2012年11月14日水曜日

active LINE-1のゲノムマップ（2003年のPNAS)

故きを温ねて新しきを知る

次のマップは今から10年前、2003年にペンシルバニア大学Kazazian教授のところから出たactive LINE-1のゲノムマップである。（今年のENCODE関連の論文と比較すると面白いかもしれない）

PNAS vol. 100 no. 9 5280-5285 

Hot L1s account for the bulk of retrotransposition in the human population

Brook Brouha, Joshua Schustak, Richard M. Badge, Sheila Lutz-Prigge, Alexander H. Farley, John V. Moran, and Haig H. Kazazian, Jr.

このマップの上にはすでに90個のactive LINE-1がマップされている。この論文を参考文献としてその後どのような論文が出ているか、ざっと網羅した（下記） 。 active LINE-1には当然プロモーターがあるが、このメチレーションstatusについてはブームのようでここのところ様々な論文が出ている。どのLINE-1がターゲットになっているんだろうね。

小生の知る限り、個々のプロモーターについて個別にメチル化解析をした論文は余りないように見えるのだ。10年前には、このようなマップが既に報告されているのだが、そのことは余り意識されずに LINE-1メチル化研究が進んでいるように見える。どうもすっきりしないなあ。























クリックで大きくなります。


  • Poly(A) Binding Protein C1 Is Essential for Efficient L1 Retrotransposition and Affects L1 RNP Formation Mol. Cell. Biol. 2012 32 (21) 4323-4336
  • Ionising irradiation alters the dynamics of human long interspersed nuclear elements 1 (LINE1) retrotransposon Mutagenesis 2012 27 (5) 599-607
  • Male Germline Control of Transposable Elements Biol. Reprod. 2012 86 (5) 162
  • Reprogramming somatic cells into iPS cells activates LINE-1 retroelement mobility Hum Mol Genet 2012 21 (1) 208-218
  • Methylation of L1Hs promoters is lower on the inactive X, has a tendency of being higher on autosomes in smaller genomes and shows inter-individual variability at some loci Hum Mol Genet 2012 21 (1) 219-235
  • Telomerase and Retrotransposons: Reverse Transcriptases That Shaped Genomes Special Feature Sackler Colloquium: Similarities between long interspersed element-1 (LINE-1) reverse transcriptase and telomerase Proc. Natl. Acad. Sci. USA 2011 108 (51) 20345-20350
  • Telomerase and Retrotransposons: Reverse Transcriptases That Shaped Genomes Special Feature Sackler Colloquium: Ataxia telangiectasia mutated (ATM) modulates long interspersed element-1 (L1) retrotransposition in human neural stem cells Proc. Natl. Acad. Sci. USA 2011 108 (51) 20382-20387
  • Retrofitting the Genome: L1 Extinction Follows Endogenous Retroviral Expansion in a Group of Muroid Rodents J. Virol. 2011 85 (23) 12315-12323
  • Endogenous APOBEC3B Restricts LINE-1 Retrotransposition in Transformed Cells and Human Embryonic Stem Cells J. Biol. Chem. 2011 286 (42) 36427-36437
  • Retrotransposition of marked SVA elements by human L1s in cultured cells Hum Mol Genet 2011 20 (17) 3386-3400
  • Reading TE leaves: New approaches to the identification of transposable element insertions Genome Res 2011 21 (6) 813-820
  • Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans Genome Res 2011 21 (6) 985-990
  • Characterization of L1 retrotransposition with high-throughput dual-luciferase assays Nucleic Acids Res 2011 39 (3) e16
  • Epigenetic Control of Retrotransposon Expression in Human Embryonic Stem Cells Mol. Cell. Biol. 2011 31 (2) 300-316
  • Identification of human-specific transcript variants induced by DNA insertions in the human genome Bioinformatics 2011 27 (1) 14-21
  • Recent Expansion of a New Ingi-Related Clade of Vingi non-LTR Retrotransposons in Hedgehogs Mol Biol Evol 2011 28 (1) 17-20
  • From the Cover: Induction of long interspersed nucleotide element-1 (L1) retrotransposition by 6-formylindolo[3,2-b]carbazole (FICZ), a tryptophan photoproduct Proc. Natl. Acad. Sci. USA 2010 107 (43) 18487-18492
  • High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes Genome Res 2010 20 (9) 1262-1270
  • Colloquium Paper: Footprints of nonsentient design inside the human genome Proc. Natl. Acad. Sci. USA 2010 107 (Supplement_2) 8969-8976
  • Discrete subcellular partitioning of human retrotransposon RNAs despite a common mechanism of genome insertion Hum Mol Genet 2010 19 (9) 1712-1725
  • Long Interspersed Nuclear Element 1 Hypomethylation Is a Marker of Poor Prognosis in Stage IA Non-Small Cell Lung Cancer Clin. Cancer Res. 2010 16 (8) 2418-2426
  • Association of Nuclear Localization of a Long Interspersed Nuclear Element-1 Protein in Breast Tumors with Poor Prognostic Outcomes Genes & Cancer 2010 1 (2) 115-124
  • Retrotransposons and non-protein coding RNAs Briefings in Functional Genomics 2009 8 (6) 493-501
  • L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism Genes Dev. 2009 23 (11) 1303-1312
  • AID can restrict L1 retrotransposition suggesting a dual role in innate and adaptive immunity Nucleic Acids Res 2009 37 (6) 1854-1867
  • Sole copy of Z2-type human cytidine deaminase APOBEC3H has inhibitory activity against retrotransposons and HIV-1 FASEB J. 2009 23 (1) 279-287
  • L1 recombination-associated deletions generate human genomic variation Proc. Natl. Acad. Sci. USA 2008 105 (49) 19366-19371
  • Active Alu retrotransposons in the human genome Genome Res 2008 18 (12) 1875-1883
  • A single amino acid substitution in ORF1 dramatically decreases L1 retrotransposition and provides insight into nucleic acid chaperone activity Nucleic Acids Res 2008 36 (18) 5845-5854
  • Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition Genome Res 2008 18 (6) 869-880
  • Microarray-based global mapping of integration sites for the retrotransposon, intracisternal A-particle, in the mouse genome Nucleic Acids Res 2008 36 (10) e59
  • Functional endogenous LINE-1 retrotransposons are expressed and mobilized in rat chloroleukemia cells Nucleic Acids Res 2008 36 (2) 648-665
  • Loss of LINE-1 Activity in the Megabats Genetics 2008 178 (1) 393-404
  • The necessary junk: new functions for transposable elements Hum Mol Genet 2007 16 (R2) R159-R167
  • LINE-1 ORF1 Protein Localizes in Stress Granules with Other RNA-Binding Proteins, Including Components of RNA Interference RNA-Induced Silencing Complex Mol. Cell. Biol. 2007 27 (18) 6469-6483
  • Identification and Solution Structure of a Highly Conserved C-terminal Domain within ORF1p Required for Retrotransposition of Long Interspersed Nuclear Element-1 J. Biol. Chem. 2007 282 (34) 24893-24904
  • L1 retrotransposition can occur early in human embryonic development Hum Mol Genet 2007 16 (13) 1587-1592
  • LINE-1 retrotransposition in human embryonic stem cells Hum Mol Genet 2007 16 (13) 1569-1577
  • All APOBEC3 family proteins differentially inhibit LINE-1 retrotransposition Nucleic Acids Res 2007 35 (9) 2955-2964
  • Distinct mechanisms for trans-mediated mobilization of cellular RNAs by the LINE-1 reverse transcriptase Genome Res 2007 17 (5) 602-611
  • Mobile DNA in Old World Monkeys: A Glimpse Through the Rhesus Macaque Genome Science 2007 316 (5822) 238-240
  • Active retrotransposition by a synthetic L1 element in mice Proc. Natl. Acad. Sci. USA 2006 103 (49) 18662-18667
  • Phylogenomic Analysis of the L1 Retrotransposons in Deuterostomia Syst Biol 2006 55 (6) 886-901
  • APOBEC3 Proteins Inhibit Human LINE-1 Retrotransposition J. Biol. Chem. 2006 281 (31) 22161-22172
  • APOBEC3B and APOBEC3F Inhibit L1 Retrotransposition by a DNA Deamination-independent Mechanism J. Biol. Chem. 2006 281 (25) 16837-16841
  • Fitness cost of LINE-1 (L1) activity in humans Proc. Natl. Acad. Sci. USA 2006 103 (25) 9590-9594
  • Cellular inhibitors of long interspersed element 1 and Alu retrotransposition Proc. Natl. Acad. Sci. USA 2006 103 (23) 8780-8785
  • Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity Proc. Natl. Acad. Sci. USA 2006 103 (17) 6611-6616
  • LINE-1 RNA splicing and influences on mammalian gene expression Nucleic Acids Res 2006 34 (5) 1512-1521
  • L1 integration in a transgenic mouse model Genome Res 2006 16 (2) 240-250
  • Unconventional translation of mammalian LINE-1 retrotransposons Genes Dev. 2006 20 (2) 210-224
  • Ribonucleoprotein particle formation is necessary but not sufficient for LINE-1 retrotransposition Hum Mol Genet 2005 14 (21) 3237-3248
  • Genomewide Screening Reveals High Levels of Insertional Polymorphism in the Human Endogenous Retrovirus Family HERV-K(HML2): Implications for Present-Day Activity J. Virol. 2005 79 (19) 12507-12514
  • Evolutionary Diversity and Potential Recombinogenic Role of Integration Targets of Non-LTR Retrotransposons Mol Biol Evol 2005 22 (10) 1983-1991
  • Multiple Fates of L1 Retrotransposition Intermediates in Cultured Human Cells Mol. Cell. Biol. 2005 25 (17) 7780-7795
  • Gene-breaking: A new paradigm for human retrotransposon-mediated gene evolution Genome Res 2005 15 (8) 1073-1078
  • CpG Mutation Rates in the Human Genome Are Highly Dependent on Local GC Content Mol Biol Evol 2005 22 (3) 650-658
  • Isolation and Characterization of Active LINE and SINEs from the Eel Mol Biol Evol 2005 22 (3) 673-682
  • The human L1 promoter: Variable transcription initiation sites and a major impact of upstream flanking sequence on promoter activity Genome Res 2004 14 (11) 2253-2260
  • The Innate Antiretroviral Factor APOBEC3G Does Not Affect Human LINE-1 Retrotransposition in a Cell Culture Assay J. Biol. Chem. 2004 279 (42) 43371-43373
  • Natural Genetic Variation Caused by Transposable Elements in Humans Genetics 2004 168 (2) 933-951
  • A YY1-binding site is required for accurate human LINE-1 transcription initiation Nucleic Acids Res 2004 32 (13) 3846-3855
  • The Insertional History of an Active Family of L1 Retrotransposons in Humans Genome Res 2004 14 (7) 1221-1231
  • Cell Type-specific Expression of LINE-1 Open Reading Frames 1 and 2 in Fetal and Adult Human Tissues J. Biol. Chem. 2004 279 (26) 27753-27763
  • A potential role for the nucleolus in L1 retrotransposition Hum Mol Genet 2004 13 (10) 1041-1048
  • Mobile Elements: Drivers of Genome Evolution Science 2004 303 (5664) 1626-1632
時刻:

0 件のコメント:

コメントを投稿