PubMed journal article Genomic abundance and transcriptional activity of diverse gypsy and copia long terminal repeat retrotransposons in three wild sunflower specie were found in PRIME PubMed. Download Prime PubMed App to iPhone or iPad.
LTR retrotransposons are class I transposable element characterized by the presence of Long Terminal Repeats (LTR) directly flanking an internal coding region. As retrotransposons, they mobilize through reverse-transcription of their mRNA and integration of the newly created cDNA into another location. Their mechanism of retrotransposition is shared with retroviruses, with the difference that most LTR-retrotransposons do not form infectious particles that leave the cells and therefore only replicate inside their genome of origin. Their size ranges from a few hundred base pairs to 25kb, like the Ogre retrotransposon in the Pea genome In plant genomes, LTR retrotransposons are the major repetitive sequence class, e.g. able to constitute more than 75% of the maize genome. LTR retrotransposons have direct long terminal repeat that range from ~100 bp to over 5 kb in size. LTR retrotransposons are further sub-classified into the Ty1-copia-like (Pseudoviridae), Ty3-gypsy-like (Metaviridae), and ...
Converting the single-stranded retroviral RNA into integration-competent double-stranded DNA is achieved through a multi-step process mediated by the virus-coded reverse transcriptase (RT). With the exception that it is restricted to an intracellular life cycle, replication of the Saccharomyces cerevisiae long terminal repeat (LTR)-retrotransposon Ty3 genome is guided by equivalent events that, while generally similar, show many unique and subtle differences relative to the retroviral counterparts. Until only recently, our knowledge of RT structure and function was guided by a vast body of literature on the human immunodeficiency virus (HIV) enzyme. Although the recently-solved structure of Ty3 RT in the presence of an RNA/DNA hybrid adds little in terms of novelty to the mechanistic basis underlying DNA polymerase and ribonuclease H activity, it highlights quite remarkable topological differences between retroviral and LTR-retrotransposon RTs. The theme of overall similarity but distinct ...
In the PhD project the successful candidate will characterize integration site selection by the non-long terminal repeat retrotransposon TRE5-A upstream of tRNA genes. In vivo chromatin immunoprecipitation will be combined with Illumina sequencing (ChIP-seq) to evaluate whether sites of TRE5-A integration coincide with RNA polymerase III complexes. To analyze the influence of local chromatin structure upstream of tRNA genes on TRE5-A integration, we use nucleosome profiling (MNase-seq), comparing D. discoideum wildtype and a particular mutant in which TRE5-A retrotransposition is compromised. Further, an in vivo tRNA gene targeting assay with genetically tagged TRE5-A retrotransposons will be established to directly test requirements of protein interactions between the retrotransposon and its target sites ...
Reverse transcription-derived sequences account for at least half of the human genome. Although these retroelements are formidable motors of evolution, they can occasionally cause disease, and accordingly are inactivated during early embryogenesis through epigenetic mechanisms. In the mouse, at least for endogenous retroviruses, important mediators of this process are the tetrapod-specific KRAB-containing zinc finger proteins (KRAB-ZFPs) and their cofactor TRIM28. The present study demonstrates that KRAB/TRIM28-mediated regulation is responsible for controlling a very broad range of human-specific endogenous retroelements (EREs) in human embryonic stem (ES) cells and that it exerts, as a consequence, a marked effect on the transcriptional dynamics of these cells. It further reveals reciprocal dependence between TRIM28 recruitment at specific families of EREs and DNA methylation. It finally points to the importance of persistent TRIM28-mediated control of ERE transcriptional impact beyond their ...
Background In contrast to DNA-mediated transposable elements (TEs), retrotransposons, particularly non-long terminal repeat retrotransposons (non-LTRs), are generally considered to have a much lower propensity towards horizontal transfer. selection due to functional constraint. Vertical transmission of Juan and a few cases of phylogenetic incongruence Comparison of host phylogeny with TE phylogeny is one method used to address the question of vertical vs. horizontal transmission. A detailed mosquito phylogeny has been previously constructed using Vg-C [30]. We have only included Vg-C sequences from species for which Juan sequences were obtained in this study (Figure ?(Figure2A).2A). In addition, we have also obtained sequence for Vg-C from Ae. simpsoni, which was not available from the previous dataset [30]. We used nt sequences for phylogenetic inference as in the previous study, and our phylogeny is consistent with the phylogeny based on the larger Vg-C dataset [30]. Phylogenetic inference ...
Transposable elements constitute about half of the mammalian genome, and can be divided into two classes: the class I (retrotransposons) and the class II (DNA transposons). A few hundred types of retrotransposons, which are dynamic and stage specific, have been annotated. The copy numbers and genomic locations are significantly varied in species. Retrotransposons are active in germ cells, early embryos and pluripotent stem cells (PSCs) correlated with low levels of DNA methylation in epigenetic regulation. Some key pluripotency transcriptional factors (such as OCT4, SOX2, and NANOG) bind retrotransposons and regulate their activities in PSCs, suggesting a vital role of retrotransposons in pluripotency maintenance and self-renewal. In response to retrotransposons transposition, cells employ a number of silencing mechanisms, such as DNA methylation and histone modification. This review summarizes expression patterns, functions, and regulation of retrotransposons in PSCs and early embryonic development.
We present data on the relationship between the rate of transposition and copy number in the genome for the copia and Doc retrotransposons of Drosophila melanogaster. copia and Doc transposition rates were directly measured in sublines of the isogenic 2b line using individual males or females, respectively, with a range of copia copy numbers from 49 to 103 and Doc copy numbers from 112 to 235 per genome. Transposition rates varied from 3 x 10(-4) to 2 x 10(-2) for copia and from 2 x 10(-4) to 2 x 10(-3) for Doc. A positive relationship between transposition rate and copy number was found both for copia and for Doc when the data were analysed across all the 2b individuals; no significant correlation was found when the data were analysed across the subline means for both retrotransposons tested. Overall, correlation between copia and Doc transposition rate and their copy number in the genome, if any, was not negative, which would be expected if transposable elements (TEs) self-regulate their copy number.
TY - JOUR. T1 - Retrotransposons manipulating mammalian skeletal development in chondrocytes. AU - Kubota, Satoshi. AU - Ishikawa, Takanori. AU - Kawata, Kazumi. AU - Hattori, Takako. AU - Nishida, Takashi. PY - 2020/3/1. Y1 - 2020/3/1. N2 - Retrotransposons are genetic elements that copy and paste themselves in the host genome through transcription, reverse‐transcription, and integration processes. Along with their proliferation in the genome, retrotransposons inevitably modify host genes around the integration sites, and occasionally create novel genes. Even now, a number of retrotransposons are still actively editing our genomes. As such, their profound role in the evolution of mammalian genomes is obvious; thus, their contribution to mammalian skeletal evolution and development is also unquestionable. In mammals, most of the skeletal parts are formed and grown through a process entitled endochondral ossification, in which chondrocytes play central roles. In this review, current knowledge ...
Active retrotransposons play important roles during evolution and continue to shape our genomes today, especially in genetic polymorphisms underlying a diverse set of diseases. However, studies of human retrotransposon insertion polymorphisms (RIPs) based on whole-genome deep sequencing at the population level have not been sufficiently undertaken, despite the obvious need for a thorough characterization of RIPs in the general population.|br| Herein, we present a novel and efficient computational tool named Specific Insertions Detector (SID) for the detection of non-reference RIPs. We demonstrate that SID is suitable for high depth whole-genome sequencing (WGS) data using paired-end reads obtained from simulated and real datasets. We construct a comprehensive RIP database using a large population of 90 Han Chinese individuals with a mean 68× depth per individual. In total, we identify 9342 recent RIPs, and 8433 of these RIPs are novel compared with dbRIP, including 5826 Alu, 2169 long interspersed
Evolutionary changes in genome size result from the combined effects of mutation, natural selection, and genetic drift. Insertion and deletion mutations (indels) directly impact genome size by adding or removing sequences. Most species lose more DNA through small indels (i.e., ∼1-30 bp) than they gain, which can result in genome reduction over time. Because this rate of DNA loss varies across species, small indel dynamics have been suggested to contribute to genome size evolution. Species with extremely large genomes provide interesting test cases for exploring the link between small indels and genome size; however, most large genomes remain relatively unexplored. Here, we examine rates of DNA loss in the tetrapods with the largest genomes-the salamanders. We used low-coverage genomic shotgun sequence data from four salamander species to examine patterns of insertion, deletion, and substitution in neutrally evolving non-long terminal repeat (LTR) retrotransposon sequences. For comparison, we ...
Retroposons are repetitive DNA fragments which are inserted into chromosomes after they had been reverse transcribed from any RNA molecule. In contrast to retrotransposons, they never encode reverse transcriptase (RT) (but see below). Therefore, they are non-autonomous elements with regard to transposition activity (as opposed to transposons). Non-long terminal repeat (LTR) retrotransposons such as the human LINE1 elements are sometimes falsely referred to as retroposons. However, this depends on the author. For example, Howard Temin published the following definition: Retroposons encode RT but are devoid of long terminal repeats (LTRs), for example Long interspersed elements (LINEs). Retrotransposons also feature LTRs and retroviruses, in addition, are packaged as viral particles (virions). Retrosequences are non-autonomous elements devoid of RT. They are retroposed with the aid of the machinery of autonomous elements, such as LINEs; examples are Short interspersed nuclear elements (SINEs) or ...
Department of Zoology and Genetics, Iowa State University, Ames 50011, USA.. DNA sequence analysis near the Arabidopsis thaliana ABI3 gene revealed the presence of a non-LTR retrotransposon insertion that we have designated Ta11-1. This insertion is 6.2 kb in length and encodes two overlapping reading frames with similarity to non-LTR retrotransposon proteins, including reverse transcriptase. A polymerase chain reaction assay was developed based on conserved amino acid sequences shared between the Ta11-1 reverse transcriptase and those of non-LTR retrotransposons from other species. Seventeen additional A. thaliana reverse transcriptases were identified that range in nucleotide similarity from 48-88% (Ta12-Ta28). Phylogenetic analyses indicated that the A. thaliana sequences are more closely related to each other than to elements from other organisms, consistent with the vertical evolution of these sequences over most of their evolutionary history. One sequence, Ta17, is located in the ...
Sigma-Aldrich offers abstracts and full-text articles by [Ryuichi Ono, Masayuki Ishii, Yoshitaka Fujihara, Moe Kitazawa, Takako Usami, Tomoko Kaneko-Ishino, Jun Kanno, Masahito Ikawa, Fumitoshi Ishino].
Reverse transcriptases (RTs) are usually thought of as eukaryotic enzymes, but they are also present in bacteria and likely originated in bacteria and migrated to eukaryotes. Only three types of bacterial retroelements have been substantially characterized: group II introns, diversity-generating retroelements, and retrons. Recent work, however, has identified a myriad of uncharacterized RTs and RT-related sequences in bacterial genomes, which exhibit great sequence diversity and a range of domain structures. Apart from group II introns, none of these putative RTs show evidence of active retromobility. Instead, available information suggests that they are involved in useful processes, sometimes related to phages or phage resistance. This article reviews our knowledge of both characterized and uncharacterized RTs in bacteria. The range of their sequences and genomic contexts promises the discovery of new biochemical reactions and biological phenomena.
IntroductionRetroelements are mobile genetic elements (MGEs) that retrotranspose via a RNA intermediate that is reverse-transcribed to DNA by the encoded reverse transcriptase and integrated into a ne
Sigma-Aldrich offers abstracts and full-text articles by [Tianxiang Hu, Xingguo Zhu, Wenhu Pi, Miao Yu, Huidong Shi, Dorothy Tuan].
Additionally, several other structural elements are required for successful transposition. These include the primer binding site (PBS), which is essential as the start point for reverse transcription[6-8]. Typically the PBS is 8 to 18 base pairs long and expected to be found directly downstream of the inner 5 LTR boundary. In this region of 8 to 18 nucleotides, it is also highly complementary to the 3 region of a transfer RNA of the host organism. Another important feature is the polypurine tract (PPT), needed as a primer for plus-strand DNA synthesis. The A/G-rich polypurine tracts vary in length and are usually in the range of 8 to 22 bases[8]. Often a U-rich section (the so-called U-box) can be found just upstream of the PPT[9].. The presence of these distinctive structural features have led to the development of various software tools using these features as markers to identify potential LTR retrotransposon insertions (called candidates in the scope of this paper)[10-14]. These tools do ...
Significant number of exons created from junk DNA seem to play a role in gene regulation Friday, 17 October 2008 For about 15 years, scientists have known that certain "junk" DNA - repetitive DNA segments previously thought to have no function - could evolve into exons, which are the building blocks for protein-coding genes in higher organisms like animals and plants. Now, a University of Iowa study has found evidence that a significant number of exons created from junk DNA seem to play a role in gene regulation. The findings, which increase understanding of how humans differ from other animals, including non-human primates, appear Oct. 17 in the open-access journal PLoS Genetics. Nearly half of human DNA consists of repetitive DNA, including transposons, which can "transpose" or move around to different positions within the genome. A type of transposon called retrotransposons are transcribed into RNA and then reintegrated into the genomic DNA. The most common form of retrotransposons in the ...
Small RNAs derived from the DIRS-1 retrotransposon (A) Distribution of cloned DIRS-1 sequences in the two cDNA libraries in sense (top) and antisense (bottom) o
The use of bi-allelic markers such as retrotransposable element insertion polymorphisms or Innuls (for insertion/null) can overcome some limitations of sho
L1 retrotransposons replicate (amplify) by copying (reverse transcribing) their RNA transcript into genomic DNA. The evolutionary history of L1 in mammals has been unique. In mice and humans ~80 million years of L1 evolution and replication produced a single evolutionary lineage of L1 elements while generating ~20% of the genomic mass in each species. By contrast, zebrafish contain |30 distinct L1 lineages that have generated approximately one-tenth as much DNA. We contend that, by becoming far more permissive of interspersed repeated DNA than other organisms, mammals are conducive to competition between L1 families for replicative dominance, and that this competition, perhaps for the host factors required for L1 replication, results in a single L1 lineage.
The cover for issue 3 of Aging features Figure 1 Preferential Ty1 retromobility in mother cells and nonquiescent stationary phase cells is associated with increased concentrations of total Gag or processed Gag and is inhibited by exposure to a high concentration of calcium from Peifer and Maxwell.
Inge de Waard, Sean Abajian, Michael Sean Gallagher, Rebecca Hogue, Nilgün Keskin, Apostolos Koutropoulos, Osvaldo C. Rodriguez ...
Hamdy4「緩解能藉由維持良好的飲食與規律的運動而延長》「. 患有二型糖尿病的人只要吃得正確3並持續保持身材就能讓此疾病保持在不需要藥物或是胰島素幫助治療的狀態》只是擁有計畫跟確實執行是完全不同的兩件事情》. Parrish4「我寫下每一個單一食物的熱量與碳水化合物的重量3並在一天的最後將它們加總起來》一旦我停下來作這件事情3我的體重就又開始增加》「. Hamdy 說3幹勁是能否長期成功的關鍵3而維持幹勁最好的方法就是設定可達到的目標》. 「當病患看到接近目標的成效便會被激勵》而當他們看到改善3他們甚至會變得更有幹勁》「. 以上是 Parrish ...
研究證實聽音樂或處在歡笑的情境下可能是另一種降低高血壓的方法》. 新研究指出中年男女或許能藉由多笑與聽他們喜歡的音樂來減少血壓計的讀數》 日本大阪大學的研究者們為了確定音樂與笑聲能否降低血壓3因此安排了兩種情況41. 聽到音樂或笑聲後立即測量》2. 在三個月期間內每週一次3讓參與者聽音樂或讓他們歡笑一個小時3並在結束後測量血壓》 科學家讓 79 位年齡在 40 ~ 74 歲的參與者隨機分成三組》32 位聽音樂 30 位是笑聲組3而最後的 17 位既不聽音樂也沒被安排到歡笑的情境》 在每種音樂或是歡笑情境的前後均會測量血壓》 ...
The identification of cellular factors that regulate the replication of exogenous viruses and endogenous mobile elements provides fundamental understanding of host-pathogen relationships. MOV10 is a superfamily 1 putative RNA helicase that controls the replication of several RNA viruses and whose homologs are necessary for the repression of endogenous mobile elements. Here, we employ both ectopic expression and gene knockdown approaches to analyse the role of human MOV10 in the replication of a panel of exogenous retroviruses and endogenous retroelements. MOV10 overexpression substantially decreased the production of infectious retrovirus particles, as well the propagation of LTR and non-LTR endogenous retroelements. Most significantly, RNAi-mediated silencing of endogenous MOV10 enhanced the replication of both LTR and non-LTR endogenous retroelements, but not the production of infectious retrovirus particles demonstrating that natural levels of MOV10 suppress retrotransposition, but have no impact on
Retroviruses have a unique evolutionary association with their host; having a fossil record on the genomic DNA of the host chromosome. Most mammalian genomes carry, as part of their genetic make-up, retroviruses in the form of endogenous proviruses that are inherited like cellular genes following germ-line transmission of some retroviral genomes, accumulated throughout evolution in many organisms. Indeed, recently available genomic data revealed that a large portion of the mammalian genome is derived from ancient transposable elements. In particular, retroelements, transported by an intracellular copy-and-paste process involving an RNA intermediate, constitute a majority of these mobile genetic elements. Endogenous retroviruses, also called long-terminal-repeat (LTR)-type retroelements, are structurally similar to infectious retroviruses and constitute one class of these retroelements in a range of mammalian species. The non-LTR members, with reverse transcription occurring exclusively within the
elements are a distinct group of grow Ty3/gypsy-like retrotransposons characterized by several specific features, one of which is a separation of the region into two non-overlapping open reading frames: ORF2 coding for Gag-Pro, and ORF3 coding for RT/RH-INT proteins. buy PHA-680632 region between ORF2 and ORF3 is usually spliced from transcripts and showed that this process is only partial, probably due to poor splice signals. This is one of very few known cases of spliced LTR retrotransposons and the only one where splicing does not involve parts of the elements coding sequences, thus resembling intron splicing found in most cellular genes. Electronic supplementary material The online version of this article (doi:10.1007/s00438-008-0376-8) contains supplementary material, which is available to authorized users. gene codes for proteins needed for an assembly of virus-like particles and RNA packaging. The gene encodes enzymes protease (Pro), reverse transcriptase/RNaseH (RT/RH) and integrase ...
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Retrotransposons encompass half of the human genome and contribute to the formation of heterochromatin, which provides nuclear structure and regulates gene expression. Here, we asked if the human silencing hub (HUSH) complex is necessary to silence retrotransposons and whether it collaborates with TRIM28 and the chromatin remodeler ATRX at specific genomic loci. We show that the HUSH complex contributes to de novo repression and DNA methylation of a SVA retrotransposon reporter. By using naïve vs. primed mouse pluripotent stem cells, we reveal a critical role for the HUSH complex in naïve cells, implicating it in programming epigenetic marks in development. While the HUSH component TASOR binds to endogenous retroviruses (ERVs) and L1s, it is mainly required to repress evolutionarily young L1s. TRIM28, in contrast, is necessary to repress both ERVs and young L1s. Genes co-repressed by TRIM28 and TASOR are evolutionarily young, or exhibit tissue-specific expression, are enriched in young L1s and display
Repeated DNA in heterochromatin presents enormous difficulties for whole-genome sequencing; hence, sequence organization in a significant portion of the genomes of multicellular organisms is relatively unknown. Two sequenced BACs now allow us to compare telomeric retrotransposon arrays from Drosophila melanogaster telomeres with an array of telomeric retrotransposons that transposed into the centromeric region of the Y chromosome ,13 MYA, providing a unique opportunity to compare the structural evolution of this retrotransposon in two contexts. We find that these retrotransposon arrays, both heterochromatic, are maintained quite differently, resulting in sequence organizations that apparently reflect different roles in the two chromosomal environments. The telomere array has grown only by transposition of new elements to the chromosome end; the centromeric array instead has grown by repeated amplifications of segments of the original telomere array. Many elements in the telomere have been ...
The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. The mapping population parents (IAC66-6 and TUC71-7) contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM
Although accurate long-distance neuronal migration is a cardinal feature of cerebral cortical development, little is known about control of this migration. The scrambler (scm) mouse shows abnormal cortical lamination that is indistinguishable from reeler. Genetic and physical mapping of scm identifies yeast artificial chromosomes containing an exon of mdab1, a homolog of Drosophila Disabled, which encodes a phosphoprotein that binds nonreceptor tyrosine kinases. mdab1 transcripts show abnormal splicing in scm homozygotes, with 1.5 kb of intracisternal A particle retrotransposon sequence inserted into the mdab1 coding region in antisense orientation, producing a mutated and truncated predicted protein. Therefore, mdab1 is most likely the scm gene, thus implicating nonreceptor tyrosine kinases in neuronal migration and lamination in developing cerebral cortex (Ware, 1997). Formation of the mammalian brain requires choreographed migration of neurons to generate highly ordered laminar structures, ...
Despite the recent large-scale efforts dedicated to comprehensive phylogenetic analyses using mitochondrial and nuclear DNA sequences, several relationships among mammalian orders remain controversial. Here, we present an extensive application of retroposon (L1) insertion analysis to the phylogeneti …
Around half of our genetic content is composed of retrotransposons that are thought to be ancient viruses that have stably integrated into our genomes. These ancient viruses, as mobile genetic elements, have been drivers of evolution, creating new genes and plasticity of genomes, and many of them are species-specific.. Endogenous retroviruses are one type of retrotransposon family that resemble present day retroviruses like HIV, and as such, they are thought to have arisen from germ-line integrations of retroviruses. While these viruses that were once mobile are now mostly inactive through mutation, they have co-evolved with our genes to adopt normal functions in gene regulation. For example, exciting data including ours has shown that endogenous retroviruses retain regulatory sequences that can act as enhancers, repressors or alternative promoters for cellular genes in a temporal or tissue-specific way. Very little is known about which transcription factors and complexes are recruited to ...
The Long INterspersed Element-1 (L1, LINE-1) is the only autonomous mobile DNA element in humans and has generated as much as half of the genome. Due to increasing clinical interest in the roles of L1 in cancer, embryogenesis and neuronal development, it has become a priority to understand L1-host interactions and identify host factors required for its activity. Apropos to this, we recently reported that L1 retrotransposition in HeLa cells requires phosphorylation of the L1 protein ORF1p at motifs targeted by host cell proline-directed protein kinases (PDPKs), which include the family of mitogen-activated protein kinases (MAPKs). Using two engineered L1 reporter assays, we continued our investigation into the roles of MAPKs in L1 activity. We found that the MAPK p38δ phosphorylated ORF1p on three of its four PDPK motifs required for L1 activity. In addition, we found that a constitutively active p38δ mutant appeared to promote L1 retrotransposition in HeLa cells. However, despite the consistency of
Retrotransposons are small genetic sequences that have the ability to replicate and position themselves in new locations in their hosts genome. "The ability of retrotransposons to copy themselves and integrate these new copies into the host genome makes them genetic parasites," says geneticist and principal investigator, Manuel Aranda. "Every integration event is basically a new mutation in the host genome. Very often these new copies disable or disrupt host genes. However, sometimes they can also change how certain genes behave. They are often bad, like most mutations, but some can produce advantageous effects ...
Schatz, M. C. (2017) Nanopore sequencing meets epigenetics. Nat Methods, 14 (4). pp. 347-348. ISSN 1548-7091 Scholes, D. R., Dalrymple, J., Mesa, J. M., Banta, J. A., Paige, K. N. (2017) An assessment of the molecular mechanisms contributing to tolerance to apical damage in natural populations of Arabidopsis thaliana. Plant Ecology, 218 (3). pp. 265-276. ISSN 1385-0237 Schorn, A. J., Gutbrod, M. J., LeBlanc, C., Martienssen, R. (2017) LTR-Retrotransposon Control by tRNA-Derived Small RNAs. Cell, 170 (1). 61-71.e11. ISSN 0092-8674 Sekiya, Michiko, Maruko-Otake, Akiko, Hearn, Stephen, Sakakibara, Yasufumi, Fujisaki, Naoki, Suzuki, Emiko, Ando, Kanae, Iijima, Koichi M. (2017) EDEM Function in ERAD Protects against Chronic ER Proteinopathy and Age-Related Physiological Decline in Drosophila. Developmental Cell, 41 (6). 652-664.e5. ISSN 1534-5807 Senturk, S., Shirole, N. H., Nowak, D. G., Corbo, V., Pal, D., Vaughan, A., Tuveson, D. A., Trotman, L. C., Kinney, J. B., Sordella, R. (2017) Rapid and ...
The human genome is densely populated with transposons and transposon-like repetitive elements. Although the impact of these transposons and elements on human genome evolution is recognized, the significance of subtle variations in their sequence remains mostly unexplored. This study reports homozygosity mapping of an infantile neurodegenerative disease locus in a genetic isolate. Complete DNA sequencing of the 400-kb linkage locus revealed a point mutation in a primate-specific retrotransposon that was transcribed as part of a unique noncoding RNA, which was expressed in the brain. In vitro knockdown of this RNA increased neuronal apoptosis, consistent with the inappropriate dosage of this RNA in vivo and with the phenotype. Moreover, structural analysis of the sequence revealed a small RNA-like hairpin that was consistent with the putative gain of a functional site when mutated. This study show here that a mutation in a unique transposable element-containing RNA is associated with lethal ...
What factors might have led to the L1 extinction seen here? Was it a stochastic process, or was there some change in selective forces that increased the probability of an extinction? The genomes of bats are known to be smaller than the other major groups of mammals (Bachmann 1972; Redi et al. 2005). For example, the average haploid genome size (C-value) of the 83 Chiropteran species present in the Animal Genome Size Database, Release 2.0 (Gregory 2006) is 2.55 pg, while the C-values of the 517 other mammalian species within that database average 3.57 pg. When the two suborders of the Chiroptera within that database are examined, the 7 species of Yinpterochiroptera, which include the megabats, are found to have an average C-value of 2.16 pg, while the 76 species of Yangochiroptera have an average C-value of 2.59 pg. It is known that retroelements are major contributors to increases in genome size in mammals (Kidwell 2002), so it is reasonable that reduction in L1 activity might have been a factor ...
The Long interspersed element 1 (LINE1 or L1) retrotransposon constitutes 17% of the human genome. There are currently 80-100 human L1 elements that are thought to be active in any diploid human genome. These elements can mobilize into new locations of the genome, resulting in changes in genomic information. Active L1s are thus considered to be a type of endogenous mutagen, and L1 insertions can cause disease. Certain stresses, such as gamma radiation, oxidative stress, and treatment with some agents, can induce transcription and/or mobilization of retrotransposons. In this study, we used a reporter gene assay in HepG2 cells to screen compounds for the potential to enhance the transcription of human L1. We assessed 95 compounds including genotoxic agents, substances that induce cellular stress, and commercially available drugs. Treatment with 15 compounds increased the L1 promoter activity by |1.5-fold (p|0.05) after 6 or 24 hours of treatment. In particular, genotoxic agents (benzo[a]pyrene,
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Also in great numbers are transposons. About a third of the genome are Gypsy-type retrotransposons. Several other classes of transposons are present also. In the end, just over a quarter (26%) of the genome is non-repetitive. While these transposons do not themselves appear to contain phytopathological genes, their presence appears to be driving expansion of some key families of such genes. Comparison of genomic scaffolds with the other two sequenced Phytophora show striking overall conservation of conserved genes, but with local rearrangements and expansion of the zones between conserved genes (Figure 1 plus S18 and S19). Continuing evolutionary activity in this space is shown by the fact that some of these genes are apparently inactivated but have only small numbers of mutations, suggesting very recent conversion to pseudogenes. A transposon polymorphism was also found -- an insertion in one haplotype which is absent in another (figure S9 ...
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From BioPortfolio: Transfer RNA fragments prevent jumping genes from hopping around in the mouse embryo, when histone methylation can
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InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their individual strengths to produce a powerful integrated database and diagnostic tool.
Jafnréttisþing föstudaginn 16. janúar kl. 9-17 á Hilton Nordica.. Félags- og tryggingamálaráðherra og Jafnréttisráð boða til Jafnréttisþings í samræmi við lög um jafnan rétt og jafna stöðu kvenna og karla nr. 10/2008.. Á jafnréttisþingi leggur félags- og tryggingamálaráðherra fram skýrslu um stöðu og þróun jafnréttismála og drög að framkvæmdaáætlun í jafnréttismálum, en við endanlega gerð hennar skal samkvæmt jafnréttislögum taka mið af umræðum á jafnréttisþingi. Á þinginu verður fjallað um helstu svið jafnréttismála í fyrirlestrum, pallborðsumræðum og málstofum þar sem vænst er þátttöku og hugmynda frá þeim sem þingið sækja.. Forseti ASÍ, Gylfi Arnbjörnsson er meðal þátttakenda ...