長鎖散在反復配列、長散在型反復配列、長い散在反復配列、長い散在性反復配列

関: L1 element、LINE、LINE-1 element、long interspersed element、long interspersed nuclear element

WordNet

primarily temporal sense; being or indicating a relatively great or greater than average duration or passage of time or a duration as specified; "a long life"; "a long boring speech"; "a long time"; "a long friendship"; "a long game"; "long ago"; "an hour long"
(of speech sounds or syllables) of relatively long duration; "the English vowel sounds in `bate, `beat, `bite, `boat, `boot are long"
for an extended distance
for an extended time or at a distant time; "a promotion long overdue"; "something long hoped for"; "his name has long been forgotten"; "talked all night long"; "how long will you be gone?"; "arrived long before he was expected"; "it is long after your bedtime"
having or being more than normal or necessary:"long on brains"; "in long supply"
holding securities or commodities in expectation of a rise in prices; "is long on coffee"; "a long position in gold"
involving substantial risk; "long odds"
of relatively great height; "a race of long gaunt men"- Sherwood Anderson; "looked out the long French windows"
primarily spatial sense; of relatively great or greater than average spatial extension or extension as specified; "a long road"; "a long distance"; "contained many long words"; "ten miles long"
a straight line that generates a cylinder or cone
one of four substances thought in ancient and medieval cosmology to constitute the physical universe; "the alchemists believed that there were four elements"
the situation in which you are happiest and most effective; "in your element"
the most favorable environment for a plant or animal; "water is the element of fishes"
place at intervals in or among; "intersperse exclamation marks in the text"
introduce ones writing or speech with certain expressions (同)interlard
prolonged unfulfilled desire or need (同)yearning, hungriness
a phosphoric ester of a nucleoside; the basic structural unit of nucleic acids (DNA or RNA) (同)base

PrepTutorEJDIC

(距離・物の長さが)『長い』 / (時間が)『長い』,長く続く / 《時間・距離などを表離などを表す語を伴って》長さが…の / 『長々しい』,あきあきする / (数量が標準よりも)『多い』,長い / (人が)やせてひょろ長い / 長く,長い間,久しく / …じゅう / ずっと(前に,後に) / 長い間
『熱望する』
〈C〉(物質を構成する)元素 / 〈C〉《修飾語[句]を伴って》(…の)(基本的な)『要素』,『成分』;《しばしば複数形で》構成分子 / 〈C〉(生物に固有の)生息場所,環境;(人の)適所,本領 / 〈C〉《古》四大(しだい)[元素](自然界の基本的構成要素と考えられていた地(earth)・水(water)・風(air)・火(fire)の4大要素の一つ) / 《the elements》(雨・風・雪などの)自然力・風雨,(特に)悪天候 / 《the elements》(学問の)原理,初歩,概論
(…の間に)…‘を'散らばせる,まき散らす《+『名』+『among』(『between』)+『名』》 / 《通例受動態で》(他のものを散りばめて)…‘に'変化を与える;(他のものを)…‘に'散りばめる《+『名』+『with』+『名』》
『あこがれ』,熱望 / (目の表情などが)あこがれの,熱望している

Wikipedia preview

出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2016/03/03 16:44:36」(JST)

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Long interspersed elements (LINEs) are a group of non-LTR (long terminal repeat) retrotransposons which are widespread in the genome of many eukaryotes.^[1] They make up around 20% of the human genome.^[2] Some sources also give "Long interspersed nuclear element" as the long form for LINE.^[3]

History of discovery

The first description of an approximately 6.4 kb long LINE-derived sequence was published by J. Adams et al. in 1980.^[4]

Types of LINE elements

Based on structural features and the phylogeny of its key enzyme, the reverse transcriptase (RT), LINEs are grouped into five main groups, called L1, RTE, R2, I and Jockey, which can be subdivided into at least 28 clades.^[5] The LINE-1/L1-element is the only element that is still active in the human genome today. It is found in all mammals.^[6] However, remnants of L2 and L3 elements are also found in the human genome.^[2]

In plant genomes, so far only LINEs of the L1 and RTE clade have been reported.^[7]^[8] Whereas L1 elements diversify into several subclades, RTE-type LINEs are highly conserved often constituting a single family.^[9]^[10]

In fungi, Tad , L1, CRE, Deceiver and Inkcap-like elements have been identified,^[11] with Tad-like elements appearing exclusively in fungal genomes.^[12]

Structure

A typical L1 element is approximately 6,000 base pairs long and consists of two non-overlapping open reading frames (ORF) which are flanked by UTR and target site duplications.

First ORF

The first ORF encodes a RNA-binding protein of 500 amino acid lengths that weighs 40 kDA. This protein contains a leucine zipper motif and functions as a chaperone.^[13]

Trimeric structure and flexibility of the L1ORF1 protein in human L1 retrotransposition.

Second ORF

The second ORF of the L1 encodes a protein-complex that has endonuclease and reverse transcriptase activity. The encoded protein has a molecular weight of 150 kDA.

Crystal structure of the targeting endonuclease of the human LINE-1 retrotransposon

UTR

The 5' Untranslated region (UTR) of the L1 element contains a strong, internal RNA Polymerase II transcription promoter in sense^[14] and a less strong anti-sense promoter.^[15]

Incidence

In human

In the first human genome draft the fraction of LINE elements of the human genome was given as 21% and their copy number as 850,000. Of these, L1, L2 and L3 elements made up 516,000, 315,000 and 37,000 copies, respectively. The non-autonomous SINE elements which depend on L1 elements for their proliferation make up 13% of the human genome and have a copy number of around 1.5 million.^[2] Recent estimates show the typical human genome contains on average 100 L1 elements with potential for mobilization, however there is a fair amount of variation and some individuals may contain a larger number of active L1 elements, making these individuals more prone to L1-induced mutagenesis.^[16]

Increased L1 copy numbers have also been found in the brains of people with schizophrenia, indicating that LINE elements may play a role in some neuronal diseases.^[17]

Propagation

LINE elements propagate by a so-called target primed reverse transcription mechanism. This mechanism was first described for the R2 element from Bombyx mori: A specific nick on one of the DNA strands at the target site is generated by the endonuclease encoded by the R2 element. Thus, a 3'OH group is freed for the R2 reverse transcriptase to prime reverse transcription of the LINE RNA transcript. Following the reverse transcription the target strand is cleaved and the thus created cDNA integrated^[18]

Regulation of LINE activity

It has been shown that host cells regulate L1 retrotransposition activity, for example through epigenetic silencing. For example, the RNA interference (RNAi) mechanism of small interfering RNAs derived from L1 sequences can cause suppression of L1 retrotransposition.^[19]

In plant genomes, epigenetic modification of LINEs can lead to expression changes of nearby genes and even to phenotypic changes: In the oil palm genome, methylation of a Karma-type LINE underlies the somaclonal, 'mantled' variant of this plant, responsible for drastic yield loss.^[20]

Cancer risk

L1 mobilization leads to epithelial cell cancer (carcinoma).^[21] Shift work sleep disorder is associated with increased cancer risk because light exposure at night reduces melatonin, a hormone that has been shown to reduce L1-induced genome instability.^[22]

References

^ Jurka, J. (1998). "Repeats in genomic DNA: Mining and meaning". Current Opinion in Structural Biology 8 (3): 333–337. doi:10.1016/S0959-440X(98)80067-5.
^ ^a ^b ^c Lander ES, Linton LM, Birren B, et al. (February 2001). "Initial sequencing and analysis of the human genome". Nature 409 (6822): 860–921. doi:10.1038/35057062. PMID 11237011.
^ Ewing, A. D.; Kazazian, H. H. (27 October 2010). "Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans". Genome Research 21 (6): 985–990. doi:10.1101/gr.114777.110.
^ Adams, J. W.; Kaufman, R. E.; Kretschmer, P. J.; Harrison, M.; Nienhuis, A. W. (1980). "A family of long reiterated DNA sequences, one copy of which is next to the human beta globin gene". Nucleic Acids Research 8 (24): 6113–6128. doi:10.1093/nar/8.24.6113.
^ Kapitonov, VV; Tempel, S; Jurka, J (15 December 2009). "Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences.". Gene 448 (2): 207–13. doi:10.1016/j.gene.2009.07.019. PMC 2829327. PMID 19651192.
^ Warren, W. C.; Hillier, L. W.; Marshall Graves, J. A.; Birney, E.; Ponting, C. P.; Grützner, F.; Belov, K.; Miller, W.; Clarke, L.; Chinwalla, A. T.; Yang, S. P.; Heger, A.; Locke, D. P.; Miethke, P.; Waters, P. D.; Veyrunes, F. D. R.; Fulton, L.; Fulton, B.; Graves, T.; Wallis, J.; Puente, X. S.; López-Otín, C.; Ordóñez, G. R.; Eichler, E. E.; Chen, L.; Cheng, Z.; Deakin, J. E.; Alsop, A.; Thompson, K.; Kirby, P. (2008). "Genome analysis of the platypus reveals unique signatures of evolution". Nature 453 (7192): 175–183. doi:10.1038/nature06936. PMC 2803040. PMID 18464734.
^ Zupunski, V; Gubensek, F; Kordis, D (October 2001). "Evolutionary dynamics and evolutionary history in the RTE clade of non-LTR retrotransposons.". Molecular Biology and Evolution 18 (10): 1849–63. doi:10.1093/oxfordjournals.molbev.a003727. PMID 11557792.
^ Komatsu, M; Shimamoto, K; Kyozuka, J (August 2003). "Two-step regulation and continuous retrotransposition of the rice LINE-type retrotransposon Karma". The Plant Cell 15 (8): 1934–44. doi:10.1105/tpc.011809. PMC 167180. PMID 12897263.
^ Heitkam, T; Holtgräwe, D; Dohm, JC; Minoche, AE; Himmelbauer, H; Weisshaar, B; Schmidt, T (August 2014). "Profiling of extensively diversified plant LINEs reveals distinct plant-specific subclades.". The Plant Journal 79 (3): 385–97. doi:10.1111/tpj.12565. PMID 24862340.
^ Smyshlyaev, G; Voigt, F; Blinov, A; Barabas, O; Novikova, O (10 December 2013). "Acquisition of an Archaea-like ribonuclease H domain by plant L1 retrotransposons supports modular evolution.". Proceedings of the National Academy of Sciences of the United States of America 110 (50): 20140–5. doi:10.1073/pnas.1310958110. PMC 3864347. PMID 24277848.
^ Novikova, O; Fet, V; Blinov, A (February 2009). "Non-LTR retrotransposons in fungi.". Functional & Integrative Genomics 9 (1): 27–42. doi:10.1007/s10142-008-0093-8. PMID 18677522.
^ Malik, HS; Burke, WD; Eickbush, TH (June 1999). "The age and evolution of non-LTR retrotransposable elements". Molecular Biology and Evolution 16 (6): 793–805. doi:10.1093/oxfordjournals.molbev.a026164. PMID 10368957.
^ Ewing, A. D.; Ballinger, T. J.; Earl, D.; Harris, C. C.; Ding, L.; Wilson, R. K.; Haussler, D. (2013). "Retrotransposition of gene transcripts leads to structural variation in mammalian genomes". Genome Biology 14 (3): R22. doi:10.1186/gb-2013-14-3-r22.
^ Swergold, G. D. (1990). "Identification, characterization, and cell specificity of a human LINE-1 promoter". Molecular and Cellular Biology 10 (12): 6718–6729. doi:10.1128/MCB.10.12.6718 (inactive 2015-01-13). PMC 362950. PMID 1701022.
^ Mätlik, K; Redik, K; Speek, M (2006). "L1 antisense promoter drives tissue-specific transcription of human genes". Journal of Biomedicine and Biotechnology 2006 (1): 71753. doi:10.1155/JBB/2006/71753. PMC 1559930. PMID 16877819.
^ Streva, Vincent (21 March 2015). "Sequencing, identification and mapping of primed L1 elements (SIMPLE) reveals significant variation in full length L1 elements between individuals". BMC Genomics 16 (220). doi:10.1186/s12864-015-1374-y. PMC 4381410. PMID 25887476.
^ Bundo M, Toyoshima M, Okada Y, et al. (22 January 2014). "Increased L1 Retrotransposition in the Neuronal Genome in Schizophrenia". Neuron 81 (2): 306–313. doi:10.1016/j.neuron.2013.10.053. PMID 24389010.
^ Luan, D. D.; Korman, M. H.; Jakubczak, J. L.; Eickbush, T. H. (1993). "Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: A mechanism for non-LTR retrotransposition". Cell 72 (4): 595–605. doi:10.1016/0092-8674(93)90078-5. PMID 7679954.
^ Yang, N; Kazazian Jr, H. H. (2006). "L1 retrotransposition is suppressed by endogenously encoded small interfering RNAs in human cultured cells". Nature Structural & Molecular Biology 13 (9): 763–71. doi:10.1038/nsmb1141. PMID 16936727.
^ Ong-Abdullah, M; Ordway, JM; Jiang, N; Ooi, SE; Kok, SY; Sarpan, N; Azimi, N; Hashim, AT; Ishak, Z; Rosli, SK; Malike, FA; Bakar, NA; Marjuni, M; Abdullah, N; Yaakub, Z; Amiruddin, MD; Nookiah, R; Singh, R; Low, ET; Chan, KL; Azizi, N; Smith, SW; Bacher, B; Budiman, MA; Van Brunt, A; Wischmeyer, C; Beil, M; Hogan, M; Lakey, N; Lim, CC; Arulandoo, X; Wong, CK; Choo, CN; Wong, WC; Kwan, YY; Alwee, SS; Sambanthamurthi, R; Martienssen, RA (24 September 2015). "Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm.". Nature 525 (7570): 533–7. doi:10.1038/nature15365. PMID 26352475.
^ Carreira PE1, Richardson SR, Faulkner GJ (2014). "L1 retrotransposons, cancer stem cells and oncogenesis". FEBS Journal 281 (1): 63–67. doi:10.1111/febs.12601. PMID 24286172.
^ deHaro D, Kines KJ, Sokolowski M, Dauchy RT, Streva VA, Hill SM, Hanifin JP, Brainard GC, Blask DE, Belancio VP (2014). "Regulation of L1 expression and retrotransposition by melatonin and its receptor: implications for cancer risk associated with light exposure at night". Nucleic Acids Research 42 (12): 7694–7707. doi:10.1093/nar/gku503. PMID 24914052.

UpToDate Contents

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1. 先天性および後天性ＱＴ延長症候群の遺伝学 genetics of congenital and acquired long qt syndrome
2. 遺伝性疾患の基本原則 basic principles of genetic disease
3. 成人におけるメチシリン耐性黄色ブドウ球菌感染症の疫学 epidemiology of methicillin resistant staphylococcus aureus infection in adults
4. 鉄のバランス調節 regulation of iron balance
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English Journal

Novel polymorphisms in UTR and coding region of inducible heat shock protein 70.1 gene in tropically adapted Indian zebu cattle (Bos indicus) and riverine buffalo (Bubalus bubalis).

Sodhi M, Mukesh M, Kishore A, Mishra BP, Kataria RS, Joshi BK.SourceNational Bureau of Animal Genetic resources, Karnal 132001, India. Electronic address: monikasodhi@yahoo.com.
Gene.Gene.2013 Sep 25;527(2):606-15. doi: 10.1016/j.gene.2013.05.078. Epub 2013 Jun 19.
Due to evolutionary divergence, cattle (taurine, and indicine) and buffalo are speculated to have different responses to heat stress condition. Variation in candidate genes associated with a heat-shock response may provide an insight into the dissimilarity and suggest targets for intervention. The p
PMID 23792016

L1-ORF1p, a Smad4 Interaction Protein, Promotes Proliferation of HepG2 Cells and Tumorigenesis in Mice.

Zhu Y, Feng F, Yu J, Song B, Hu M, Gao X, Wang Y, Zhang Q.Source1 The Institute of Life Sciences and Bio-Engineering in Beijing Jiaotong University , Beijing, China .
DNA and cell biology.DNA Cell Biol.2013 Sep;32(9):531-40. doi: 10.1089/dna.2013.2097. Epub 2013 Jul 17.
Long interspersed nucleotide element (LINE-1; L1) as an autonomous retrotransposon is localized usually in AT-rich, low-recombined, and gene-poor regions of genome. It is transiently activated in embryonic development and continuously activated in all tumor cells tested so far. Full-length L1 gene c
PMID 23863096

Influence of ambient air pollution on global DNA methylation in healthy adults: A seasonal follow-up.

De Prins S, Koppen G, Jacobs G, Dons E, Van de Mieroop E, Nelen V, Fierens F, Int Panis L, De Boever P, Cox B, Nawrot TS, Schoeters G.SourceEnvironmental Risk and Health unit, VITO (Flemish Institute for Technological Research), Boeretang 200, B-2400 Mol, Belgium; Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium. Electronic address: sofie.deprins@vito.be.
Environment international.Environ Int.2013 Sep;59:418-24. doi: 10.1016/j.envint.2013.07.007. Epub 2013 Aug 3.
BACKGROUND: DNA methylation changes are potential pathways of environmentally induced health effects. We investigated whether exposure to ambient concentrations of NO2, PM10, PM2.5 and O3 and traffic parameters were associated with global DNA methylation in blood of healthy adults.METHODS: 48 non-sm
PMID 23917442

Japanese Journal

Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration

Zhu Wei,Kuo Dwight,Nathanson Jason [他]
Development, growth & differentiation 54(7), 673-685, 2012-09-00
NAID 40019424904

Involvement of retrotransposition of long interspersed nucleotide element-1 in skin tumorigenesis induced by 7,12-dimethylbenz[a]anthracene and 12-O-tetradecanoylphorbol-13-acetate

OKUDAIRA Noriyuki,GOTO Motohito,YANOBU TAKANASHI Rieko,TAMURA Masato,AN Akihiro,ABE Yukiko,KANO Shigeyuki,HAGIWARA Shotaro,ISHIZAKA Yukihito,OKAMURA Tadashi
Cancer science 102(11), 2000-2006, 2011-11-10
NAID 10030244955

Mouse Processed Pseudogenes (Apexp1 and Cbx3p1) for Apex Nuclease and Chromobox Homolog 3

関周司,真鍋芳江,NakamuraTakashi,YaoMing,関雄一
Chugokugakuen journal 1, 13-17, 2002-00-00
… These pseudogenes are located in inactive LINE (long interspersed repetitive element) sequences. … Calculation of nucleotide substitution rates suggests that the non-functional mouse Apexp1 arose 24 million years ago, and that the non-functional mouse Cbx3p1 arose even earlier, 56 million years ago. …
NAID 110004706320

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★リンクテーブル★

リンク元	「LINE」「長散在型反復配列」「長い散在性反復配列」「長鎖散在反復配列」「L1 element」
関連記事	「element」「intersperse」「interspersed」「long」

「LINE」

　　[★]

日: 長い散在反復配列、長散在型反復配列、長い散在性反復配列、ライン、広範囲散在反復配列
英: long interspersed nuclear element, long interspersed nucleotide element, long interspersed element, long interspersed repetitive elements, LINEs, long interspersed repeat sequences
関: レトロトランスポゾン

quoted from http://en.wikipedia.org/wiki/Long_interspersed_nucleotide_elements#LINEs

Long interspersed nuclear elements[8] are a group of genetic elements that are found in large numbers in eukaryotic genomes. They are transcribed (or are the evolutionary remains of what was once transcribed) to an RNA using an RNA polymerase II promoter that resides inside the LINE. LINEs code for the enzyme reverse transcriptase, and many LINEs also code for an endonuclease (e.g. RNase H). The reverse transcriptase has a higher specificity for the LINE RNA than other RNA, and makes a DNA copy of the RNA that can be integrated into the genome at a new site.

The 5' UTR contains the promoter sequence, while the 3' UTR contains a polyadenylation signal (AATAAA) and a poly-A tail.[10] Because LINEs move by copying themselves (instead of moving, like transposons do), they enlarge the genome. The human genome, for example, contains about 20,000-40,000 LINEs, which is roughly 21% of the genome.