenous transposable elements in these malignancies by identifying evidence of somatic retrotransposition in glioblastomas (GBM). We performed transposon insertion profiling of the active subfamily of Long INterspersed Element-1 (LINE-1) elements by deep sequencing (TIPseq) on genomic DNA of low passage oncosphere cell lines derived from 7 primary GBM biopsies, 3 secondary GBM tissue samples, and matched normal intravenous blood samples from the same individuals...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27843499/evidence-for-l1-associated-dna-rearrangements-and-negligible-l1-retrotransposition-in-glioblastoma-multiforme
#14
Patricia E Carreira, Adam D Ewing, Guibo Li, Stephanie N Schauer, Kyle R Upton, Allister C Fagg, Santiago Morell, Michaela Kindlova, Patricia Gerdes, Sandra R Richardson, Bo Li, Daniel J Gerhardt, Jun Wang, Paul M Brennan, Geoffrey J Faulkner
BACKGROUND: LINE-1 (L1) retrotransposons are a notable endogenous source of mutagenesis in mammals. Notably, cancer cells can support unusual L1 retrotransposition and L1-associated sequence rearrangement mechanisms following DNA damage. Recent reports suggest that L1 is mobile in epithelial tumours and neural cells but, paradoxically, not in brain cancers. RESULTS: Here, using retrotransposon capture sequencing (RC-seq), we surveyed L1 mutations in 14 tumours classified as glioblastoma multiforme (GBM) or as a lower grade glioma...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27832372/isolation-and-application-of-p-genome-specific-dna-sequences-of-agropyron-gaertn-in-triticeae
#15
Haiming Han, Weihua Liu, Yuqing Lu, Jinpeng Zhang, Xinming Yang, Xiuquan Li, Zanmin Hu, Lihui Li
Different types of P genome sequences and markers were developed, which could be used to analyze the evolution of P genome in Triticeae and identify precisely wheat- A. cristatum introgression lines. P genome of Agropyron Gaertn. plays an important role in Triticeae and could provide many desirable genes conferring high yield, disease resistance, and stress tolerance for wheat genetic improvement. Therefore, it is significant to develop specific sequences and functional markers of P genome. In this study, 126 sequences were isolated from the degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR) products of microdissected chromosome 6PS...
November 10, 2016: Planta
https://www.readbyqxmd.com/read/27821059/recent-and-dynamic-transposable-elements-contribute-to-genomic-divergence-under-asexuality
#16
Julie Ferreira de Carvalho, Victor de Jager, Thomas P van Gurp, Niels C A M Wagemaker, Koen J F Verhoeven
BACKGROUND: Transposable elements (TEs) are mobile pieces of genetic information with high mutagenic potential for the host genome. Transposition is often neutral or deleterious but may also generate potentially adaptive genetic variation. This additional source of variation could be especially relevant in non-recombining species reproducing asexually. However, evidence is lacking to determine the relevance of TEs in plant asexual genome evolution and their associated effects. Here, we characterize the repetitive fraction of the genome of the common dandelion, Taraxacum officinale and compare it between five accessions from the same apomictic lineage...
November 7, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27814350/retrotransposons-jump-into-alternative-splicing-regulation-via-a-long-noncoding-rna
#17
Reini F Luco
No abstract text is available yet for this article.
November 4, 2016: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/27807467/a-map-of-mobile-dna-insertions-in-the-nci-60-human-cancer-cell-panel
#18
John G Zampella, Nemanja Rodić, Wan Rou Yang, Cheng Ran Lisa Huang, Jane Welch, Veena P Gnanakkan, Toby C Cornish, Jef D Boeke, Kathleen H Burns
BACKGROUND: The National Cancer Institute-60 (NCI-60) cell lines are among the most widely used models of human cancer. They provide a platform to integrate DNA sequence information, epigenetic data, RNA and protein expression, and pharmacologic susceptibilities in studies of cancer cell biology. Genome-wide studies of the complete panel have included exome sequencing, karyotyping, and copy number analyses but have not targeted repetitive sequences. Interspersed repeats derived from mobile DNAs are a significant source of heritable genetic variation, and insertions of active elements can occur somatically in malignancy...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27799657/lkb1-loss-links-serine-metabolism-to-dna-methylation-and-tumorigenesis
#19
Filippos Kottakis, Brandon N Nicolay, Ahlima Roumane, Rahul Karnik, Hongcang Gu, Julia M Nagle, Myriam Boukhali, Michele C Hayward, Yvonne Y Li, Ting Chen, Marc Liesa, Peter S Hammerman, Kwok Kin Wong, D Neil Hayes, Orian S Shirihai, Nicholas J Dyson, Wilhelm Haas, Alexander Meissner, Nabeel Bardeesy
Intermediary metabolism generates substrates for chromatin modification, enabling the potential coupling of metabolic and epigenetic states. Here we identify a network linking metabolic and epigenetic alterations that is central to oncogenic transformation downstream of the liver kinase B1 (LKB1, also known as STK11) tumour suppressor, an integrator of nutrient availability, metabolism and growth. By developing genetically engineered mouse models and primary pancreatic epithelial cells, and employing transcriptional, proteomics, and metabolic analyses, we find that oncogenic cooperation between LKB1 loss and KRAS activation is fuelled by pronounced mTOR-dependent induction of the serine-glycine-one-carbon pathway coupled to S-adenosylmethionine generation...
October 31, 2016: Nature
https://www.readbyqxmd.com/read/27797947/the-evolution-of-line-1-in-vertebrates
#20
Stéphane Boissinot, Akash Sookdeo
The abundance and diversity of the LINE-1 (L1) retrotransposon differ greatly among vertebrates. Mammalian genomes contain hundred of thousands L1s that have accumulated since the origin of mammals. A single group of very similar elements is active at a time in mammals, thus a single lineage of active families has evolved in this group. In contrast, non-mammalian genomes (fish, amphibians, reptiles) harbor a large diversity of concurrently transposing families, which are all represented by very small number of recently inserted copies...
October 19, 2016: Genome Biology and Evolution
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