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https://www.readbyqxmd.com/read/28729554/comparison-of-traditional-and-new-generation-dna-markers-declares-high-genetic-diversity-and-differentiated-population-structure-of-wild-almond-species
#1
Karim Sorkheh, Mehrana Koohi Dehkordi, Sezai Ercisli, Attila Hegedus, Júlia Halász
Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28723946/the-mitochondrial-genome-of-the-terrestrial-carnivorous-plant-utricularia-reniformis-lentibulariaceae-structure-comparative-analysis-and-evolutionary-landmarks
#2
Saura R Silva, Danillo O Alvarenga, Yani Aranguren, Helen A Penha, Camila C Fernandes, Daniel G Pinheiro, Marcos T Oliveira, Todd P Michael, Vitor F O Miranda, Alessandro M Varani
The carnivorous plants of the family Lentibulariaceae have attained recent attention not only because of their interesting lifestyle, but also because of their dynamic nuclear genome size. Lentibulariaceae genomes span an order of magnitude and include species with the smallest genomes in angiosperms, making them a powerful system to study the mechanisms of genome expansion and contraction. However, little is known about mitochondrial DNA (mtDNA) sequences of this family, and the evolutionary forces that shape this organellar genome...
2017: PloS One
https://www.readbyqxmd.com/read/28715998/detection-of-active-transposable-elements-in-arabidopsis-thaliana-using-oxford-nanopore-sequencing-technology
#3
Emilie Debladis, Christel Llauro, Marie-Christine Carpentier, Marie Mirouze, Olivier Panaud
BACKGROUND: Transposables elements (TEs) contribute to both structural and functional dynamics of most eukaryotic genomes. Because of their propensity to densely populate plant and animal genomes, the precise estimation of the impact of transposition on genomic diversity has been considered as one of the main challenges of today's genomics. The recent development of NGS (next generation sequencing) technologies has open new perspectives in population genomics by providing new methods for high throughput detection of Transposable Elements-associated Structural Variants (TEASV)...
July 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28714502/insights-into-the-rna-binding-mechanism-of-human-l1-orf1p-a-molecular-dynamics-study
#4
Muthukumaran Rajagopalan, Sangeetha Balasubramanian, Amutha Ramaswamy
The recognition and binding of nucleic acids by ORF1p, an L1 retrotransposon protein, have not yet been clearly understood due to the lack of structural knowledge. The present study attempts to identify the probable single-stranded RNA binding pathway of trimeric ORF1p using computational methods like ligand mapping methodology combined with molecular dynamics simulations. Using the ligand mapping methodology, the possible RNA interacting sites on the surface of the trimeric ORF1p were identified. The crystal structure of the ORF1p timer and an RNA molecule of 29 nucleotide bases in length were used to generate the structure of the ORF1p complex based on information on predicted binding sites as well as the functional states of the CTD...
July 17, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28700586/systematic-identification-and-characterization-of-regulatory-elements-derived-from-human-endogenous-retroviruses
#5
Jumpei Ito, Ryota Sugimoto, Hirofumi Nakaoka, Shiro Yamada, Tetsuaki Kimura, Takahide Hayano, Ituro Inoue
Human endogenous retroviruses (HERVs) and other long terminal repeat (LTR)-type retrotransposons (HERV/LTRs) have regulatory elements that possibly influence the transcription of host genes. We systematically identified and characterized these regulatory elements based on publicly available datasets of ChIP-Seq of 97 transcription factors (TFs) provided by ENCODE and Roadmap Epigenomics projects. We determined transcription factor-binding sites (TFBSs) using the ChIP-Seq datasets and identified TFBSs observed on HERV/LTR sequences (HERV-TFBSs)...
July 12, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28698226/loss-of-dna-methylation-in-zebrafish-embryos-activates-retrotransposons-to-trigger-antiviral-signaling
#6
Yelena Chernyavskaya, Raksha Mudbhary, Debra Tokarz, Vinitha Jacob, Smita Gopinath, Chi Zhang, Xiaochen Sun, Shuang Wang, Elena Magnani, Bhavani P Madakashira, Jeffrey A Yoder, Yujin Hoshida, Kirsten C Sadler
Complex cytoplasmic nucleotide sensing mechanisms can recognize foreign DNA based on a lack of methylation and initiate an immune response to clear the infection. Zebrafish embryos with global DNA hypomethylation caused by mutations in the ubiquitin-like, with PHD and RING finger domains 1 (uhrf1) or DNA methyltransferase 1 (dnmt1) genes exhibit a robust interferon induction characteristic of first line of defense against viral infection. We found that this interferon induction occurred in non-immune cells and asked whether intracellular viral sensing pathways in these cells were the trigger...
July 11, 2017: Development
https://www.readbyqxmd.com/read/28688038/dadd1-and-dxnp-prevent-genome-instability-by-maintaining-hp1a-localization-at-drosophila-telomeres
#7
Joselyn Chavez, Juan Manuel Murillo-Maldonado, Vanessa Bahena, Ana Karina Cruz, América Castañeda-Sortibrán, Rosario Rodriguez-Arnaiz, Mario Zurita, Viviana Valadez-Graham
Telomeres are important contributors to genome stability, as they prevent linear chromosome end degradation and contribute to the avoidance of telomeric fusions. An important component of the telomeres is the heterochromatin protein 1a (HP1a). Mutations in Su(var)205, the gene encoding HP1a in Drosophila, result in telomeric fusions, retrotransposon regulation loss and larger telomeres, leading to chromosome instability. Previously, it was found that several proteins physically interact with HP1a, including dXNP and dAdd1 (orthologues to the mammalian ATRX gene)...
July 7, 2017: Chromosoma
https://www.readbyqxmd.com/read/28687080/inhibition-of-rna-polymerase-ii-allows-controlled-mobilisation-of-retrotransposons-for-plant-breeding
#8
Michael Thieme, Sophie Lanciano, Sandrine Balzergue, Nicolas Daccord, Marie Mirouze, Etienne Bucher
BACKGROUND: Retrotransposons play a central role in plant evolution and could be a powerful endogenous source of genetic and epigenetic variability for crop breeding. To ensure genome integrity several silencing mechanisms have evolved to repress retrotransposon mobility. Even though retrotransposons fully depend on transcriptional activity of the host RNA polymerase II (Pol II) for their mobility, it was so far unclear whether Pol II is directly involved in repressing their activity...
July 7, 2017: Genome Biology
https://www.readbyqxmd.com/read/28679751/aim2-like-receptors-positively-and-negatively-regulate-the-interferon-response-induced-by-cytosolic-dna
#9
Yuki Nakaya, Jingtao Lilue, Spyridon Stavrou, Eileen A Moran, Susan R Ross
Cytosolic DNAs derived from retrotransposons serve as pathogen-associated molecular patterns for pattern recognition receptors (PRRs) that stimulate the induction of interferons (IFNs) and other cytokines, leading to autoimmune disease. Cyclic GMP-AMP synthase is one PRR that senses retrotransposon DNA, activating type I IFN responses through the stimulator of IFN genes (STING). Absent in melanoma 2 (AIM2)-like receptors (ALRs) have also been implicated in these pathways. Here we show that the mouse ALR IFI205 senses cytosolic retrotransposon DNA independently of cyclic GMP-AMP production...
July 5, 2017: MBio
https://www.readbyqxmd.com/read/28678163/genome-sequences-of-marine-shrimp-exopalaemon-carinicauda-holthuis-provide-insights-into-genome-size-evolution-of-caridea
#10
Jianbo Yuan, Yi Gao, Xiaojun Zhang, Jiankai Wei, Chengzhang Liu, Fuhua Li, Jianhai Xiang
Crustacea, particularly Decapoda, contains many economically important species, such as shrimps and crabs. Crustaceans exhibit enormous (nearly 500-fold) variability in genome size. However, limited genome resources are available for investigating these species. Exopalaemoncarinicauda Holthuis, an economical caridean shrimp, is a potential ideal experimental animal for research on crustaceans. In this study, we performed low-coverage sequencing and de novo assembly of the E. carinicauda genome. The assembly covers more than 95% of coding regions...
July 5, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28677663/inter-strain-differences-in-line-1-dna-methylation-in-the-mouse-hematopoietic-system-in-response-to-exposure-to-ionizing-radiation
#11
Isabelle R Miousse, Jianhui Chang, Lijian Shao, Rupak Pathak, Étienne Nzabarushimana, Kristy R Kutanzi, Reid D Landes, Alan J Tackett, Martin Hauer-Jensen, Daohong Zhou, Igor Koturbash
Long Interspersed Nuclear Element 1 (LINE-1) retrotransposons are the major repetitive elements in mammalian genomes. LINE-1s are well-accepted as driving forces of evolution and critical regulators of the expression of genetic information. Alterations in LINE-1 DNA methylation may lead to its aberrant activity and are reported in virtually all human cancers and in experimental carcinogenesis. In this study, we investigated the endogenous DNA methylation status of the 5' untranslated region (UTR) of LINE-1 elements in the bone marrow hematopoietic stem cells (HSCs), hematopoietic progenitor cells (HPCs), and mononuclear cells (MNCs) in radioresistant C57BL/6J and radiosensitive CBA/J mice and in response to ionizing radiation (IR)...
July 4, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28675832/epigenetic-control-of-retrotransposons-in-adult-tissues-implications-for-immune-regulation
#12
REVIEW
Christopher Hc Tie, Helen M Rowe
Retrotransposons tune immune reactivity in differentiated cells because when they are transcribed, their nucleic acids can be viewed as non-self leading to innate immune sensing. Most retrotransposons, however, are subject to transcriptional regulation by a multitude of epigenetic pathways, which have coevolved with them for millions of years. While a lot is known about the epigenetic control of retrotransposons in germ cells and early embryos, surprisingly little is understood about these pathways in adult tissues, particularly in human cells...
July 1, 2017: Current Opinion in Virology
https://www.readbyqxmd.com/read/28667019/retrotransposons-are-the-major-contributors-to-the-expansion-of-the-drosophila-ananassae-muller-f-element
#13
Wilson Leung, Christopher D Shaffer, Elizabeth J Chen, Thomas J Quisenberry, Kevin Ko, John M Braverman, Thomas C Giarla, Nathan T Mortimer, Laura K Reed, Sheryl T Smith, Srebrenka Robic, Shannon R McCartha, Danielle R Perry, Lindsay M Prescod, Zenyth A Sheppard, Ken J Saville, Allison McClish, Emily A Morlock, Victoria R Sochor, Brittney Stanton, Isaac C Veysey-White, Dennis Revie, Luis A Jimenez, Jennifer J Palomino, Melissa D Patao, Shane M Patao, Edward T Himelblau, Jaclyn D Campbell, Alexandra L Hertz, Maddison F McEvilly, Allison R Wagner, James Youngblom, Baljit Bedi, Jeffery Bettincourt, Erin Duso, Maiye Her, William Hilton, Samantha House, Masud Karimi, Kevin Kumimoto, Rebekah Lee, Darryl Lopez, George Odisho, Ricky Prasad, Holly Lyn Robbins, Tanveer Sandhu, Tracy Selfridge, Kara Tsukashima, Hani Yosif, Nighat P Kokan, Latia Britt, Alycia Zoellner, Eric P Spana, Ben T Chlebina, Insun Chong, Harrison Friedman, Danny A Mammo, Chun L Ng, Vinayak S Nikam, Nicholas U Schwartz, Thomas Q Xu, Martin G Burg, Spencer M Batten, Lindsay M Corbeill, Erica Enoch, Jesse J Ensign, Mary E Franks, Breanna Haiker, Judith A Ingles, Lyndsay D Kirkland, Joshua M Lorenz-Guertin, Jordan Matthews, Cody M Mittig, Nicholaus Monsma, Katherine J Olson, Guillermo Perez-Aragon, Alen Ramic, Jordan R Ramirez, Christopher Scheiber, Patrick A Schneider, Devon E Schultz, Matthew Simon, Eric Spencer, Adam C Wernette, Maxine E Wykle, Elizabeth Zavala-Arellano, Mitchell J McDonald, Kristine Ostby, Peter Wendland, Justin R DiAngelo, Alexis M Ceasrine, Amanda H Cox, James E B Docherty, Robert M Gingras, Stephanie M Grieb, Michael J Pavia, Casey L Personius, Grzegorz L Polak, Dale L Beach, Heaven L Cerritos, Edward A Horansky, Karim A Sharif, Ryan Moran, Susan Parrish, Kirsten Bickford, Jennifer Bland, Juliana Broussard, Kerry Campbell, Katelynn E Deibel, Richard Forka, Monika C Lemke, Marlee B Nelson, Catherine O'Keeffe, S Mariel Ramey, Luke Schmidt, Paola Villegas, Christopher J Jones, Stephanie L Christ, Sami Mamari, Adam S Rinaldi, Ghazal Stity, Amy T Hark, Mark Scheuerman, Cathy Silver Key, Briana D McRae, Adam S Haberman, Sam Asinof, Harriette Carrington, Kelly Drumm, Terrance Embry, Richard McGuire, Drew Miller-Foreman, Stella Rosen, Nadia Safa, Darrin Schultz, Matt Segal, Yakov Shevin, Petros Svoronos, Tam Vuong, Gary Skuse, Don W Paetkau, Rachael K Bridgman, Charlotte M Brown, Alicia R Carroll, Francesca M Gifford, Julie Beth Gillespie, Susan E Herman, Krystal L Holtcamp, Misha A Host, Gabrielle Hussey, Danielle M Kramer, Joan Q Lawrence, Madeline M Martin, Ellen N Niemiec, Ashleigh P O'Reilly, Olivia A Pahl, Guadalupe Quintana, Elizabeth A S Rettie, Torie L Richardson, Arianne E Rodriguez, Mona O Rodriguez, Laura Schiraldi, Joanna J Smith, Kelsey F Sugrue, Lindsey J Suriano, Kaitlyn E Takach, Arielle M Vasquez, Ximena Velez, Elizabeth J Villafuerte, Laura T Vives, Victoria R Zellmer, Jeanette Hauke, Charles R Hauser, Karolyn Barker, Laurie Cannon, Perouza Parsamian, Samantha Parsons, Zachariah Wichman, Christopher W Bazinet, Diana E Johnson, Abubakarr Bangura, Jordan A Black, Victoria Chevee, Sarah A Einsteen, Sarah K Hilton, Max Kollmer, Rahul Nadendla, Joyce Stamm, Antoinette E Fafara-Thompson, Amber M Gygi, Emmy E Ogawa, Matt Van Camp, Zuzana Kocsisova, Judith L Leatherman, Cassie M Modahl, Michael R Rubin, Susana S Apiz-Saab, Suzette M Arias-Mejias, Carlos F Carrion-Ortiz, Patricia N Claudio-Vazquez, Debbie M Espada-Green, Marium Feliciano-Camacho, Karina M Gonzalez-Bonilla, Mariela Taboas-Arroyo, Dorianmarie Vargas-Franco, Raquel Montañez-Gonzalez, Joseph Perez-Otero, Myrielis Rivera-Burgos, Francisco J Rivera-Rosario, Heather L Eisler, Jackie Alexander, Samatha K Begley, Deana Gabbard, Robert J Allen, Wint Yan Aung, William D Barshop, Amanda Boozalis, Vanessa P Chu, Jeremy S Davis, Ryan N Duggal, Robert Franklin, Katherine Gavinski, Heran Gebreyesus, Henry Z Gong, Rachel A Greenstein, Averill D Guo, Casey Hanson, Kaitlin E Homa, Simon C Hsu, Yi Huang, Lucy Huo, Sarah Jacobs, Sasha Jia, Kyle L Jung, Sarah Wai-Chee Kong, Matthew R Kroll, Brandon M Lee, Paul F Lee, Kevin M Levine, Amy S Li, Chengyu Liu, Max Mian Liu, Adam P Lousararian, Peter B Lowery, Allyson P Mallya, Joseph E Marcus, Patrick C Ng, Hien P Nguyen, Ruchik Patel, Hashini Precht, Suchita Rastogi, Jonathan M Sarezky, Adam Schefkind, Michael B Schultz, Delia Shen, Tara Skorupa, Nicholas C Spies, Gabriel Stancu, Hiu Man Vivian Tsang, Alice L Turski, Rohit Venkat, Leah E Waldman, Kaidi Wang, Tracy Wang, Jeffrey W Wei, Dennis Y Wu, David D Xiong, Jack Yu, Karen Zhou, Gerard P McNeil, Robert W Fernandez, Patrick Gomez Menzies, Tingting Gu, Jeremy Buhler, Elaine R Mardis, Sarah C R Elgin
The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (~5.2 Mb) is the smallest chromosome in Drosophila melanogaster, but it is substantially larger (>18.7 Mb) in Drosophila ananassae To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4 Mb region of the D. ananassae F element, and a 1.7 Mb region from the D element for comparison...
June 30, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28666125/ltr-retrotransposon-control-by-trna-derived-small-rnas
#14
Andrea J Schorn, Michael J Gutbrod, Chantal LeBlanc, Rob Martienssen
Transposon reactivation is an inherent danger in cells that lose epigenetic silencing during developmental reprogramming. In the mouse, long terminal repeat (LTR)-retrotransposons, or endogenous retroviruses (ERV), account for most novel insertions and are expressed in the absence of histone H3 lysine 9 trimethylation in preimplantation stem cells. We found abundant 18 nt tRNA-derived small RNA (tRF) in these cells and ubiquitously expressed 22 nt tRFs that include the 3' terminal CCA of mature tRNAs and target the tRNA primer binding site (PBS) essential for ERV reverse transcription...
June 29, 2017: Cell
https://www.readbyqxmd.com/read/28664156/ltrs-of-endogenous-retroviruses-as-a-source-of-tbx6-binding-sites
#15
Yukuto Yasuhiko, Yoko Hirabayashi, Ryuichi Ono
Retrotransposons are abundant in mammalian genomes and can modulate the gene expression of surrounding genes by disrupting endogenous binding sites for transcription factors (TFs) or providing novel TFs binding sites within retrotransposon sequences. Here, we show that a (C/T)CACACCT sequence motif in ORR1A, ORR1B, ORR1C, and ORR1D, Long Terminal Repeats (LTRs) of MaLR endogenous retrovirus (ERV), is the direct target of Tbx6, an evolutionary conserved family of T-box TFs. Moreover, by comparing gene expression between control mice (Tbx6 +/-) and Tbx6-deficient mice (Tbx6 -/-), we demonstrate that at least four genes, Twist2, Pitx2, Oscp1, and Nfxl1, are down-regulated with Tbx6 deficiency...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/28663342/comparative-genomics-of-two-sequential-candida-glabrate-clinical-isolates
#16
Luis Vale-Silva, Emmanuel Beaudoing, Van Du T Tran, Dominique Sanglard
Candida glabrate is an important fungal pathogen which develops rapidly antifungal resistance in treated patients. It is known that azole treatments lead to antifungal resistance in this fungal species and that multidrug efflux transporters are involved in this process. Specific mutations in the transcriptional regulator PDR1 result in upregulation of the transporters. In addition, we showed that the PDR1 mutations can contribute to enhance virulence in animal models. We were interested in this study to compare genomes of two specific C...
June 29, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28662698/mov10-suppresses-retroelements-and-regulates-neuronal-development-and-function-in-the-developing-brain
#17
Geena Skariah, Joseph Seimetz, Miles Norsworthy, Monica C Lannom, Phillip J Kenny, Mohamed Elrakhawy, Craig Forsthoefel, Jenny Drnevich, Auinash Kalsotra, Stephanie Ceman
BACKGROUND: Moloney leukemia virus 10 (Mov10) is an RNA helicase that mediates access of the RNA-induced silencing complex to messenger RNAs (mRNAs). Until now, its role as an RNA helicase and as a regulator of retrotransposons has been characterized exclusively in cell lines. We investigated the role of Mov10 in the mouse brain by examining its expression over development and attempting to create a Mov10 knockout mouse. Loss of both Mov10 copies led to early embryonic lethality. RESULTS: Mov10 was significantly elevated in postnatal murine brain, where it bound retroelement RNAs and mRNAs...
June 29, 2017: BMC Biology
https://www.readbyqxmd.com/read/28659950/mapping-and-characterization-of-the-fefe-gene-that-controls-iron-uptake-in-melon-cucumis-melo-l
#18
Raghuprakash Kastoori Ramamurthy, Brian M Waters
Iron (Fe) deficiency in plants limits crop growth and productivity. Molecular mechanisms that plants use to sense and respond to Fe deficiency by coordinated expression of Fe-uptake genes are not fully understood. The C940-fe chlorotic melon (Cucumis melo) mutant known as fefe is unable to upregulate Fe-uptake genes, however, the FeFe gene had not been identified. In this study, we used two F2 mapping populations to map and identify the FeFe gene as bHLH38, a homolog of subgroup Ib bHLH genes from Arabidopsis thaliana that are involved in transcriptional regulation of Fe-uptake genes in partnership with the FIT gene...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28659723/helitrons-and-retrotransposons-are-co-localized-in-bos-taurus-genomes
#19
A Babii, S Kovalchuk, T Glazko, G Kosovsky, V Glazko
BACKGROUND: DNA transposons helitrons are mobile genetic elements responsible for major movements of the genetic material within and across different genomes. This ability makes helitrons suitable candidate elements for the development of new approaches of multilocus genotyping of live-stock animals, along with the well-known microsatellite loci. OBJECTIVE: We aimed to estimate the informativeness of helitron and microsatellite markers in assessing the consolidation and the "gene pool" standards of two commercial dairy cattle breeds (Ayrshire breed and holsteinized Black-and-White cattle) and one local breed of Kalmyk cattle, and to reveal any inter-breed difference in the organization of genomic regions flanked by helitrons in the studied cattle breeds...
June 2017: Current Genomics
https://www.readbyqxmd.com/read/28655292/insertionally-polymorphic-sites-of-human-endogenous-retrovirus-k-hml-2-with-long-target-site-duplications
#20
Tomoaki Kahyo, Hidetaka Yamada, Hong Tao, Nobuya Kurabe, Haruhiko Sugimura
BACKGROUND: Human endogenous retroviruses (HERVs) belong to the LTR-retrotransposon family, where the complete HERV sequence contains two long terminal repeats (LTRs) located at each end. Intact LTRs possess highly conserved transcriptional promoter and enhancer sequences, so analyses of HERV insertional polymorphisms are expected to provide greater insights into human genomic variation compared with the conventional analysis of single nucleotide variations. High-throughput sequencing technology is developing but genome-wide investigations of HERVs are methodically challenging, and thus a comprehensive understanding of HERV insertional polymorphisms and target site duplications (TSDs) remains elusive...
June 27, 2017: BMC Genomics
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