keyword
MENU ▼
Read by QxMD icon Read
search

transposable elements

keyword
https://www.readbyqxmd.com/read/29048487/the-genome-draft-of-coconut-cocos-nucifera
#1
Yong Xiao, Pengwei Xu, Haikuo Fan, Luc Baudouin, Wei Xia, Stéphanie Bocs, Junyang Xu, Qiong Li, Anping Guo, Lixia Zhou, Jing Li, Yi Wu, Zilong Ma, Alix Armero, Auguste Emmanuel Issali, Na Liu, Ming Peng, Yaodong Yang
Background: Coconut palm (Cocos nucifera, 2n = 32), a member of genus Cocos and family Arecaceae (Palmaceae), is an important tropical fruit and oil crop. Currently, coconut palm is cultivated in 93 countries, including Central and South America, East and West Africa, Southeast Asia and the Pacific island, with a total growth area of more than 12 million hectares (www.fao.org/faostat/en/). Coconut palm is generally classified into two main categories: "Tall" (flowering 8-10 years after planting) and "Dwarf" (flowering 4-6 years after planting), based on morphological characteristics and breeding habits...
October 5, 2017: GigaScience
https://www.readbyqxmd.com/read/29046683/the-diversity-of-sequence-and-chromosomal-distribution-of-new-transposable-element-related-segments-in-the-rye-genome-revealed-by-fish-and-lineage-annotation
#2
Yingxin Zhang, Chengming Fan, Shuangshuang Li, Yuhong Chen, Richard R-C Wang, Xiangqi Zhang, Fangpu Han, Zanmin Hu
Transposable elements (TEs) in plant genomes exhibit a great variety of structure, sequence content and copy number, making them important drivers for species diversity and genome evolution. Even though a genome-wide statistic summary of TEs in rye has been obtained using high-throughput DNA sequencing technology, the accurate diversity of TEs in rye, as well as their chromosomal distribution and evolution, remains elusive due to the repetitive sequence assembling problems and the high dynamic and nested nature of TEs...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29046402/the-hybrid-incompatibility-genes-lhr-and-hmr%C3%A2-are-required-for-sister-chromatid-detachment-during-anaphase-but-not-for-centromere-function
#3
Jacob A Blum, Silvia Bonaccorsi, Marta Marzullo, Valeria Palumbo, Yukiko M Yamashita, Daniel A Barbash, Maurizio Gatti
Crosses between Drosophila melanogaster females and Drosophila simulans males produce hybrid sons that die at the larval stage. This hybrid lethality is suppressed by loss-of-function mutations in the D. melanogasterHybrid male rescue (Hmr) or in the D. simulansLethal hybrid rescue (Lhr) genes. Previous studies have shown that Hmr and Lhr interact with heterochromatin proteins and suppress expression of transposable elements within D. melanogaster It also has been proposed that Hmr and Lhr function at the centromere...
October 18, 2017: Genetics
https://www.readbyqxmd.com/read/29044423/cultured-bovine-embryo-biopsy-conserves-methylation-marks-from-original-embryo
#4
Noelia Fonseca Balvís, Soledad Garcia-Martinez, Serafín Pérez-Cerezales, Elena Ivanova, Isabel Gomez-Redondo, Meriem Hamdi, Dimitrios Rizos, Pilar Coy, Gavin Kelsey, Alfonso Gutierrez-Adan
A major limitation of embryo epigenotyping by chromatin immunoprecipitation analysis is the reduced amount of sample available from an embryo biopsy. We developed an in vitro system to expand trophectoderm cells from an embryo biopsy to overcome this limitation. This work analyzes whether expanded trophectoderm (EX) is representative of the trophectoderm (TE) methylation or adaptation to culture has altered its epigenome. We took a small biopsy from the trophectoderm (30-40 cells) of in vitro produced bovine-hatched blastocysts and cultured it on fibronectin-treated plates until we obtained ∼4 × 104 cells...
August 1, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/29042411/a-horizontally-transferred-autonomous-helitron-became-a-full-polydnavirus-segment-in-cotesia-vestalis
#5
Pedro Heringer, Guilherme B Dias, Gustavo C S Kuhn
Bracoviruses associate symbiotically with thousands of parasitoid wasp species in the family Braconidae, working as virulence gene vectors, and allowing the development of wasp larvae within hosts. These viruses are composed by multiple DNA circles that are packaged into infective particles and injected together with wasp's eggs during parasitization. One of the viral segments of Cotesia vestalis bracovirus contains a gene that has been previously described as a helicase of unknown origin. Here we demonstrate that this gene is a Rep/Helicase from an intact Helitron transposable element that covers the viral segment almost entirely...
October 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29040764/rif1-promotes-a-repressive-chromatin-state-to-safeguard-against-endogenous-retrovirus-activation
#6
Pishun Li, Li Wang, Brian D Bennett, Jiajia Wang, Jialun Li, Yufeng Qin, Motoki Takaku, Paul A Wade, Jiemin Wong, Guang Hu
Transposable elements, including endogenous retroviruses (ERVs), constitute a large fraction of the mammalian genome. They are transcriptionally silenced during early development to protect genome integrity and aberrant transcription. However, the mechanisms that control their repression are not fully understood. To systematically study ERV repression, we carried out an RNAi screen in mouse embryonic stem cells (ESCs) and identified a list of novel regulators. Among them, Rif1 displays the strongest effect...
October 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040293/mapping-of-important-taxonomic-and-productivity-traits-using-genic-and-non-genic-transposable-element-markers-in-peanut-arachis-hypogaea-l
#7
Anil A Hake, Kenta Shirasawa, Arati Yadawad, M Sukruth, Malagouda Patil, Spurthi N Nayak, S Lingaraju, P V Patil, H L Nadaf, M V C Gowda, R S Bhat
A mapping population of recombinant inbred lines (RILs) derived from TMV 2 and its mutant, TMV 2-NLM was employed for mapping important taxonomic and productivity traits using genic and non-genic transposable element markers in peanut. Single nucleotide polymorphism and copy number variation using RAD-Sequencing data indicated very limited polymorphism between TMV 2 and TMV 2-NLM. But phenotypically they differed significantly for many taxonomic and productivity traits. Also, the RIL population showed significant variation for a few additional agronomic traits...
2017: PloS One
https://www.readbyqxmd.com/read/29039003/tissue-culture-somatic-embryogenesis-induced-tnt1-retrotransposon-based-mutagenesis-in-brachypodium-distachyon
#8
Upinder S Gill, Juan C Serrani-Yarce, Hee-Kyung Lee, Kirankumar S Mysore
Brachypodium distachyon is a model grass species for economically important cereal crops. Efforts are in progress to develop useful functional genomic resources in Brachypodium. A tobacco retrotransposon, Tnt1, has been used successfully in recent past to generate insertional mutagenesis in several dicot plant species. Tnt1 retrotransposon replicates, transposes, and inserts at multiple random genomic locations in the plant genome. Transposition occurs only during somatic embryogenesis but not during seed transmission...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29038910/analysis-of-somaclonal-variation-in-transgenic-and-regenerated-plants-of-arabidopsis-thaliana-using-methylation-related-metaflp-and-tmd-markers
#9
Carlos J Coronel, Ana I González, María L Ruiz, Carlos Polanco
We provide evidence that nucleotide sequence and methylation status changes occur in the Arabidopsis genome during in vitro tissue culture at a frequency high enough to represent an important source of variation. Somaclonal variation is a general consequence of the tissue culture process that has to be analyzed specifically when regenerated plants are obtained in any plant species. Currently, there are few studies about the variability comprising sequence changes and methylation status at the DNA level, generated by the culture of A...
October 16, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/29037146/comparative-genomic-analyses-highlight-the-contribution-of-pseudogenized-protein-coding-genes-to-human-lincrnas
#10
Wan-Hsin Liu, Zing Tsung-Yeh Tsai, Huai-Kuang Tsai
BACKGROUND: The regulatory roles of long intergenic noncoding RNAs (lincRNAs) in humans have been revealed through the use of advanced sequencing technology. Recently, three possible scenarios of lincRNA origins have been proposed: de novo origination from intergenic regions, duplication from other long noncoding RNAs, and pseudogenization from protein-coding genes. The first two scenarios are largely studied and supported, yet few studies focused on the evolution from pseudogenized protein-coding sequence to lincRNA...
October 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29036710/a-disulfide-bond-a-like-oxidoreductase-is-a-strong-candidate-gene-for-self-incompatibility-in-apricot-prunus-armeniaca-pollen
#11
Juan Vicente Muñoz-Sanz, Elena Zuriaga, María L Badenes, Carlos Romero
S-RNase based gametophytic self-incompatibility (SI) is a widespread prezygotic reproductive barrier in flowering plants. In the Solanaceae, Plantaginaceae and Rosaceae gametophytic SI is controlled by the pistil-specific S-RNases and the pollen S-locus F-box proteins but non-S-specific factors, namely modifiers, are also required. In apricot, Prunus armeniaca (Rosaceae), we previously mapped two pollen-part mutations that confer self-compatibility in cultivars Canino and Katy at the distal end of chromosome 3 (M-locus) unlinked to the S-locus...
September 25, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29036642/striking-a-balance-regulation-of-transposable-elements-by-zfp281-and-mll2-in-mouse-embryonic-stem-cells
#12
Qian Dai, Yang Shen, Yan Wang, Xin Wang, Joel Celio Francisco, Zhuojuan Luo, Chengqi Lin
Transposable elements (TEs) compose about 40% of the murine genome. Retrotransposition of active TEs such as LINE-1 (L1) tremendously impacts genetic diversification and genome stability. Therefore, transcription and transposition activities of retrotransposons are tightly controlled. Here, we show that the Krüppel-like zinc finger protein Zfp281 directly binds and suppresses a subset of retrotransposons, including the active young L1 repeat elements, in mouse embryonic stem (ES) cells. In addition, we find that Zfp281-regulated L1s are highly enriched for 5-hydroxymethylcytosine (5hmC) and H3K4me3...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036592/gain-and-loss-of-small-rna-classes-characterization-of-small-rnas-in-the-parasitic-nematode-family-strongyloididae
#13
Anja Holz, Adrian Streit
The nematode family Strongyloididae is of particular interest because it contains important parasites of medical and veterinary relevance. In addition, species of this family can form parasitic and free-living generations and it also occupies an interesting phylogenetic position within the nematodes. Nematodes differ in several ways from other taxa with respect to their small non-coding RNAs. Recent comparative studies revealed that there is also considerable variability within the nematodes. However, no Strongyloididae species or close relative was included in these studies...
September 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29036316/the-role-of-small-rna-based-epigenetic-silencing-for-purifying-selection-on-transposable-elements-in-capsella-grandiflora
#14
Robert Horvath, Tanja Slotte
To avoid negative effects of transposable element (TE) proliferation, plants epigenetically silence TEs using a number of mechanisms, including RNA-directed DNA methylation. These epigenetic modifications can extend outside the boundaries of TE insertions and lead to silencing of nearby genes, resulting in a trade-off between TE silencing and interference with nearby gene regulation. Therefore, purifying selection is expected to remove silenced TE insertions near genes more efficiently and prevent their accumulation within a population...
September 27, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29032547/genome-wide-mutagenesis-in-borrelia-burgdorferi
#15
Tao Lin, Lihui Gao
Signature-tagged mutagenesis (STM) is a functional genomics approach to identify bacterial virulence determinants and virulence factors by simultaneously screening multiple mutants in a single host animal, and has been utilized extensively for the study of bacterial pathogenesis, host-pathogen interactions, and spirochete and tick biology. The signature-tagged transposon mutagenesis has been developed to investigate virulence determinants and pathogenesis of Borrelia burgdorferi. Mutants in genes important in virulence are identified by negative selection in which the mutants fail to colonize or disseminate in the animal host and tick vector...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29032444/modulating-signaling-networks-by-crispr-cas9-mediated-transposable-element-insertion
#16
REVIEW
Luis María Vaschetto
In a recent past, transposable elements (TEs) were referred to as selfish genetic components only capable of copying themselves with the aim of increasing the odds of being inherited. Nonetheless, TEs have been initially proposed as positive control elements acting in synergy with the host. Nowadays, it is well known that TE movement into host genome comprises an important evolutionary mechanism capable of increasing the adaptive fitness. As insights into TE functioning are increasing day to day, the manipulation of transposition has raised an interesting possibility of setting the host functions, although the lack of appropriate genome engineering tools has unpaved it...
October 14, 2017: Current Genetics
https://www.readbyqxmd.com/read/29030848/profiling-open-chromatin-structure-in-the%C3%A2-ovarian-somatic-cells-using-atac-seq
#17
Kensaku Murano, Yuka W Iwasaki, Haruhiko Siomi
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) was recently established as a method to profile open chromatin, which overcomes the sample size limitations of the alternative methods DNase/MNase-seq. To investigate the role of Piwi in heterochromatin formation around transposable element loci, we have used ATAC-seq to examine chromatin accessibility at target transposable elements in a Drosophila cultured cell line, ovarian somatic cells (OSCs). In this chapter, we describe our method to profile open chromatin structure in OSCs using ATAC-seq...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29029740/a-quantitative-homogeneous-assay-for-global-dna-methylation-levels-using-cpg-binding-domain-and-methyl-cpg-binding-domain-fused-luciferase
#18
Wataru Yoshida, Yuji Baba, Kyoko Banzawa, Isao Karube
Global DNA methylation levels have been considered as biomarkers for cancer diagnostics because transposable elements that constitute approximately 45% of the human genome are hypomethylated in cancer cells. We have previously reported a homogeneous assay for measuring methylated CpG content of genomic DNA based on bioluminescence resonance energy transfer (BRET) using methyl-CpG-binding domain (MBD)-fused luciferase (MBD-luciferase). In this study, a homogeneous assay for measuring unmethylated CpG content of genomic DNA in the same platform was developed using CXXC domain-fused luciferase (CXXC-luciferase) that specifically recognizes unmethylated CpG...
October 16, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29025411/maize-rna-poliv-affects-the-expression-of-genes-with-nearby-te-insertions-and-has-a-genome-wide-repressive-impact-on-transcription
#19
Cristian Forestan, Silvia Farinati, Riccardo Aiese Cigliano, Alice Lunardon, Walter Sanseverino, Serena Varotto
BACKGROUND: RNA-directed DNA methylation (RdDM) is a plant-specific epigenetic process that relies on the RNA polymerase IV (Pol IV) for the production of 24 nucleotide small interfering RNAs (siRNA) that guide the cytosine methylation and silencing of genes and transposons. Zea mays RPD1/RMR6 gene encodes the largest subunit of Pol IV and is required for normal plant development, paramutation, transcriptional repression of certain transposable elements (TEs) and transcriptional regulation of specific alleles...
October 12, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29023226/contrasting-evolutionary-paths-among-indo-pacific-pomacentrus-species-promoted-by-extensive-pericentric-inversions-and-genome-organization-of-repetitive-sequences
#20
Nuntaporn Getlekha, Marcelo de Bello Cioffi, Nuntiya Maneechot, Luiz Antônio Carlos Bertollo, Weerayuth Supiwong, Alongklod Tanomtong, Wagner Franco Molina
Pomacentrus (damselfishes) is one of the most characteristic groups of fishes in the Indo-Pacific coral reef. Its 77 described species exhibit a complex taxonomy with cryptic lineages across their extensive distribution. Periods of evolutionary divergences between them are very variable, and the cytogenetic events that followed their evolutionary diversification are largely unknown. In this respect, analyses of chromosomal divergence, within a phylogenetic perspective, are particularly informative regarding karyoevolutionary trends...
October 12, 2017: Zebrafish
keyword
keyword
68633
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"