バイオ研究とバイオ研究者の情報チャンネル
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2006年分


DNA

8902871

Nucleic Acids Res. 2006 Dec 20
Specific targeting of cytosine methylation to DNA sequences in vivo. メチル化パターンを決めるメカニズムの研究は、ノーベル賞級の結果をもたらすかも。
遺伝子発現のオンオフだけでなく、突然変異にもかかわっていますから。

Nucleic Acids Res. 2006 Dec 14
G-quadruplexes in promoters throughout the human genome. プロモーター部分のG4重鎖

Nat Genet. 2006 Dec 3
Cdkn1a deletion improves stem cell function and lifespan of mice with dysfunctional telomeres without accelerating cancer formation. テロメアを維持しがん化を抑える遺伝子

Nat Genet. 2006 Dec;38(12):1362-1363.
Making the commitment to meiosis. 発生学を突き詰めると、減数分裂の研究になる

Nature. 2006 Nov 19
Clustered DNA motifs mark X chromosomes for repression by a dosage compensation complex. X染色体の配列中にあった遺伝子発現を抑制する仕組み

Nat Methods. 2006 Nov;3(11):917-22.
Rational design of a super core promoter that enhances gene expression. 強力な発現プロモーターを設計

EMBO J. 2006 Nov 16
MDMX regulation of p53 response to ribosomal stress. MDMX、p53、薬剤耐性との関係

Science. 2006 Nov 17;314(5802):1144-1147
Initial Transcription by RNA Polymerase Proceeds Through a DNA-Scrunching Mechanism. 転写を観察する

Nat Genet. 2006 Nov 12
Regional copy number-independent deregulation of transcription in cancer. がん細胞において、調節領域のメチル化で、遺伝子発現が抑えられる

Nucleic Acids Res. 2006 Nov 7
Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing. ウィルスによって適合するDICERが異なる

Cis-urocanic acid, a sunlight-induced immunosuppressive factor, activates immune suppression via the 5-HT2A receptor. cis-UCAや紫外線で起こる免疫低下の機構

Cell. 2006 Nov 3;127(3):481-93
New Histone Incorporation Marks Sites of UV Repair in Human Cells. DNA修復の際のヒストンの挙動

A cryptochrome/photolyase class of enzymes with single-stranded DNA-specific photolyase activity. 光回復とサーカディアンリズムの仲介をしているような分子だと面白いのですが

Mol Cell. 2006 Oct 20;24(2):245-255
A Mechanism of Nucleotide Misincorporation during Transcription due to Template-Strand Misalignment. T7RNAポリメラーゼで転写のエラーが起こる仕組み

Hum Gene Ther. 2006 Sep 26
DNA Vaccines: Recent Developments and Future Possibilities.

Science. 2006 Oct 13;314(5797):236.
Nobel Prize in chemistry. Solo winner detailed path From DNA to RNA.


Nucleic Acids Res. 2006 Sep 29
Quadruplex DNA: sequence, topology and structure. レビュー

Nat Genet. 2006 Oct;38(10):1104-5
New evidence that DNA encodes its packaging. ヌクレオソームの位置

Bioessays. 2006 Sep 22;28(10):963-967
Detrimental deletions: mitochondria, aging and Parkinson's disease.

Nucleic Acids Res. 2006 Sep 22
Covalent binding of the natural antimicrobial peptide indolicidin to DNA abasic sites. 有用なペプチド

Nat Mater. 2006 Sep 24
Co-delivery of drugs and DNA from cationic core-shell nanoparticles self-assembled from a biodegradable copolymer.

Nature. 2006 Sep 21;443(7109):340-4.
Topical drug rescue strategy and skin protection based on the role of Mc1r in UV-induced tanning.
日焼けによる発ガンを防ぐ

Nucleic Acids Res. 2006 Sep 14
Human replication protein A unfolds telomeric G-quadruplexes. G4重鎖をほどく

Nature. 2006 Sep 10
The neurodegenerative disease protein aprataxin resolves abortive DNA ligation intermediates.

Nature. 2006 Sep
The pathological response to DNA damage does not contribute to p53-mediated tumour suppression.
p53に依存しないがん抑制反応

Nucleic Acids Res. 2006 Aug 31
A mass spectrometry-based approach for identifying novel DNA polymerase substrates from a pool of dNTP analogues. 複製の際に取り込まれた塩基をMSで分析

Nat Methods. 2006 Sep;3(9):729-35.
An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA.
複製転写ができる、新しい合成鎖

Nat Rev Genet. 2006 Aug 15
Insulators: exploiting transcriptional and epigenetic mechanisms. 新しい調節因子、インシュレーター

Nature. 2006 Aug 13
Autophosphorylation at serine 1987 is dispensable for murine Atm activation in vivo. ATMが働く仕組みが、だいぶわかってきました。

Science. 2006 Aug 11;313(5788):848-51
Escherichia coli induces DNA double-strand breaks in eukaryotic cells. 大腸菌のペプチドとポリケタイドの働き

Nat Med. 2006 Aug;12(8):945-9. Epub 2006 Jul 30.
A previously unidentified alternatively spliced isoform of t(8;21) transcript promotes leukemogenesis.
染色体の転座でできる新しい転写産物ががんを引き起こすかもしれない

Nat Biotechnol. 2006 Jul 30
Gene targeting in vivo by adeno-associated virus vectors. ウィルスを使ってノックアウト

Cell. 2006 Jul 28;126(2):297-308.
Endonucleolytic Function of MutLalpha in Human Mismatch Repair.
in vitroでのミスマッチ修復系


Proc Natl Acad Sci U S A.
2006 Jul 27

Involvement of Rad18 in somatic hypermutation. Rad18の新しい役割

EMBO J. 2006 Jul 27
DNA-PK autophosphorylation facilitates Artemis endonuclease activity.
アルテミスの切断活性とリン酸化

Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. 5-メチルシトシンを取り除く酵素

Nature. 2006 Jul 12
DNA overwinds when stretched.
DNA分子の挙動

Nucleic Acids Res. 2006 Jul 19;34(12):3476-83. Print 2006
Synthesis and properties of 4'-ThioDNA: unexpected RNA-like behavior of 4'-ThioDNA.
RNAのようなヌクレアーゼ耐性の修飾DNA

Mol Cell. 2006 Jul 21;23(2):155-60.
DNA replication: keep moving and don't mind the gap.
レビュー

Proc Natl Acad Sci U S A. 2006 Jul 17
Influence of sex chromosome constitution on the genomic imprinting of germ cells.
性染色体のメチル化

Cancer Res. 2006 Jul 15;66(14):6899-902.
ChIP-chip Comes of Age for Genome-wide Functional Analysis.
クロモゾームIPをアレイで行う

Cell. 2006 Jul 14;126(1):93-106.
An ARGONAUTE4-Containing Nuclear Processing Center Colocalized with Cajal Bodies in Arabidopsis thaliana.
Li CF, Pontes O, El-Shami M, Henderson IR, Bernatavichute YV, Chan SW, Lagrange T, Pikaard CS, Jacobsen SE.
Cell. 2006 Jul 14;126(1):79-92.
The Arabidopsis Chromatin-Modifying Nuclear siRNA Pathway Involves a Nucleolar RNA Processing Center.
Pontes O, Li CF, Nunes PC, Haag J, Ream T, Vitins A, Jacobsen SE, Pikaard CS.
siRNAと脱メチル化との関係

J Biol Chem. 2006 Jul 7
Characterization of an active spore photoproduct lyase, a DNA repair enzyme in the radical SAM superfamily.
Buis JM, Cheek J, Kalliri E, Broderick JB.
チミンの新しい紫外線損傷の修復に、SAMが必要

Cell. 2006 Jun 30;125(7):1297-308.
Live-cell imaging reveals replication of individual replicons in eukaryotic replication factories.
Kitamura E, Blow JJ, Tanaka TU.
Cell. 2006 Jun 30;125(7):1233-5.
In and out of the Replication Factory.
Meister P, Taddei A, Gasser SM.
酵母の複製工場を観察する


EMBO Rep. 2006 Jun 16
Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome.
Blot N, Mavathur R, Geertz M, Travers A, Muskhelishvili G.
ゲノムDNAのスーパーコイルと転写との関係

Science. 2006 Jun 23;312(5781):1798-802.
A topoisomerase IIbeta-mediated dsDNA break required for regulated transcription.
Ju BG, Lunyak VV, Perissi V, Garcia-Bassets I, Rose DW, Glass CK, Rosenfeld MG.
トポイソメラーゼが関与する転写の活性化

J Biol Chem. 2006 Jun 16
Interdomain communication in DNA topoisomerase II: DNA binding and enzyme activation.
Mueller-Planitz F, Herschlag D.
分子内ドメイン間での活性情報の伝達

Proc Natl Acad Sci U S A. 2006 Jun 15
Selective utilization of nonhomologous end-joining and homologous recombination DNA repair pathways during nervous system development.
Orii KE, Lee Y, Kondo N, McKinnon PJ.
神経系発生時の、HR、NHEJ、アポトーシス

Science. 2006 Jun 16;312(5780):1614-20.
Positive natural selection in the human lineage.
Sabeti PC, Schaffner SF, Fry B, Lohmueller J, Varilly P, Shamovsky O, Palma A, Mikkelsen TS, Altshuler D, Lander ES.
自然選択とゲノム配列

Nat Rev Genet. 2006 Jun 13
Designed DNA molecules: principles and applications of molecular nanotechnology.
Condon A.
DNAの調節因子をデザインする

Nat Methods. 2006 Jun;3(6):424.
Getting a DNA to do an RNA's job.
Eisenstein M.
DNA enzymeを設計する

Proc Natl Acad Sci U S A. 2006 Jun 9
Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement of Streptomyces kanamyceticus.
Yanai K, Murakami T, Bibb M.
カナマイシン合成遺伝子群を増幅させるだけで、カナマイシンの生産性が上がる

Science. 2006 Jun 8
Selective Silencing of Foreign DNA with Low GC Content by the H-NS Protein in Salmonella.
Navarre WW, Porwollik S, Wang Y, McClelland M, Rosen H, Libby SJ, Fang FC.
外来遺伝子を抑制するサルモネラの仕組み

Proc Natl Acad Sci U S A. 2006 Jun 6
Remarkably high activities of testicular cytochrome c in destroying reactive oxygen species and in triggering apoptosis.
Liu Z, Lin H, Ye S, Liu QY, Meng Z, Zhang CM, Xia Y, Margoliash E, Rao Z, Liu XJ.
精巣のチトクロームcの働き

Nat Cell Biol. 2006 Jun;8(6):640-2.
The Y-family DNA polymerase kappa (pol kappa) functions in mammalian nucleotide-excision repair.
Ogi T, Lehmann AR.
ヌクレオチド除去修復に関与するポリメラーゼkappa

Nat Biotechnol. 2006 May 28
Sequencing genomes from single cells by polymerase cloning.
Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, Church GM.
1細胞からの、ゲノムのシーケンシング

Nature. 2006 May 21
ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression.
Shi X, Hong T, Walter KL, Ewalt M, Michishita E, Hung T, Carney D, Pena P, Lan F, Kaadige MR, Lacoste N, Cayrou C, Davrazou F, Saha A, Cairns BR, Ayer DE, Kutateladze TG, Shi Y, Cote J, Chua KF, Gozani O.
ヒストンのメチル化による、遺伝子発現の抑制


Nat Cell Biol. 2006 May 21
Molecular architecture of a kinetochore-microtubule attachment site.
Joglekar AP, Bouck DC, Molk JN, Bloom KS, Salmon ED.
染色体分離の仕組み


Nucleic Acids Res. 2006 May 17;34(9):2579-86. Print 2006.
RNA aptamers selected against DNA polymerase {beta} inhibit the polymerase activities of DNA polymerases beta and kappa.
Gening LV, Klincheva SA, Reshetnjak A, Grollman AP, Miller H.
DNAポリメラーゼを阻害するアプタマー

Science. 2006 May 19;312(5776):1027-30.
Oligonucleotide-modified gold nanoparticles for intracellular gene regulation.
Rosi NL, Giljohann DA, Thaxton CS, Lytton-Jean AK, Han MS, Mirkin CA.
金の微粒子にくっつけると、オリゴがヌクレアーゼ耐性になる


EMBO J. 2006 May 18
Topoisomerase II, not topoisomerase I, is the proficient relaxase of nucleosomal DNA.
Salceda J, Fernandez X, Roca J.
ヌクレオゾームをリラックスさせる

Nature. 2006 May 14
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise.
Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, Derisi JL, Weissman JS.
1細胞レベルでのプロテオミクスの分析

EMBO J. 2006 May 11
Histone H2B mutations in inner region affect ubiquitination, centromere function, silencing and chromosome segregation.
Maruyama T, Nakamura T, Hayashi T, Yanagida M.
ヒストンH2Bの重要な働き

Proc Natl Acad Sci U S A. 2006 May 8
The X chromosome is organized into a gene-rich outer rim and an internal core containing silenced nongenic sequences.
Clemson CM, Hall LL, Byron M, McNeil J, Lawrence JB.
X染色体の中の遺伝子の位置


EMBO J. 2006 May 4
Opposing effects of the UV lesion repair protein XPA and UV bypass polymerase eta on ATR checkpoint signaling.
Bomgarden RD, Lupardus PJ, Soni DV, Yee MC, Ford JM, Cimprich KA.
NERとTLSとの関係


Science. 2006 Apr 28;312(5773):570-2.
Population size does not influence mitochondrial genetic diversity in animals.
Bazin E, Glemin S, Galtier N.
ミトコンドリアDNAの進化

Cell. 2006 Apr 21;125(2):315-26.
A bivalent chromatin structure marks key developmental genes in embryonic stem cells.
Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber SL, Lander ES.
DNAの配列でクロマチンの状態をコントロールしている

Nucleic Acids Res. 2006 Apr 13;34(7):1974-81.
Aspects of large-scale chromatin structures in mouse liver nuclei can be predicted from the DNA sequence.
Cioffi A, Fleury TJ, Stein A.
配列から、クロマチンの構造を予測する。

Mol Cell Biol. 2006 May;26(9):3672-9.
An HMG Protein, Hmo1, Associates with Promoters of Many Ribosomal Protein Genes and throughout the rRNA Gene Locus in Saccharomyces cerevisiae.
Hall DB, Wade JT, Struhl K.


Proc Natl Acad Sci U S A. 2006 Apr 10
A Dirichlet process model for detecting positive selection in protein-coding DNA sequences.
Huelsenbeck JP, Jain S, Frost SW, Kosakovsky Pond SL.
DNA配列を選択する進化過程

Nat Cell Biol. 2006 Apr;8(4):308-10.
Chromosomes walk the line.
Compton DA.
クロモゾームが分離する仕組み

Nat Cell Biol. 2006 Apr;8(4):303-5.
Deubiquitinating PCNA: a downside to DNA damage tolerance.
Ulrich HD.
PCNAの脱ユビキチン化

Nat Genet. 2006 Apr 9
High levels of mitochondrial DNA deletions in substantia nigra neurons in aging and Parkinson disease.
Bender A, Krishnan KJ, Morris CM, Taylor GA, Reeve AK, Perry RH, Jaros E, Hersheson JS, Betts J, Klopstock T, Taylor RW, Turnbull DM.
Nat Genet. 2006 Apr 9
Mitochondrial DNA deletions are abundant and cause functional impairment in aged human substantia nigra neurons.
Kraytsberg Y, Kudryavtseva E, McKee AC, Geula C, Kowall NW, Khrapko K.
ミトコンドリアDNAの欠失と加齢病



Nature. 2006 Apr 6;440(7085):824-8.
Semi-conservative DNA replication through telomeres requires Taz1.
Miller KM, Rog O, Cooper JP.
テロメア複製時のtaz1の機能


Nat Cell Biol. 2006 Mar 26
DNA methyltransferases control telomere length and telomere recombination in mammalian cells.
Gonzalo S, Jaco I, Fraga MF, Chen T, Li E, Esteller M, Blasco MA.
メチルトランスフェラーゼがないと、テロメアが異常に伸長する


Curr Biol. 2006 Mar 21;16(6):R209-11.
DNA replication fidelity: proofreading in trans.
Albertson TM, Preston BD.


Curr Biol. 2006 Mar 21;16(6):R186-9.
Directed DNA deamination by AID/APOBEC3 in immunity.
Macduff DA, Harris RS.


Nucleic Acids Res. 2006 Mar 15;34(5):e40. Print 2006.
Enhancement of the efficiency of non-viral gene delivery by application of pulsed magnetic field.
Kamau SW, Hassa PO, Steitz B, Petri-Fink A, Hofmann H, Hofmann-Amtenbrink M, von Rechenberg B, Hottiger MO.
磁石と磁場を使って、遺伝子を導入する


Nature. 2006 Mar 16;440(7082):297-302.
Folding DNA to create nanoscale shapes and patterns.
Rothemund PW.
1本鎖DNAで、様々な形を作る。


Proc Natl Acad Sci U S A. 2006 Mar 10
Self-catalyzed site-specific depurination of guanine residues within gene sequences.
Amosova O, Coulter R, Fresco JR.
グアニンの脱プリン化が高頻度に起こる


Proc Natl Acad Sci U S A. 2006 Mar 14
Self-synthesizing DNA transposons in eukaryotes.
Kapitonov VV, Jurka J.
真核生物のトランスポゾン

Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4056-61. Epub 2006 Mar 6.
Repair of DNA-polypeptide crosslinks by human excision nuclease.
Reardon JT, Sancar A.
DNA-タンパク質間のクロスリンクを修復するヌクレオチド除去修復

Mol Cell Biol. 2006 Apr;26(7):2550-9.
Cooperative Activity of BRG1 and Z-DNA Formation in Chromatin Remodeling.
Liu H, Mulholland N, Fu H, Zhao K.
Z-DNA(逆巻きの2重らせんDNA)を作る因子


Nucleic Acids Res. 2006 Mar 6;34(5):1405-15. Print 2006.
Human replication protein A can suppress the intrinsic in vitro mutator phenotype of human DNA polymerase lambda.
Maga G, Shevelev I, Villani G, Spadari S, Hubscher U.
ポリメラーゼラムダとRPAとの関係。


Mol Cell Biol. 2006 Mar;26(6):2093-108.
Normal cells, but not cancer cells, survive severe plk1 depletion.
Liu X, Lei M, Erikson RL.
plk1遺伝子の抑制で、がん細胞がよく死ぬ。


J Biol Chem. 2006 Feb 28
Postreplicative mismatch repair factors are recruited to epstein-barr virus replication compartments.
Daikoku T, Kudoh A, Sugaya Y, Iwahori S, Shirata N, Isomura H, Tsurumi T.
ウィルスの複製タンパク質に、ミスマッチ修復タンパク質が結合している。


EMBO J. 2006 Mar 2
Extension of G-quadruplex DNA by ciliate telomerase.
Oganesian L, Moon IK, Bryan TM, Jarstfer MB.
G4重鎖の安定性


EMBO J. 2006 Feb 16
DNA interstrand crosslink repair during G1 involves nucleotide excision repair and DNA polymerase zeta.
Sarkar S, Davies AA, Ulrich HD, McHugh PJ.
NERとTLSが協調して、ICLを修復するのではないか。

EMBO J. 2006 Feb 16
14-3-3 proteins integrate E2F activity with the DNA damage response.
Milton AH, Khaire N, Ingram L, O'donnell AJ, La Thangue NB.
14-3-3が、DNA損傷に反応して、転写を引き起こす。


Nucleic Acids Res. 2006 Feb 14;34(3):e27.
Affinity selection of DNA-binding protein complexes using mRNA display.
Tateyama S, Horisawa K, Takashima H, Miyamoto-Sato E, Doi N, Yanagawa H.
mRNAのライブラリーを用いることによって、結合タンパク質のグループをセレクションしてくることができるようになりました。

Proc Natl Acad Sci U S A. 2006 Feb 10
Z-DNA-forming sequences generate large-scale deletions in mammalian cells.
Wang G, Christensen LA, Vasquez KM
Z型のDNAのところで2本鎖切断が起こりやすく、欠失しやすい。


Nucleic Acids Res. 2006 Feb 9;34(3):e18.
SNP genotyping using alkali cleavage of RNA/DNA chimeras and MALDI time-of-flight mass spectrometry.
Mauger F, Jaunay O, Chamblain V, Reichert F, Bauer K, Gut IG, Gelfand DH.
MSでSNPを検出する技術


Proc Natl Acad Sci U S A. 2006 Feb 6
Fast complementation of split fluorescent protein triggered by DNA hybridization.
Demidov VV, Dokholyan NV, Witte-Hoffmann C, Chalasani P, Yiu HW, Ding F, Yu Y, Cantor CR, Broude NE.
DNAの対合を利用して、蛍光タンパク質を光らせる技術です。


Chem Rev. 2006 Feb;106(2):607-86.
NMR structures of damaged DNA.
Lukin M, de Los Santos C.
損傷DNAのNMRによる解析


Nat Biotechnol. 2006 Feb;24(2):139.
A DNA flu vaccine in practice.
Dunnill P.


Nucleic Acids Res. 2006 Feb 2;34(3):796-805.
Engineering a rare-cutting restriction enzyme: genetic screening and selection of NotI variants.
Samuelson JC, Morgan RD, Benner JS, Claus TE, Packard SL, Xu SY.
制限酵素遺伝子を改変して、新しい活性を持つ酵素遺伝子をセレクションしました。


Science.
2006 Jan 20;311(5759):395-8.
Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2.
Goll MG, Kirpekar F, Maggert KA, Yoder JA, Hsieh CL, Zhang X, Golic KG, Jacobsen SE, Bestor TH.
DNAメチルトランスフェレースのホモログが、tRNAをメチル化するという論文です。
生物種によってそれぞれメチル化のパターンが異なるようです。メチル化のパターンの生物種による違いがどういった意味を持つのでしょうか。今後の研究に期待します。

Cancer Res. 2006 Jan 15;66(2):748-54.
Critical Roles for Polymerase {zeta} in Cellular Tolerance to Nitric Oxide-Induced DNA Damage.
Wu X, Takenaka K, Sonoda E, Hochegger H, Kawanishi S, Kawamoto T, Takeda S, Yamazoe M.
ポリメレースζ(zeta)欠損の細胞は、NO剤に高感受性になることから、鎖切断の修復に関与しているのではないかという論文です。
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