(Online version in colour. Epub 2013 Apr 4. However, no family-specific preference or clustering was observed. Short-interspersed nuclear elements are characterized by their size and method of retrotransposition. This finding suggests that SINE insertions in genic regions might account for only a small fraction of alterations in gene structure. Our results showed that there was a highly significant depletion of SINEs in genic regions, which might be the result of the transposition of SINEs under selective constraints. doi: 10.1093/gbe/evab232. Das Genom enthlt die Deutsch Wikipedia, Families of short (150-300 bp), moderately, Glossary of Biotechnology for Food and Agriculture. The families CitruS-II and CitruS-VI were assigned to two subfamilies and grouped on separate branches (Fig. Miyagawa wase, 360 Mbp) were downloaded via the resources for citrus genomics homepage (http://www.citrusgenome.jp/).27 The expression data of sweet orange were queried from the Citrus sinensis annotation project database homepage (http://citrus.hzau.edu.cn).28. Genomic gems: SINE RNAs regulate mRNA production. The only requirement for application is installation of the Python software (at least version 2.5). (1997). 8600 Rockville Pike Epub 2018 Jan 16. Deragon J.M., Landry B.S., Plissier T., Tutois S., Tourmente S., Picard G. (1994). Considerations include not only the number of 3UTR Alus but also their orientation(s), the extent to which they have diverged from the original Alu sequence that was inserted, and their position(s) within the 3UTR relative to one another, should multiple 3UTR Alus exist, as well as relative to the translation termination codon, any additional cis-acting regulatory sequences, and the cleavage and polyadenylation site(s). By contrast, most SolS families described here have sequence similarities below 80% among members. Varshney Identification of the CypS-I family in the zebra fish (Cyprinidae) demonstrated the successful application of the SINE-Finder for an animal genome sequence. Tajaddod M, Tanzer A, Licht K, Wolfinger MT, Badelt S, Huber F, Pusch O, Schopoff S, Janisiw M, Hofacker I, Jantsch MF. Epub 2010 Feb 20. SINEs are also DNA While SINEs have been intensively investigated in humans and other animal systems, they are poorly studied in plants, especially in wheat (Triticum aestivum).We used quantitative PCR of various wheat species to determine Peters Resulting polymorphic loci were mapped to the reference sequences of citrus using MUSCLE.29. Accessibility The full-length rate of citrus SINEs characterized on the SINE family and genome level. 7A). +86 371 63579623. 6E and F). 2000; 85: 101106. SINEs were assigned to a single family when they shared at least 60% similarity; they were used as queries for BLAST searches to retrieve the majority of all family members, resulting in 1489 full-length and 870 5 truncated copies in potato. We detected a polymorphic SINE copy that was mainly derived from CitruS-IIa (CitruS-composite) in 14 citrus accessions (Fig. After splitting of potato and tomato 7.3 MYA, the SINE families SolS-IV (Figure 3, right panel) and SolS-IIIb (Figure 3, middle panel) were highly amplified in potato. (b) Cellular stress, including ultraviolet irradiation or heat shock, activate the MKK6p38mitogen and stress-activated protein kinase (MSK)1/2 signalling cascade so that MSK1 and MSK2 phosphorylate nuclear ADAR1p110 (details provided in Sakurai et al. All rights reserved. Recently, four SINE families from Medicago truncatula were identified by screening of public genome sequences (Gadzalski and Sakowicz, 2011). Identification of a short interspersed repetitive element in partially spliced transcripts of the bell pepper (. Host Noncoding Retrotransposons Induced by DNA Viruses: a SINE of Infection? The candidate sequences were clustered based on similarity using NCBI-BLAST 2.2.31+ toolkits.29 The procedure consisted of three steps: clustering of candidate sequences, verification of SINE copies, and family assignment. 1996; 6: 959961. These data suggest that there is no stringent correlation between plant genome size and number of SINEs as has also been observed for LTR retrotransposons (Vitte and Bennetzen, 2006). The SINE-Finder (see Supplemental Data Set 1 online) is a Python script (http://www.python.org/). Short interspersed nuclear elements (SINEs) are non-autonomous, non-coding transposable elements (TEs) that are 50-500 base pairs long. Short interspersed nuclear element (SINE) sequences are short repetitive, non-coding sequences ranging in size from 100600 bp. We used MAPCHART37 to display the chromosomal localization of the citrus SINEs. HSCLs were divided into unique HSCLs and multiple HSCLs according to their number of occurrences in each genome. 2014, DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis. 2019 Jan 2;20(1):140. doi: 10.3390/ijms20010140. 3UTR Alu-mediated SMD has been shown to be important for wound-healing [17,18] and adipogenesis [26], and future work will undoubtedly expand on its realm of influence. SINEs from N. advena and Pinaceae (Table 2) were involved as distant outgroup sequences. S1 SINE retroposons are methylated at symmetrical and non-symmetrical positions in. Target sites for SINE integration in Brassica genomes display nuclear matrix binding activity. Mapping of SINE -like sequences of the A . Families of 5S rRNA-related SINE sequences, nominated as AfuSINE3, were also identified and their 5'-5S rRNA-related regions show 50-65% and 60-75% similarity to respectively A. fumigatus 5S rRNAs and SINE3-1_AO found in A. oryzae. Yoshioka Y., Matsumoto S., Kojima S., Ohshima K., Okada N., Machida Y. The comprehensive analyses described here enabled insights into the evolution and age of Solanaceae SINEs. Citrus SINEs were identified that (A) created a new exon and contributed two splice sites, (B and F) provided the first exon donating a start codon and (B) a 5 splice site, (C and D) donated stop codons, and (E, F) created novel genes. Short interspersed nuclear elements (SINEs) are non-long terminal repeat retrotransposons that are highly abundant, heterogeneous, and mostly not annotated in eukaryotic genomes. In addition, tobacco-specific occurrence was observed for some SINE families (gray-shaded branches in Figure 1). The family CitruS-I accounted for at least 29.8% of SINEs located in cds in sweet orange, Satsuma mandarin, and Clementine mandarin, but no genic SINEs in the remaining four genomes (Supplementary Fig. Currently, it is difficult to establish rules for whether a TE has been co-opted for function and, if it has, whether that function is advantageous to the host for many reasons. 2021 Oct 28;9(11):1560. doi: 10.3390/biomedicines9111560. Like 3UTR Alus in humans, 3UTR B1, B2, B4 and ID SINEs in mice can trigger SMD by imperfectly base-pairing with a partially complementary SINE in another transcript that recruits STAU1, STAU2 or both [22,29]. Furthermore, we conducted a search in 10 angiosperm genome sequences of different taxonomic clades to investigate the occurrence of SINEs in diverse plant genomes (Table 2; see Supplemental Data Set 2 online). Molecular characterization of a short interspersed repetitive element from tobacco that exhibits sequence homology to specific tRNAs, BoS: A large and diverse family of short interspersed elements (SINEs) in. These data suggested that citrus SINEs experienced family specific evolutionary histories. Southern blot hybridization of AfuSINE, Fig 7. Loci in which SINE copies shared identical flanking sequences (identity 80%) were designated HSCLs. Accessibility For one, the proportion of SINEs that regulates gene expression post-transcriptionally, and which genes are affected, remains unclear. A short interspersed nuclear element, Mg-SINE, was isolated and characterized from the genome of the rice blast fungus, Magnaporthe grisea. Learn more Moreover, TS SINEs share the poly(GTT) tail with SolRTE-I (Figure 6; see Supplemental Data Set 7 online). We identified 1039 potato, 1127 tomato, and 5265 tobacco truncated SINEs. We propose an evolutionary scenario for the formation of TS as a spontaneous event, which could be typical for the emergence of SINE families. A typical member of the SolRTE-I family is SolRTE-I_St1, which is 4174 bp long and belongs to the RTE clade (Malik and Eickbush, 1998) of LINEs (see Supplemental Figures 3 and 4 and Supplemental Data Set 7 online). The words at the top of the list are the ones most associated with short interspersed nuclear (a) Staufen (STAU) binding to 3UTR IRAlus can enhance 3UTR IRAlus gene expression by two consecutive mechanisms. Southern blot hybridization of AfuSINE sequences in the genome of A . SINEs werden hufig zu den . {"type":"entrez-nucleotide","attrs":{"text":"EF647616","term_id":"209977157","term_text":"EF647616"}}, {"type":"entrez-nucleotide","attrs":{"text":"AC233388","term_id":"215744962","term_text":"AC233388"}}, {"type":"entrez-nucleotide","attrs":{"text":"AC232878","term_id":"229368260","term_text":"AC232878"}}, {"type":"entrez-nucleotide","attrs":{"text":"AC219014","term_id":"170671787","term_text":"AC219014"}}, {"type":"entrez-nucleotide","attrs":{"text":"FH227950","term_id":"191755310","term_text":"FH227950"}}, {"type":"entrez-nucleotide","attrs":{"text":"ET774464","term_id":"191210802","term_text":"ET774464"}}, {"type":"entrez-nucleotide","attrs":{"text":"AC234546","term_id":"222537810","term_text":"AC234546"}}, {"type":"entrez-nucleotide","attrs":{"text":"CU459061","term_id":"156764013","term_text":"CU459061"}}, {"type":"entrez-nucleotide","attrs":{"text":"ET727010","term_id":"190840675","term_text":"ET727010"}}, {"type":"entrez-nucleotide","attrs":{"text":"HE583424","term_id":"356471988","term_text":"HE583424"}}, {"type":"entrez-nucleotide","attrs":{"text":"HE583588","term_id":"356472151","term_text":"HE583588"}}, Nuclear DNA content of some important plant species. Federal government websites often end in .gov or .mil. Unable to load your collection due to an error, Unable to load your delegates due to an error, Intermolecular base-pairing via partially complementary SINEs can create Staufen (STAU)-binding sites that trigger STAU-mediated mRNA decay (SMD). Nevertheless, the use of unique HSCLs in evolution research has limitations, because the mining of syntenic HSCLs depends on high-quality genome assembly. RepeatMasker34 searches against genome sequences were conducted using consensus sequences as queries to retrieve all copies of each family (including intact and truncated SINE copies) with the following settings: -nolow, -no_is, -par 28, -xsmall, and -gff. J.S., Proulx S.R., Rapp R.A., Wendel J.F. Then, 200bp sequences flanking both ends of these SINE copies were extracted and aligned. The author thanks Max Popp and Xavier Rambout for comments on the manuscript, Manny Ares for helpful discussions and Tatsuaki Kurosaki for generating figures. For example, because SMD competes with nonsense-mediated mRNA decay (NMD) for available UPF1 [27], when cells vary the efficiency of NMD in response to changes in developmental and environmental conditions [28], the efficiency of SMD is probably simultaneously varied. Only a small number of active SINEs are required as master elements for constant amplification, while most copies are transpositional inactive (Deininger and Batzer, 2002). Hirochika H., Fukuchi A., Kikuchi F. (1992). Shih Epub 2006 May 22. will also be available for a limited time. Keywords: Lucas Due to the heterogeneity in sequence and length, the criteria for family assignment suggested by Wicker et al. 2011, Genome size and transposable element content as determined by high-throughput sequencing in maize and zea luxurians, Dynamics of genome size evolution in birds and mammals. Would you like email updates of new search results? The consensus sequences of CitruS-II a/b and CitruS-VI a/b showed identity values of 82.2 and 82.1%, respectively. A summary of these results is provided in Table 1, Supplemental Data Set 2 online, and Supplemental Data Set 3 online. See this image and copyright information in PMC. The lengths of TSDs and poly(A) tails are indicators of the relative insertion time of individual SINE copies.15,17,42,43 In citrus, the lengths of the TSDs and poly(A) tails were not eligible as an age indicator because more than half of the full-length copies did not have detectable TSDs, and the poly(A) tails were likely to overlap with short adenine stretches of the TSDs. (2007). Short interspersed nuclear elements (SINEs) (100300 bp, 15% of the genome) are retrotransposons, which are regions of DNA capable of copying and pasting themselves into The Zea mays genome sequence was obtained from the PlantGDB (http://zoneannfu.gdcb.iastate.edu/XGDB/phplib/download.php?GDB=Zm) and the Danio rerio genome from the Danio rerio Sequencing Project (http://hgdownload.cse.ucsc.edu/goldenPath/danRer6/bigZips/; Wellcome Trust Sanger Institute). TE co-options are involved in changing the patterns of gene expression, changing the functions of the proteins they encode, or both.62 We believe that in citrus, SINEs were co-opted into genes by providing new potential regulatory sequences to adjacent genes, altering gene structure, and creating novel genes. genes primarily encoding messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs), SINEs can function as cis- or trans-regulatory RNA elements. The non-autonomous SINE elements which depend on L1 elements for their proliferation make up Okada N., Hamada M., Ogiwara I., Ohshima K. (1997). 2010, Genomic gems: SINE RNAs regulate mRNA production. J., Hodge R., Andrade-Navarro M.A. Huang Capy P, Gasperi G, Bimont C and Bazin C. Stress and transposable elements: Co-evolution or useful parasites? Analysis of the complete Solanaceae sequence data set including many novel members of the AU and TS family, revealed a similar number of full-length (8153) and 5 truncated (7431) SINEs. The DNA samples were isolated using Tiangen DP360 DNA extraction kit (Tiangen Biotech, Beijing, China). Alignments and BLAST searches were performed using stand-alone versions of MUSCLE (Edgar, 2004) and FASTA (ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/fasta36/), respectively. Site-preferential insertion might be one possible explanation for the distribution patterns of SINEs on chromosomes. 3C). In brief, a BLAST search was performed using consensus sequences as queries against all full-length copies, and then histograms were created using R script (https://www.R-project.org/) based on the resulting sequence identity data. Because the convergent evolution of at least one human-mouse gene pair could be extended to the African green monkey, evidence exists that 3UTR Alu acquisition preceded the divergence of their last shared common ancestor approximately 28 Ma. Short branches in the dendrogram (Figure 1) indicate ancestry and close phylogenetic relationships of some SINE subfamilies, such as SolS-Ia/b and SolS-IIIa/b. The chromosomal localization of the SINE copies in the unique HSCLs based on their physical positions was visualized on chromosomal pseudomolecules of sweet orange, pummelo, and the nine longest scaffolds (>10 Mbp) of Clementine mandarin (Supplementary Fig. As inferred from previous reports,14,17 site-preferential insertion may be a reason for the enrichment of citrus SINEs near genes. Similarity profiles of SINE families were calculated with a modified protocol as described by Schwichtenberg et al.,17 which was based on the sequence identity to the consensus sequence in each SINE family. Gene association and chromosomal distribution of citrus SINEs. An official website of the United States government. (Online version in colour.). )Download figureOpen in new tabDownload PowerPoint, Figure 1. Short interspersed nuclear elements (SINEs) are non-autonomous, non-coding transposable elements (TEs) that are about 100 to 700 base pairs in length. Goubely C., Arnaud P., Tatout C., Heslop-Harrison J.S., Deragon J.M. When residing within RNA polymerase II-transcribed genes, i.e. A number of mRNA 3UTRs contain multiple Alus and, among them, those with inverted-repeat Alus (IRAlus) are the best characterized. M., Schein J., Birol I., et al. A.M., Salem A.H., Oyeniran O.O., et al. Seven SINE families and subfamilies (SolS-Ia, Ib, II, IIIa, IIIb, IV, and V) were highly amplified in potato. No significant similarity to specific tRNA genes was found. Kim WR, Park EG, Lee YJ, Bae WH, Lee DH, Kim HS. Novel families of short interspersed nuclear element (SINE) sequences in the human pathogenic fungus Aspergillus fumigatus, clinical isolate Af293, were identified and categorised into tRNA-related and 5S rRNA-related SINEs. doi: 10.1128/JVI.00982-17. In addition, we found tandem amplification and dispersed duplications derived from truncated SINEs (Supplementary Fig. In these methods, poly(A) is largely but incompletely removed using oligo(dT) and RNase H, the resulting 3-ends are ligated to an adapter that is also used to prime reverse transcription, and any short poly(A) that cannot be aligned to the genome is taken as an indication of bona fide polyadenylation site usage. 2014 Mar;64:36-44. doi: 10.1016/j.fgb.2014.01.002. Mol Gen Genet. Graphical representation of insertion site preferences and dendrogram showing the divergence and grouping of citrus SINE families. Functional noncoding sequences derived from SINEs in the mammalian genome. However, the annotation of raw data still lags behind and is a cumbersome process. Cells. Structure of the AfuSINE2-1a tRNA-derived SINE found, Fig 5. Highly repeated sequences in mammalian genomes. The search algorithm designated as pattern is as follows: pattern = (('TSD_region_1', {,40}), ('a_box', [GA][CGA]TGG), ('spacer_1', {25,50}), ('b_box', GTTC[AG]A), ('spacer_2', {20,500}? Alus J, S and Y, whose retrotransposition activities peaked approximately 65, 30 and 46 mega annum (Ma), the latter of which took place after the divergence of humans and African apes. government site. Otto They emerged more than 23 million years ago and were species specifically amplified during the radiation of potato, tomato (Solanum lycopersicum), and tobacco (Nicotiana tabacum). Primate-specific Alu short interspersed nuclear elements (SINEs) and rodent-specific B and ID (B/ID) SINEs are non-autonomous and generally non-coding retrotransposons that have been copied and pasted into the respective genomes so as to constitute what is estimated to be a remarkable 13% and 8% of those genomes. Prevention allows for export to the cytoplasm, where if the level of cytoplasmic STAU proteins is sufficient to compete with protein kinase R (PKR) for binding to IRAlus, then PKR-mediated translational repression can be avoided (figure 2a). 2021 Aug 31;22:199-218. doi: 10.1146/annurev-genom-111620-100736. SINEs are short nonautonomous retroelements that range in size up to 500 nucleotides and have a composite structure, and their retrotransposition relies on proteins encoded by a partner LINE (Singer, 1982; Weiner et al., 1986; Boeke, 1997; Kajikawa and Okada, 2002; Dewannieux et al., 2003). The .gov means its official. Pummelo harboured the highest copy number, with 2,118 full-length copies, and citron harboured the lowest copy number, with 1,339 full-length copies. Most plant SINEs have been randomly identified, for example, by insertional polymorphisms, and a systematic and targeted search for SINEs is not possible, even in the era where complete genome sequences are available in an ever increasing rate. P.D., Walters R.D., Espinoza C.A., et al. In the first, STAU binding in the nucleus inhibits binding by the paraspeckle constituent p54nrb, thereby preventing 3UTR IRAlus mRNA retention in nuclear paraspeckles via the lncRNA NEAT1 and allowing export to the cytoplasm. However, we were also able to identify the four SINE families from the maize (Zea mays) genome reported so far (Baucom et al., 2009). We show that tobacco TS retrotransposons are composite SINEs consisting of the 3 end of a long interspersed nuclear element integrated downstream of a nonhomologous SINE family followed by successfully colonization of the genome. This is why the full-length SINE copies in our study showed an average sequence similarity of 8491% to the consensus, while the average sequence similarity ranged from 60 to 100% in Wenke et al.14 and Schwichtenberg et al.17. official website and that any information you provide is encrypted By contrast, SolS-IIIb SINEs were identified in all three Solanaceae species (Table 1) and hence are likely to be more ancestral and evolutionarily older. Integration of TE Induces Cancer Specific Alternative Splicing Events. 2004, MapChart: software for the graphical presentation of linkage maps and QTLs. Before The literature differs on the length of the SINEs but there is a general consensus that they often range in length from about 100 to 700 base pairs (more or less, arbitrary cut-offs). Some families, for example CitruS-XI in Satsuma mandarin, were predicted to be old, because all SINE copies had similarities of <91% to the consensus sequence (Fig. Seibt K.M., Wenke T., Muders K., Truberg B., Schmidt T. 2016, Short interspersed nuclear elements (SINEs) are abundant in Solanaceae and have a family-specific impact on Epub 2021 Apr 1. Nevertheless, a clear family structure was observed and the identified plant SINEs share similar structural features. Dendrograms were constructed by MEGA 5 software (Tamura et al., 2007), applying the neighbor-joining distance method and the maximum composite likelihood nucleotide model. H.J. Jiao Dendrogram of Representative Copies Showing the Lowest Divergence to the Consensus of the SINE Families in Solanaceae, Nymphaeaceae, and Pinaceae. Ogiwara Zhang All 12 SINE families were included. The average full-length rate of all citrus SINEs was 0.27, which indicated that most copies of citrus SINEs were truncated during evolution. These families, which consist of B1, B2, B4 and identifier (ID), are present at concentrations that vary from approximately 5.6 105 to approximately 7.9 104 copies per genome (table1).
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