人类基因组中形成三链体的寡核苷酸靶序列。
Triplex-forming oligonucleotide target sequences in the human genome.
作者信息
Goñi J Ramon, de la Cruz Xavier, Orozco Modesto
机构信息
Molecular Modelling and Bioinformatics Unit, Institut de Recerca Biomédica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.
出版信息
Nucleic Acids Res. 2004 Jan 15;32(1):354-60. doi: 10.1093/nar/gkh188. Print 2004.
Abstract
The existence of sequences in the human genome which can be a target for triplex formation, and accordingly are candidates for anti-gene therapies, has been studied by using bioinformatics tools. It was found that the population of triplex-forming oligonucleotide target sequences (TTS) is much more abundant than that expected from simple random models. The population of TTS is large in all the genome, without major differences between chromosomes. A wide analysis along annotated regions of the genome allows us to demonstrate that the largest relative concentration of TTS is found in regulatory regions, especially in promoter zones, which suggests a tremendous potentiality for triplex strategy in the control of gene expression. The dependence of the stability and selectivity of the triplexes on the length of the TTS is also analysed using knowledge-based rules.
摘要
利用生物信息学工具对人类基因组中可作为三链体形成靶点、因而可作为抗基因治疗候选靶点的序列的存在情况进行了研究。结果发现，形成三链体的寡核苷酸靶序列（TTS）群体比简单随机模型预期的要丰富得多。TTS群体在整个基因组中都很多，染色体之间没有重大差异。对基因组注释区域进行的广泛分析使我们能够证明，TTS的最大相对浓度出现在调控区域，尤其是启动子区域，这表明三链体策略在基因表达控制方面具有巨大潜力。还利用基于知识的规则分析了三链体的稳定性和选择性对TTS长度的依赖性。
相似文献
1
Triplex-forming oligonucleotide target sequences in the human genome.人类基因组中形成三链体的寡核苷酸靶序列。
Nucleic Acids Res. 2004 Jan 15;32(1):354-60. doi: 10.1093/nar/gkh188. Print 2004.
2
Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions.探究人类调控区域中三链形成寡核苷酸靶序列高密度存在的原因。
BMC Genomics. 2006 Mar 27;7:63. doi: 10.1186/1471-2164-7-63.
3
Purine- and pyrimidine-triple-helix-forming oligonucleotides recognize qualitatively different target sites at the ribosomal DNA locus.嘌呤和嘧啶三链体形成寡核苷酸在核糖体 DNA 位点上定性识别不同的靶位。
RNA. 2018 Mar;24(3):371-380. doi: 10.1261/rna.063800.117. Epub 2017 Dec 8.
4
Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data.Triplexator：在基因组和转录组数据中检测核酸三螺旋。
Genome Res. 2012 Jul;22(7):1372-81. doi: 10.1101/gr.130237.111. Epub 2012 May 1.
5
High-affinity triplex-forming oligonucleotide target sequences in mammalian genomes.哺乳动物基因组中的高亲和力三链体形成寡核苷酸靶序列。
Mol Carcinog. 2007 Jan;46(1):15-23. doi: 10.1002/mc.20261.
6
TTS mapping: integrative WEB tool for analysis of triplex formation target DNA sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome.TTS 映射：用于分析人类基因组中三聚体形成靶 DNA 序列、G-四联体和非蛋白编码调控 DNA 元件的综合 WEB 工具。
BMC Genomics. 2009 Dec 3;10 Suppl 3(Suppl 3):S9. doi: 10.1186/1471-2164-10-S3-S9.
7
Gold nanoparticle-based colorimetric assay of single-nucleotide polymorphism of triplex DNA.基于金纳米粒子的三链 DNA 单核苷酸多态性比色分析。
Biosens Bioelectron. 2010 May 15;25(9):2135-9. doi: 10.1016/j.bios.2010.02.017. Epub 2010 Feb 25.
8
Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome.全基因组范围内计算分析人类基因组中潜在的长非编码 RNA 介导的 DNA:DNA:RNA 三链体。
J Transl Med. 2017 Sep 2;15(1):186. doi: 10.1186/s12967-017-1282-9.
9
An RNA oligonucleotide corresponding to the polypyrimidine region of the rat alpha 1(I) procollagen promoter forms a stable triplex and inhibits transcription.一种与大鼠α1（I）前胶原启动子的聚嘧啶区域相对应的RNA寡核苷酸形成稳定的三链体并抑制转录。
Biochem Biophys Res Commun. 1998 Aug 10;249(1):218-21. doi: 10.1006/bbrc.1998.9113.
10
The anti-gene strategy: control of gene expression by triplex-forming-oligonucleotides.反基因策略：通过三链形成寡核苷酸控制基因表达。
Anticancer Drug Des. 1991 Dec;6(6):569-84.
引用本文的文献
1
Systematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism.对杂交三链体拓扑结构和稳定性的系统研究表明了一种普遍的三链体介导的调控机制。
Nucleic Acids Res. 2025 Feb 27;53(5). doi: 10.1093/nar/gkaf170.
2
Tracing the Chromatin: From 3C to Live-Cell Imaging.追踪染色质：从3C技术到活细胞成像
Chem Biomed Imaging. 2024 Jun 25;2(10):659-682. doi: 10.1021/cbmi.4c00033. eCollection 2024 Oct 28.
3
Peptidylprolyl isomerase A guides SENP5/GAU1 DNA-lncRNA triplex generation for driving tumorigenesis.肽基脯氨酰顺反异构酶 A 指导 SENP5/GAU1 DNA-lncRNA 三聚体的生成，从而驱动肿瘤发生。
Nat Commun. 2024 Oct 21;15(1):9068. doi: 10.1038/s41467-024-53493-x.
4
Interaction of isoquinoline alkaloids with pyrimidine motif triplex DNA by mass spectrometry and spectroscopies reveals diverse mechanisms.通过质谱和光谱法研究异喹啉生物碱与嘧啶基序三链体DNA的相互作用揭示了多种机制。
Heliyon. 2023 Mar 30;9(4):e14954. doi: 10.1016/j.heliyon.2023.e14954. eCollection 2023 Apr.
5
Recent Development in Biomedical Applications of Oligonucleotides with Triplex-Forming Ability.具有三链形成能力的寡核苷酸在生物医学应用中的最新进展。
Polymers (Basel). 2023 Feb 9;15(4):858. doi: 10.3390/polym15040858.
6
LNA units present in [ -PS]-(DNA#LNA) chimeras enhance the thermal stability of parallel duplexes and triplexes formed with (2'-OMe)-RNA strands.存在于[-PS]-(DNA#LNA)嵌合体中的锁核酸（LNA）单元增强了与（2'-O-甲基）-RNA链形成的平行双链体和三链体的热稳定性。
RSC Adv. 2020 Jun 10;10(38):22370-22376. doi: 10.1039/d0ra03934a.
7
The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7.长链非编码 RNA Smad7 通过反式招募乙酰转移酶 p300 至多个增强子位点。
Nucleic Acids Res. 2022 Mar 21;50(5):2587-2602. doi: 10.1093/nar/gkac083.
8
Gene Correction of Point Mutations Using PolyPurine Reverse Hoogsteen Hairpins Technology.利用多嘌呤反向Hoogsteen发夹技术对点突变进行基因校正
Front Genome Ed. 2020 Oct 29;2:583577. doi: 10.3389/fgeed.2020.583577. eCollection 2020.
9
A unified computational view of DNA duplex, triplex, quadruplex and their donor-acceptor interactions.DNA 双链体、三链体、四链体及其给体-受体相互作用的统一计算观点。
Nucleic Acids Res. 2021 May 21;49(9):4919-4933. doi: 10.1093/nar/gkab285.
10
Triplex Hybridization-Based Nanosystem for the Rapid Screening of Pneumocystis Pneumonia in Clinical Samples.基于三重杂交的纳米系统用于临床样本中肺孢子菌肺炎的快速筛查
J Fungi (Basel). 2020 Nov 17;6(4):292. doi: 10.3390/jof6040292.
本文引用的文献
1
A Proposed Structure For The Nucleic Acids.核酸的一种推测结构
Proc Natl Acad Sci U S A. 1953 Feb;39(2):84-97. doi: 10.1073/pnas.39.2.84.
2
Resolution of parallel and antiparallel oligonucleotide triple helices formation and melting processes by multivariate curve resolution.通过多元曲线分辨法解析平行和反平行寡核苷酸三链螺旋的形成及解链过程。
J Biomol Struct Dyn. 2003 Oct;21(2):267-78. doi: 10.1080/07391102.2003.10506922.
3
The UCSC Genome Browser Database.加州大学圣克鲁兹分校基因组浏览器数据库。
Nucleic Acids Res. 2003 Jan 1;31(1):51-4. doi: 10.1093/nar/gkg129.
4
Bias of purine stretches in sequenced chromosomes.测序染色体中嘌呤序列的偏差。
Comput Chem. 2002 Jul;26(5):531-41. doi: 10.1016/s0097-8485(02)00013-x.
5
Triplex forming oligonucleotides: sequence-specific tools for gene targeting.三链形成寡核苷酸：用于基因靶向的序列特异性工具。
Hum Mol Genet. 2001 Oct 1;10(20):2243-51. doi: 10.1093/hmg/10.20.2243.
6
Post-transcriptional gene silencing by double-stranded RNA.双链RNA介导的转录后基因沉默
Nat Rev Genet. 2001 Feb;2(2):110-9. doi: 10.1038/35052556.
7
Initial sequencing and analysis of the human genome.人类基因组的初步测序与分析。
Nature. 2001 Feb 15;409(6822):860-921. doi: 10.1038/35057062.
8
The sequence of the human genome.人类基因组序列。
Science. 2001 Feb 16;291(5507):1304-51. doi: 10.1126/science.1058040.
9
dbSNP: the NCBI database of genetic variation.dbSNP：美国国立生物技术信息中心遗传变异数据库。
Nucleic Acids Res. 2001 Jan 1;29(1):308-11. doi: 10.1093/nar/29.1.308.
10
Triplex technology takes off.三重技术腾飞。
Nat Biotechnol. 2000 Dec;18(12):1245-6. doi: 10.1038/82348.
Zotero 插件