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https://www.readbyqxmd.com/read/28096347/human-transposon-insertion-profiling-analysis-visualization-and-identification-of-somatic-line-1-insertions-in-ovarian-cancer
#1
Zuojian Tang, Jared P Steranka, Sisi Ma, Mark Grivainis, Nemanja Rodić, Cheng Ran Lisa Huang, Ie-Ming Shih, Tian-Li Wang, Jef D Boeke, David Fenyö, Kathleen H Burns
Mammalian genomes are replete with interspersed repeats reflecting the activity of transposable elements. These mobile DNAs are self-propagating, and their continued transposition is a source of both heritable structural variation as well as somatic mutation in human genomes. Tailored approaches to map these sequences are useful to identify insertion alleles. Here, we describe in detail a strategy to amplify and sequence long interspersed element-1 (LINE-1, L1) retrotransposon insertions selectively in the human genome, transposon insertion profiling by next-generation sequencing (TIPseq)...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28087610/long-non-coding-rna-exchange-during-the-oocyte-to-embryo-transition-in-mice
#2
Rosa Karlic, Sravya Ganesh, Vedran Franke, Eliska Svobodova, Jana Urbanova, Yutaka Suzuki, Fugaku Aoki, Kristian Vlahovicek, Petr Svoboda
The oocyte-to-embryo transition (OET) transforms a differentiated gamete into pluripotent blastomeres. The accompanying maternal-zygotic RNA exchange involves remodeling of the long non-coding RNA (lncRNA) pool. Here, we used next generation sequencing and de novo transcript assembly to define the core population of 1,600 lncRNAs expressed during the OET (lncRNAs). Relative to mRNAs, OET lncRNAs were less expressed and had shorter transcripts, mainly due to fewer exons and shorter 5' terminal exons. Approximately half of OET lncRNA promoters originated in retrotransposons suggesting their recent emergence...
January 13, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28086752/single-genome-retrieval-of-context-dependent-variability-in-mutation-rates-for-human-germline
#3
Aleksandr B Sahakyan, Shankar Balasubramanian
BACKGROUND: Accurate knowledge of the core components of substitution rates is of vital importance to understand genome evolution and dynamics. By performing a single-genome and direct analysis of 39,894 retrotransposon remnants, we reveal sequence context-dependent germline nucleotide substitution rates for the human genome. RESULTS: The rates are characterised through rate constants in a time-domain, and are made available through a dedicated program (Trek) and a stand-alone database...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28078450/genome-wide-methylation-profiles-in-primary-intracranial-germ-cell-tumors-indicate-a-primordial-germ-cell-origin-for-germinomas
#4
Shintaro Fukushima, Satoshi Yamashita, Hisato Kobayashi, Hirokazu Takami, Kohei Fukuoka, Taishi Nakamura, Kai Yamasaki, Yuko Matsushita, Hiromi Nakamura, Yasushi Totoki, Mamoru Kato, Tomonari Suzuki, Kazuhiko Mishima, Takaaki Yanagisawa, Akitake Mukasa, Nobuhito Saito, Masayuki Kanamori, Toshihiro Kumabe, Teiji Tominaga, Motoo Nagane, Toshihiko Iuchi, Koji Yoshimoto, Masahiro Mizoguchi, Kaoru Tamura, Keiichi Sakai, Kazuhiko Sugiyama, Mitsutoshi Nakada, Kiyotaka Yokogami, Hideo Takeshima, Yonehiro Kanemura, Masahide Matsuda, Akira Matsumura, Kazuhiko Kurozumi, Keisuke Ueki, Masahiro Nonaka, Akio Asai, Nobutaka Kawahara, Yuichi Hirose, Tatusya Takayama, Yoichi Nakazato, Yoshitaka Narita, Tatsuhiro Shibata, Masao Matsutani, Toshikazu Ushijima, Ryo Nishikawa, Koichi Ichimura
Intracranial germ cell tumors (iGCTs) are the second most common brain tumors among children under 14 in Japan. The World Health Organization classification recognizes several subtypes of iGCTs, which are conventionally subclassified into pure germinoma or non-germinomatous GCTs. Recent exhaustive genomic studies showed that mutations of the genes involved in the MAPK and/or PI3K pathways are common in iGCTs; however, the mechanisms of how different subtypes develop, often as a mixed-GCT, are unknown. To elucidate the pathogenesis of iGCTs, we investigated 61 GCTs of various subtypes by genome-wide DNA methylation profiling...
January 11, 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/28071676/transcriptome-analysis-of-neo-tetraploid-rice-reveals-specific-differential-gene-expressions-associated-with-fertility-and-heterosis
#5
Haibin Guo, Jean Nestor Mendrikahy, Lei Xie, Junfeng Deng, Zijun Lu, Jinwen Wu, Xiang Li, Muhammad Qasim Shahid, Xiangdong Liu
Polyploid rice hybrids have a powerful biological and yield potential that may become a new way for rice breeding; however, low fertility is major hindrance in commercial utilization. Here, we developed a neo-tetraploid rice that could overcome the sterility of autotetraploid rice and produce high heterosis. Transcriptome analysis of F1 hybrid developed by crossing neo-tetraploid with autotetraploid rice displayed 807, 663 and 866 differentially expressed genes that uniquely associated with F1 and specific to (DEGFu-sp) anther, ovary and leaf, respectively...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28068183/nucleolar-aggresomes-mediate-release-of-pericentric-heterochromatin-and-nuclear-destruction-of-genotoxically-treated-cancer-cells
#6
Kristine Salmina, Anda Huna, Inna Inashkina, Alexander Belyayev, Jekabs Krigerts, Ladislava Pastova, Alejandro Vazquez-Martin, Jekaterina Erenpreisa
The role of the nucleolus and autophagy in maintenance of nuclear integrity is poorly understood. In addition, the mechanisms of nuclear destruction in cancer cells senesced after conventional chemotherapy are unclear. In an attempt to elucidate these issues, we studied teratocarcinoma PA1 cells treated with Etoposide (ETO), focussing on the nucleolus. Following treatment, most cells enter G2 arrest, display persistent DNA damage and activate p53, senescence, and macroautophagy markers. 2-5 µm sized nucleolar aggresomes (NoA) containing fibrillarin (FIB) and damaged rDNA, colocalised with ubiquitin, pAMPK, and LC3-II emerge, accompanied by heterochromatin fragments, when translocated perinuclearly...
January 9, 2017: Nucleus
https://www.readbyqxmd.com/read/28062559/atrx-and-daxx-mechanisms-and-mutations
#7
Michael A Dyer, Zulekha A Qadeer, David Valle-Garcia, Emily Bernstein
Recent genome sequencing efforts in a variety of cancers have revealed mutations and/or structural alterations in ATRX and DAXX, which together encode a complex that deposits histone variant H3.3 into repetitive heterochromatin. These regions include retrotransposons, pericentric heterochromatin, and telomeres, the latter of which show deregulation in ATRX/DAXX-mutant tumors. Interestingly, ATRX and DAXX mutations are often found in pediatric tumors, suggesting a particular developmental context in which these mutations drive disease...
January 6, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28057732/satellite-dna-and-transposable-elements-in-seabuckthorn-hippophae-rhamnoides-a-dioecious-plant-with-small-y-and-large-x-chromosomes
#8
Janka Puterova, Olga Razumova, Tomas Martinek, Oleg Alexandrov, Mikhail Divashuk, Zdenek Kubat, Roman Hobza, Gennady Karlov, Eduard Kejnovsky
Seabuckthorn (Hippophae rhamnoides) is a dioecious shrub commonly used in the pharmaceutical, cosmetic and environmental industry as a source of oil, minerals and vitamins. In this study, we analyzed the transposable elements and satellites in its genome. We carried out Illumina DNA sequencing and reconstructed the main repetitive DNA sequences. For data analysis, we developed a new bioinformatics approach for advanced satellite DNA analysis and showed that about 25% of the genome consists of satellite DNA and about 24% is formed of transposable elements, dominated by Ty3/Gypsy and Ty1/Copia LTR retrotransposons...
January 4, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28057730/insertion-polymorphisms-of-mobile-genetic-elements-in-sexual-and-asexual-populations-of-daphnia-pulex
#9
Xiaoqian Jiang, Haixu Tang, Zhiqiang Ye, Michael Lynch
Transposable elements (TEs) constitute a substantial portion of many eukaryotic genomes, and can in principle contribute to evolutionary innovation as well as genomic deterioration. Daphnia pulex serves as a useful model for studying TE dynamics as a potential cause and/or consequence of asexuality. We analyzed insertion polymorphisms of TEs in 20 sexual and 20 asexual isolates of D. pulex across North American from their available whole-genome sequencing data. Our results show that the total fraction of the derived sequences of TEs is not substantially different between asexual and sexual D...
January 4, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28049704/the-nucleotide-excision-repair-pathway-limits-l1-retrotransposition
#10
Geraldine Servant, Vincent A Streva, Rebecca S Derbes, Madushani I Wijetunge, Marc Neeland, Travis B White, Victoria P Belancio, Astrid M Roy-Engel, Prescott L Deininger
Long interspersed elements 1 (L1) are active mobile elements that constitute almost 17% of the human genome. They amplify through a "copy-and-paste" mechanism termed retrotransposition, and de novo insertions related to these elements have been reported to cause 0.2% of genetic diseases. Our previous data demonstrated that the endonuclease complex ERCC1-XPF, which cleaves a 3' DNA flap structure, limits L1 retrotransposition. Although the ERCC1-XPF endonuclease participates in several different DNA repair pathways, such as single-strand annealing, or in telomere maintenance, its recruitment to DNA lesions is best characterized in the nucleotide excision repair (NER) pathway...
January 2017: Genetics
https://www.readbyqxmd.com/read/28048954/a-preliminary-molecular-and-phylogenetic-analysis-of-the-genome-of-a-novel-endogenous-retrovirus-in-the-sea-slug-elysia-chlorotica
#11
Sidney K Pierce, Padmanabhan Mahadevan, Steven E Massey, Michael L Middlebrooks
An endogenous retrovirus that is present in the sea slug Elysia chlorotica is expressed in all individuals at the end of the annual life cycle. But the precise role of the virus, if any, in slug senescence or death is unknown. We have determined the genomic sequence of the virus and performed a phylogenetic analysis of the data. The 6060-base pair genome of the virus possesses a reverse transcriptase-domain-containing protein that shows similarity to retrotransposon sequences found in Aplysia californica and Strongylocentrotus purpuratus...
December 2016: Biological Bulletin
https://www.readbyqxmd.com/read/28043823/viral-reverse-transcriptases
#12
REVIEW
Luis Menéndez-Arias, Alba Sebastián-Martín, Mar Álvarez
Reverse transcriptases (RTs) play a major role in the replication of Retroviridae, Metaviridae, Pseudoviridae, Hepadnaviridae and Caulimoviridae. RTs are enzymes that are able to synthesize DNA using RNA or DNA as templates (DNA polymerase activity), and degrade RNA when forming RNA/DNA hybrids (ribonuclease H activity). In retroviruses and LTR retrotransposons (Metaviridae and Pseudoviridae), the coordinated action of both enzymatic activities converts single-stranded RNA into a double-stranded DNA that is flanked by identical sequences known as long terminal repeats (LTRs)...
December 30, 2016: Virus Research
https://www.readbyqxmd.com/read/28025319/molecular-cytogenetic-characterization-of-chromosome-site-specific-repetitive-sequences-in-the-arctic-lamprey-lethenteron-camtschaticum-petromyzontidae
#13
Junko Ishijima, Yoshinobu Uno, Mitsuo Nunome, Chizuko Nishida, Shigehiro Kuraku, Yoichi Matsuda
All extant lamprey karyotypes are characterized by almost all dot-shaped microchromosomes. To understand the molecular basis of chromosome structure in lampreys, we performed chromosome C-banding and silver staining and chromosome mapping of the 18S-28S and 5S ribosomal RNA (rRNA) genes and telomeric TTAGGG repeats in the Arctic lamprey (Lethenteron camtschaticum). In addition, we cloned chromosome site-specific repetitive DNA sequences and characterized them by nucleotide sequencing, chromosome in situ hybridization, and filter hybridization...
December 26, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28018140/friend-or-foe-epigenetic-regulation-of-retrotransposons-in-mammalian-oogenesis-and-early-development
#14
REVIEW
Alexei V Evsikov, Caralina Marín de Evsikova
Epigenetics is the study of phenotypic variation arising from developmental and environmental factors regulating gene transcription at molecular, cellular, and physiological levels. A naturally occurring biological process driven by epigenetics is the egg-to-embryo developmental transition when two fully differentiated adult cells - egg and sperm - revert to an early stem cell type with totipotency but subsequently differentiates into pluripotent embryonic stem cells that give rise to any cell type. Transposable elements (TEs) are active in mammalian oocytes and early embryos, and this activity, albeit counterintuitive because TEs can lead to genomic instability in somatic cells, correlates to successful development...
December 2016: Yale Journal of Biology and Medicine
https://www.readbyqxmd.com/read/28013279/inducible-transposition-of-a-heat-activated-retrotransposon-in-tissue-culture
#15
Yukari Masuta, Kosuke Nozawa, Hiroki Takagi, Hiroki Yaegashi, Keisuke Tanaka, Tasuku Ito, Hideyuki Saito, Hisato Kobayashi, Wataru Matsunaga, Seiji Masuda, Atsushi Kato, Hidetaka Ito
A transposition of a heat-activated retrotransposon named ONSEN required compromise of a small RNA-mediated epigenetic regulation that includes RNA-directed DNA methylation (RdDM) machinery after heat treatment. In the current study, we analyzed the transcriptional and transpositional activation of ONSEN to better understand the underlying molecular mechanism involved in the maintenance and/or induction of transposon activation in plant tissue culture. We found the transposition of heat-primed ONSEN during tissue culture independently of RdDM mutation...
December 23, 2016: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28012829/l1-retrotransposition-alters-the-hippocampal-genomic-landscape-enabling-memory-formation
#16
Sara Bachiller, Yaiza Del-Pozo-Martín, Ángel Manuel Carrión
Somatic LINE-1 (L1) retrotransposition is a source of genomic mosaicism and potential phenotypic diversity among neurons during brain development. In the adult brain, L1 expression can be triggered by different environmental alterations, but its functional role in this context remains unknown. Here we demonstrate a neural activation-dependent increase in the number of L1 retrotransposon insertions in the hippocampus. Using both pharmacologic and genetic approaches in mice, we demonstrate that L1 expression in the adult hippocampus enables long-term memory formation...
December 21, 2016: Brain, Behavior, and Immunity
https://www.readbyqxmd.com/read/28011770/simulation-based-estimation-of-branching-models-for-ltr-retrotransposons
#17
Serge Moulin, Nicolas Seux, Stéphane Chrétien, Christophe Guyeux, Emmanuelle Lerat
MOTIVATION: LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model for studying the propagation of LTR retrotransposons in these genomes. This model allows us to take into account both the positions and the degradation level of LTR retrotransposons copies. In our model, the duplication rate is also allowed to vary with the degradation level. RESULTS: Various functions have been implemented in order to simulate their spread and visualization tools are proposed...
October 6, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28007890/multiple-transcriptional-and-post-transcriptional-pathways-collaborate-to-control-sense-and-antisense-rnas-of-tf2-retroelements-in-fission-yeast
#18
Pierre-Luc Mallet, Marc Larochelle, François Bachand
Retrotransposons are mobile genetic elements that colonize eukaryotic genomes by replicating through an RNA intermediate. As retrotransposons can move within the host genome, defense mechanisms have evolved to repress their potential mutagenic activities. In the fission yeast Schizosaccharomyces pombe, the mRNA of Tf2 long terminal repeat retrotransposons is targeted for degradation by the 3'-5' exonucleolytic activity of the exosome-associated protein Rrp6. Here, we show that the nuclear poly(A)-binding protein Pab2 functions with Rrp6 to negatively control Tf2 mRNA accumulation...
December 22, 2016: Genetics
https://www.readbyqxmd.com/read/28007835/paralog-specific-functions-of-rpl7a-and-rpl7b-mediated-by-ribosomal-protein-or-snorna-dosage-in-saccharomyces-cerevisiae
#19
Ryan J Palumbo, Gabriele Fuchs, Sheila Lutz, M Joan Curcio
Most ribosomal proteins in Saccharomyces cerevisiae are encoded by two paralogs that additively produce the optimal protein level for cell growth. Nonetheless, deleting one paralog of most ribosomal protein gene pairs results in a variety of phenotypes not observed when the other paralog is deleted. To determine whether paralog-specific phenotypes associated with deleting RPL7A or RPL7B stem from distinct functions or different levels of the encoded isoforms, the coding region and introns of one paralog, including an intron-embedded snoRNA (small nucleolar RNA) gene, were exchanged with that of the other paralog...
December 22, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28004836/an-expressed-endogenous-nodavirus-like-element-captured-by-a-retrotransposon-in-the-genome-of-the-plant-parasitic-nematode-bursaphelenchus-xylophilus
#20
James A Cotton, Sascha Steinbiss, Toshiro Yokoi, Isheng J Tsai, Taisei Kikuchi
Recently, nematode viruses infecting Caenorhabditis elegans have been reported from the family Nodaviridae, the first nematode viruses described. Here, we report the observation of a novel endogenous viral element (EVE) in the genome of Bursaphelenchus xylophilus, a plant parasitic nematode unrelated to other nematodes from which viruses have been characterised. This element derives from a different clade of nodaviruses to the previously reported nematode viruses. This represents the first endogenous nodavirus sequence, the first nematode endogenous viral element, and significantly extends our knowledge of the potential diversity of the Nodaviridae...
December 22, 2016: Scientific Reports
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