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https://www.readbyqxmd.com/read/29444933/pnldc1-mouse-pre-pirna-trimmer-is-required-for-meiotic-and-post-meiotic-male-germ-cell-development
#1
Toru Nishimura, Ippei Nagamori, Tsunetoshi Nakatani, Natsuko Izumi, Yukihide Tomari, Satomi Kuramochi-Miyagawa, Toru Nakano
PIWI-interacting RNAs (piRNAs) are germ cell-specific small RNAs essential for retrotransposon gene silencing and male germ cell development. In piRNA biogenesis, the endonuclease MitoPLD/Zucchini cleaves long, single-stranded RNAs to generate 5' termini of precursor piRNAs (pre-piRNAs) that are consecutively loaded into PIWI-family proteins. Subsequently, these pre-piRNAs are trimmed at their 3'-end by an exonuclease called Trimmer. Recently, poly(A)-specific ribonuclease-like domain-containing 1 (PNLDC1) was identified as the pre-piRNA Trimmer in silkworms...
February 14, 2018: EMBO Reports
https://www.readbyqxmd.com/read/29444236/findgse-estimating-genome-size-variation-within-human-and-arabidopsis-using-k-mer-frequencies
#2
Hequan Sun, Jia Ding, Mathieu Piednoël, Korbinian Schneeberger, Inanc Birol
Motivation: Analyzing k-mer frequencies in whole-genome sequencing data is becoming a common method for estimating genome size (GS). However, it remains uninvestigated how accurate the method is, especially if it can capture intra-species GS variation. Results: We present findGSE, which fits skew normal distributions to k-mer frequencies to estimate GS. findGSE outperformed existing tools in an extensive simulation study. Estimating GSs of 89 Arabidopsis thaliana accessions, findGSE showed the highest capability in capturing GS variations...
February 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29441061/profiling-of-human-molecular-pathways-affected-by-retrotransposons-at-the-level-of-regulation-by-transcription-factor-proteins
#3
Daniil Nikitin, Dmitry Penzar, Andrew Garazha, Maxim Sorokin, Victor Tkachev, Nicolas Borisov, Alexander Poltorak, Vladimir Prassolov, Anton A Buzdin
Endogenous retroviruses and retrotransposons also termed retroelements (REs) are mobile genetic elements that were active until recently in human genome evolution. REs regulate gene expression by actively reshaping chromatin structure or by directly providing transcription factor binding sites (TFBSs). We aimed to identify molecular processes most deeply impacted by the REs in human cells at the level of TFBS regulation. By using ENCODE data, we identified ~2 million TFBS overlapping with putatively regulation-competent human REs located in 5-kb gene promoter neighborhood (~17% of all TFBS in promoter neighborhoods; ~9% of all RE-linked TFBS)...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29435129/computational-methods-reveal-novel-functionalities-of-piwi-interacting-rnas-in-human-papillomavirus-induced-head-and-neck-squamous-cell-carcinoma
#4
Aswini R Krishnan, Yuanhao Qu, Pin Xue Li, Angela E Zou, Joseph A Califano, Jessica Wang-Rodriguez, Weg M Ongkeko
Human papillomavirus (HPV) infection is the fastest growing cause of head and neck squamous cell carcinoma (HNSCC) today, but its role in malignant transformation remains unclear. This study aimed to conduct a comprehensive investigation of PIWI-interacting RNA (piRNA) alterations and functionalities in HPV-induced HNSCC. Using 77 RNA-sequencing datasets from TCGA, we examined differential expression of piRNAs between HPV16(+) HNSCC and HPV(-) Normal samples, identifying a panel of 30 HPV-dysregulated piRNAs...
January 12, 2018: Oncotarget
https://www.readbyqxmd.com/read/29435047/gtsf1-gene-may-serve-as-a-novel-potential-diagnostic-biomarker-for-liver-cancer
#5
De-Yong Gao, Yun Ling, Xiao-Li Lou, Ying-Ying Wang, Liang-Ming Liu
The gametocyte-specific factor 1 (GTSF1) gene participates in DNA methylation and retrotransposon activation in germ cells, particularly during cell proliferation. The present study aimed to assess the level of GTSF1 gene expression in liver cancer tumor tissues, and its role in human hepatoma cell lines in vitro and in a nude mouse model in vivo. GTSF1 gene expression was detected in liver cancer tumor tissues, compared with in healthy controls, via reverse transcription quantitative polymerase chain reaction...
March 2018: Oncology Letters
https://www.readbyqxmd.com/read/29416007/genome-wide-dna-methylation-analysis-reveals-that-mouse-chemical-ipscs-have-closer-epigenetic-features-to-mescs-than-oskm-integrated-ipscs
#6
Wangfang Ping, Jian Hu, Gongcheng Hu, Yawei Song, Qing Xia, Mingze Yao, Shixin Gong, Cizhong Jiang, Hongjie Yao
Induced pluripotent stem cells can be derived from somatic cells through ectopic expression of transcription factors or chemical cocktails. Chemical iPSCs (C-iPSCs) and OSKM-iPSCs (4F-iPSCs) have been suggested to have similar characteristics to mouse embryonic stem cells (mESCs). However, their epigenetic equivalence remains incompletely understood throughout the genome. In this study, we have generated mouse C-iPSCs and 4F-iPSCs, and further compared the genome-wide DNA methylomes of C-iPSCs, 4F-iPSCs, and mESCs that were maintained in 2i and LIF...
February 7, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29396793/post-transcriptional-regulation-of-line-1-retrotransposition-by-aid-apobec-and-adar-deaminases
#7
REVIEW
Elisa Orecchini, Loredana Frassinelli, Silvia Galardi, Silvia Anna Ciafrè, Alessandro Michienzi
Long interspersed element-1 (LINE-1 or L1) retrotransposons represent the only functional family of autonomous transposable elements in humans and formed 17% of our genome. Even though most of the human L1 sequences are inactive, a limited number of copies per individual retain the ability to mobilize by a process termed retrotransposition. The ongoing L1 retrotransposition may result in insertional mutagenesis that could lead to negative consequences such as genetic disease and cancer. For this reason, cells have evolved several mechanisms of defense to restrict L1 activity...
February 2, 2018: Chromosome Research
https://www.readbyqxmd.com/read/29393154/long-interspersed-element-1-methylation-level-as-a-prognostic-biomarker-in-gastrointestinal-cancers
#8
Yoshifumi Baba, Taisuke Yagi, Hiroshi Sawayama, Yukiharu Hiyoshi, Takatsugu Ishimoto, Masaaki Iwatsuki, Yuji Miyamoto, Naoya Yoshida, Hideo Baba
Epigenetic changes play a crucial role in human cancer development. DNA methylation is a central epigenetic process that regulates levels of gene expression. Changes in DNA methylation that occur in human tumors include global DNA hypomethylation and site-specific CpG island promoter hypermethylation. Long interspersed element-1 (LINE-1) is a repetitive DNA retrotransposon that duplicates via a copy-and-paste genetic mechanism. As LINE-1 constitutes approximately 17% of the human genome, the extent of LINE-1 methylation is regarded as a surrogate marker of global DNA methylation...
February 1, 2018: Digestion
https://www.readbyqxmd.com/read/29392473/mammalian-transposable-elements-and-their-impacts-on-genome-evolution
#9
REVIEW
Roy N Platt, Michael W Vandewege, David A Ray
Transposable elements (TEs) are genetic elements with the ability to mobilize and replicate themselves in a genome. Mammalian genomes are dominated by TEs, which can reach copy numbers in the hundreds of thousands. As a result, TEs have had significant impacts on mammalian evolution. Here we summarize the current understanding of TE content in mammal genomes and find that, with a few exceptions, most fall within a predictable range of observations. First, one third to one half of the genome is derived from TEs...
February 1, 2018: Chromosome Research
https://www.readbyqxmd.com/read/29392401/ddm1-guards-against-telomere-truncation-in-arabidopsis
#10
Xiaoyuan Xie, Dorothy E Shippen
Prolonged hypomethylation of DNA leads to telomere truncation correlated with increased telomere recombination, transposon mobilization and stem cell death. Epigenetic pathways, including DNA methylation, are crucial for telomere maintenance. Deficient in DNA Methylation 1 (DDM1) encodes a nucleosome remodeling protein, required to maintain DNA methylation in Arabidopsis thaliana. Plants lacking DDM1 can be self-propagated, but in the sixth generation (G6) hypomethylation leads to rampant transposon activation and infertility...
February 1, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29388767/kinetic-parameters-of-trans-scission-by-extended-hdv-like-ribozymes-and-the-prospect-for-the-discovery-of-genomic-trans-cleaving-rnas
#11
Judy Chiu-Ho Webb, Andrej Lupták
Hepatitis delta virus (HDV)-like ribozymes are self-cleaving catalytic RNAs with widespread distribution in nature and biological roles ranging from self-scission during rolling-circle replication in viroids to co-transcriptional processing of eukaryotic retrotransposons, among others. The ribozymes fold into a double-pseudoknot with a common catalytic core motif and highly variable peripheral domains. Like other self-cleaving ribozymes, HDV-like ribozymes can be converted into trans-acting catalytic RNAs by bisecting the self-cleaving variants at non-essential loops...
February 1, 2018: Biochemistry
https://www.readbyqxmd.com/read/29386641/a-naturally-occurring-epiallele-associates-with-leaf-senescence-and-local-climate-adaptation-in-arabidopsis-accessions
#12
Li He, Wenwu Wu, Gaurav Zinta, Lan Yang, Dong Wang, Renyi Liu, Huiming Zhang, Zhimin Zheng, Huan Huang, Qingzhu Zhang, Jian-Kang Zhu
Epigenetic variation has been proposed to facilitate adaptation to changing environments, but evidence that natural epialleles contribute to adaptive evolution has been lacking. Here we identify a retrotransposon, named "NMR19" (naturally occurring DNA methylation variation region 19), whose methylation and genomic location vary among Arabidopsis thaliana accessions. We classify NMR19 as NMR19-4 and NMR19-16 based on its location, and uncover NMR19-4 as an epiallele that controls leaf senescence by regulating the expression of PHEOPHYTIN PHEOPHORBIDE HYDROLASE (PPH)...
January 31, 2018: Nature Communications
https://www.readbyqxmd.com/read/29385567/elucidating-the-small-regulatory-rna-repertoire-of-the-sea-anemone-anemonia-viridis-based-on-whole-genome-and-small-rna-sequencing
#13
Ilona Urbarova, Hardip Patel, Sylvain Forêt, Bård Ove Karlsen, Tor Erik Jørgensen, Jason M Hall-Spencer, Steinar D Johansen
Cnidarians harbour a variety of small regulatory RNAs that include microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), but detailed information is limited. Here we report the identification and expression of novel miRNAs and putative piRNAs, as well as their genomic loci, in the symbiotic sea anemone Anemonia viridis. We generated a draft assembly of the A. viridis genome with putative size of 313 Mb that appeared to be composed of about 36% repeats, including known transposable elements. We detected approximately equal fractions of DNA transposons and retrotransposons...
January 27, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29381236/centromeric-dna-characterization-in-the-model-grass-brachypodium-distachyon-provides-insights-on-the-evolution-of-the-genus
#14
Yinjia Li, Sheng Zuo, Zhiliang Zhang, Zhanjie Li, Jinlei Han, Zhaoqing Chu, Robert Hasterok, Kai Wang
Brachypodium distachyon is a well-established model monocot plant and its small and compact genome has been used as an accurate reference for the much larger and often polyploid genomes of cereals such as wheat, oats and barley. Centromeres are indispensable functional units of chromosomes and they play a core role in genome polyploidization events during evolution. Since the Brachypodium genus contains about 20 species that differ significantly in terms of their basic chromosome numbers, genome size, ploidy levels and life strategies, studying their centromeres may provide important insight into the structure and evolution of the genome in this interesting and important genus...
January 30, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29380577/-annotation-of-the-mobilomes-of-nine-teleost-species
#15
Bo Gao, Dan Shen, Cai Chen, Saisai Wang, Kunlun Yang, Wei Chen, Wei Wang, Li Zhang, Chengyi Song
In this study, the mobilomes of nine teleost species were annotated by bioinformatics methods. Both of the mobilome size and constitute displayed a significant difference in 9 species of teleost fishes. The species of mobilome content ranking from high to low were zebrafish, medaka, tilapia, coelacanth, platyfish, cod, stickleback, tetradon and fugu. Mobilome content and genome size were positively correlated. The DNA transposons displayed higher diversity and larger variation in teleost (0.50% to 38.37%), was a major determinant of differences in teleost mobilomes, and hAT and Tc/Mariner superfamily were the major DNA transposons in teleost...
January 25, 2018: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/29379155/a-genome-for-gnetophytes-and-early-evolution-of-seed-plants
#16
Tao Wan, Zhi-Ming Liu, Ling-Fei Li, Andrew R Leitch, Ilia J Leitch, Rolf Lohaus, Zhong-Jian Liu, Hai-Ping Xin, Yan-Bing Gong, Yang Liu, Wen-Cai Wang, Ling-Yun Chen, Yong Yang, Laura J Kelly, Ji Yang, Jin-Ling Huang, Zhen Li, Ping Liu, Li Zhang, Hong-Mei Liu, Hui Wang, Shu-Han Deng, Meng Liu, Ji Li, Lu Ma, Yan Liu, Yang Lei, Wei Xu, Ling-Qing Wu, Fan Liu, Qian Ma, Xin-Ran Yu, Zhi Jiang, Guo-Qiang Zhang, Shao-Hua Li, Rui-Qiang Li, Shou-Zhou Zhang, Qing-Feng Wang, Yves Van de Peer, Jin-Bo Zhang, Xiao-Ming Wang
Gnetophytes are an enigmatic gymnosperm lineage comprising three genera, Gnetum, Welwitschia and Ephedra, which are morphologically distinct from all other seed plants. Their distinctiveness has triggered much debate as to their origin, evolution and phylogenetic placement among seed plants. To increase our understanding of the evolution of gnetophytes, and their relation to other seed plants, we report here a high-quality draft genome sequence for Gnetum montanum, the first for any gnetophyte. By using a novel genome assembly strategy to deal with high levels of heterozygosity, we assembled >4 Gb of sequence encoding 27,491 protein-coding genes...
January 29, 2018: Nature Plants
https://www.readbyqxmd.com/read/29378289/pnma-family-protein-interaction-network-and-cell-signalling-pathways-implicated-in-cancer-and-apoptosis
#17
REVIEW
Siew Wai Pang, Chandrajit Lahiri, Chit Laa Poh, Kuan Onn Tan
Paraneoplastic Ma Family (PNMA) comprises a growing number of family members which share relatively conserved protein sequences encoded by the human genome and is localized to several human chromosomes, including the X-chromosome. Based on sequence analysis, PNMA family members share sequence homology to the Gag protein of LTR retrotransposon, and several family members with aberrant protein expressions have been reported to be closely associated with the human Paraneoplastic Disorder (PND). In addition, gene mutations of specific members of PNMA family are known to be associated with human mental retardation or 3-M syndrome consisting of restrictive post-natal growth or dwarfism, and development of skeletal abnormalities...
January 26, 2018: Cellular Signalling
https://www.readbyqxmd.com/read/29374788/intraspecific-and-intraorganismal-copy-number-dynamics-of-retrotransposons-and-tandem-repeat-in-aegilops-speltoides-tausch-poaceae-triticeae
#18
Imad Shams, Olga Raskina
Transposable elements (TE) and tandem repeats (TR) compose the largest fraction of the plant genome. The abundance and repatterning of repetitive DNA underlie intrapopulation polymorphisms and intraspecific diversification; however, the dynamics of repetitive elements in ontogenesis is not fully understood. Here, we addressed the genotype-specific and tissue-specific abundances and dynamics of the Ty1-copia, Ty3-gypsy, and LINE retrotransposons and species-specific Spelt1 tandem repeat in wild diploid goatgrass, Aegilops speltoides Tausch...
January 27, 2018: Protoplasma
https://www.readbyqxmd.com/read/29368664/extensive-epigenetic-reprogramming-during-the-life-cycle-of-marchantia-polymorpha
#19
Marc W Schmid, Alejandro Giraldo-Fonseca, Moritz Rövekamp, Dmitry Smetanin, John L Bowman, Ueli Grossniklaus
BACKGROUND: In plants, the existence and possible role of epigenetic reprogramming has been questioned because of the occurrence of stably inherited epialleles. Evidence suggests that epigenetic reprogramming does occur during land plant reproduction, but there is little consensus on the generality and extent of epigenetic reprogramming in plants. We studied DNA methylation dynamics during the life cycle of the liverwort Marchantia polymorpha. We isolated thalli and meristems from male and female gametophytes, archegonia, antherozoids, as well as sporophytes at early and late developmental stages, and compared their DNA methylation profiles...
January 25, 2018: Genome Biology
https://www.readbyqxmd.com/read/29364900/de-novo-characterization-of-transcriptomes-from-two-north-american-papaipema-stem-borers-lepidoptera-noctuidae
#20
Sara J Oppenheim, Wiebke Feindt, Rob DeSalle, Paul Z Goldstein
Stem-borers in the genus Papaipema (Lepidoptera: Noctuidae) range from highly polyphagous agricultural pests to specialists on more than 20 families of flowering plants, many of them highly toxic. Papaipema is the largest genus of noctuids endemic to North America and provides an excellent study system for the evolution of noctuid host plant use. To improve the availability of genomic resources for such investigations, we performed de novo transcriptome sequencing and assembly for two specialist Papaipema with unusual larval hosts: P...
2018: PloS One
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