真核基因中分支点信号的分布与一致性：计算机化统计分析
Distribution and consensus of branch point signals in eukaryotic genes: a computerized statistical analysis.
作者信息
Harris N L, Senapathy P
机构信息
Laboratory for Computer Science, Massachusetts Institute of Technology, Cambridge 02139.
出版信息
Nucleic Acids Res. 1990 May 25;18(10):3015-9. doi: 10.1093/nar/18.10.3015.
Abstract
An intermediate stage in the process of eukaryotic RNA splicing is the formation of a lariat structure. It is anchored at an adenosine residue in intron between 10 and 50 nucleotides upstream of the 3' splice site. A short conserved sequence (the branch point sequence) functions as the recognition signal for the site of lariat formation. It has been generally assumed that the branch point is recognized mainly by the presence of its unique sequence where the lariat is formed. However, the known branch point consensus sequence is found to be distributed nearly randomly throughout the gene sequence with only a slightly higher frequency in the expected lariat region. Further, the known consensus sequence is found to be clearly inadequate to specify branch points. These observations have implications for understanding the mechanism of branch point recognition in the process of splicing, and the possible evolution of the branch point signal.
摘要
真核生物RNA剪接过程中的一个中间阶段是套索结构的形成。它锚定在3'剪接位点上游10至50个核苷酸之间的内含子中的一个腺苷残基上。一个短的保守序列（分支点序列）作为套索形成位点的识别信号。一般认为，分支点主要通过其在套索形成处的独特序列来识别。然而，已知的分支点共有序列在整个基因序列中几乎是随机分布的，仅在预期的套索区域频率略高。此外，发现已知的共有序列明显不足以确定分支点。这些观察结果对于理解剪接过程中分支点识别的机制以及分支点信号的可能进化具有启示意义。
相似文献
1
Distribution and consensus of branch point signals in eukaryotic genes: a computerized statistical analysis.真核基因中分支点信号的分布与一致性：计算机化统计分析
Nucleic Acids Res. 1990 May 25;18(10):3015-9. doi: 10.1093/nar/18.10.3015.
2
Effect of mutations at the lariat branch acceptor site on beta-globin pre-mRNA splicing in vitro.套索分支接受位点突变对β-珠蛋白前体mRNA体外剪接的影响。
Nature. 1986;324(6097):589-91. doi: 10.1038/324589a0.
3
Conserved putative signals in 3' intron junctions in rodents.啮齿动物3'内含子连接处的保守推定信号。
J Biomol Struct Dyn. 1987 Jun;4(6):1051-64. doi: 10.1080/07391102.1987.10507697.
4
Self-splicing of group II introns in vitro: lariat formation and 3' splice site selection in mutant RNAs.II类内含子在体外的自我剪接：突变RNA中环套的形成及3'剪接位点选择
Cell. 1987 Dec 4;51(5):753-62. doi: 10.1016/0092-8674(87)90098-5.
5
Cooperative interaction of branch signals in the actin intron of Saccharomyces cerevisiae.酿酒酵母肌动蛋白内含子中分支信号的协同相互作用。
Nucleic Acids Res. 1998 Sep 15;26(18):4137-45. doi: 10.1093/nar/26.18.4137.
6
Intron splicing: a conserved internal signal in introns of Drosophila pre-mRNAs.内含子剪接：果蝇前体mRNA内含子中的保守内部信号。
Nucleic Acids Res. 1985 Jul 11;13(13):4971-81. doi: 10.1093/nar/13.13.4971.
7
Small sequence insertions within the branch point region dictate alternative sites of lariat formation in a yeast intron.分支点区域内的小序列插入决定了酵母内含子中套索形成的替代位点。
Nucleic Acids Res. 1992 Dec 25;20(24):6649-55. doi: 10.1093/nar/20.24.6649.
8
Branch point identification and sequence requirements for intron splicing in Plasmodium falciparum.恶性疟原虫内含子剪接的分支点识别及序列要求
Eukaryot Cell. 2011 Nov;10(11):1422-8. doi: 10.1128/EC.05193-11. Epub 2011 Sep 16.
9
Sequencing of lariat termini in S. cerevisiae reveals 5' splice sites, branch points, and novel splicing events.酿酒酵母中套索末端的测序揭示了5'剪接位点、分支点和新的剪接事件。
RNA. 2016 Feb;22(2):237-53. doi: 10.1261/rna.052829.115. Epub 2015 Dec 8.
10
Human branch point consensus sequence is yUnAy.人类分支点共有序列为yUnAy。
Nucleic Acids Res. 2008 Apr;36(7):2257-67. doi: 10.1093/nar/gkn073. Epub 2008 Feb 19.
引用本文的文献
1
Intronic RNA secondary structural information captured for the human pre-mRNA.为人类前体信使核糖核酸捕获的内含子RNA二级结构信息。
NAR Genom Bioinform. 2024 Oct 24;6(4):lqae143. doi: 10.1093/nargab/lqae143. eCollection 2024 Sep.
2
Generation of Rare Human NMDA Receptor Variants in Mice.在小鼠中生成罕见的人类 NMDA 受体变体。
Methods Mol Biol. 2024;2799:79-105. doi: 10.1007/978-1-0716-3830-9_6.
3
Exonic splicing code and coordination of divalent metals in proteins.外显子剪接代码和蛋白质中二价金属的协调。
Nucleic Acids Res. 2024 Feb 9;52(3):1090-1106. doi: 10.1093/nar/gkad1161.
4
A Mechanism Leading to Changes in Copy Number Variations Affected by Transcriptional Level Might Be Involved in Evolution, Embryonic Development, Senescence, and Oncogenesis Mediated by Retrotransposons.一种受转录水平影响导致拷贝数变异变化的机制可能参与了由逆转录转座子介导的进化、胚胎发育、衰老和肿瘤发生过程。
Front Cell Dev Biol. 2021 Feb 11;9:618113. doi: 10.3389/fcell.2021.618113. eCollection 2021.
5
Dynamic stacking of an expected branch point adenosine in duplexes containing pseudouridine-modified or unmodified U2 snRNA sites.含有假尿嘧啶核苷修饰或未修饰 U2 snRNA 位点的双链体中预期分支点腺苷的动态堆积。
Biochem Biophys Res Commun. 2019 Apr 2;511(2):416-421. doi: 10.1016/j.bbrc.2019.02.073. Epub 2019 Feb 21.
6
Chemical Inhibition of Pre-mRNA Splicing in Living Saccharomyces cerevisiae.在活酿酒酵母中化学抑制前体 mRNA 剪接。
Cell Chem Biol. 2019 Mar 21;26(3):443-448.e3. doi: 10.1016/j.chembiol.2018.11.008. Epub 2019 Jan 10.
7
Functional analysis of Hsh155/SF3b1 interactions with the U2 snRNA/branch site duplex.Hsh155/SF3b1 与 U2 snRNA/分支位点双链体相互作用的功能分析。
RNA. 2018 Aug;24(8):1028-1040. doi: 10.1261/rna.065664.118. Epub 2018 May 11.
8
A heuristic model for computational prediction of human branch point sequence.一种用于人类分支点序列计算预测的启发式模型。
BMC Bioinformatics. 2017 Oct 24;18(1):459. doi: 10.1186/s12859-017-1864-9.
9
Limb girdle myasthenia with digenic RAPSN and a novel disease gene AK9 mutations.伴有双基因RAPSN和新疾病基因AK9突变的肢带型肌无力
Eur J Hum Genet. 2017 Feb;25(2):192-199. doi: 10.1038/ejhg.2016.162. Epub 2016 Dec 14.
10
Comparative analysis of information contents relevant to recognition of introns in many species.对与识别许多物种中的内含子相关的信息含量进行比较分析。
BMC Genomics. 2011 Jan 19;12:45. doi: 10.1186/1471-2164-12-45.
本文引用的文献
1
Intron splicing: a conserved internal signal in introns of animal pre-mRNAs.内含子剪接：动物前体mRNA内含子中的保守内部信号。
Proc Natl Acad Sci U S A. 1984 Dec;81(23):7417-20. doi: 10.1073/pnas.81.23.7417.
2
Excision of an intact intron as a novel lariat structure during pre-mRNA splicing in vitro.在体外前体mRNA剪接过程中，完整内含子作为一种新型套索结构被切除。
Cell. 1984 Aug;38(1):317-31. doi: 10.1016/0092-8674(84)90553-1.
3
A catalogue of splice junction and putative branch point sequences from plant introns.植物内含子的剪接连接和假定分支点序列目录。
Nucleic Acids Res. 1986 Dec 22;14(24):9549-59. doi: 10.1093/nar/14.24.9549.
4
RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression.不同类真核生物的RNA剪接连接：序列统计及其在基因表达中的功能意义
Nucleic Acids Res. 1987 Sep 11;15(17):7155-74. doi: 10.1093/nar/15.17.7155.
5
Recognition of the TACTAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA.酵母中mRNA剪接过程中对TACTAAC框的识别涉及与U2样snRNA的碱基配对。
Cell. 1987 Apr 24;49(2):229-39. doi: 10.1016/0092-8674(87)90564-2.
6
Splicing of messenger RNA precursors.信使核糖核酸前体的剪接
Science. 1987 Feb 13;235(4790):766-71. doi: 10.1126/science.3544217.
7
Origin of eukaryotic introns: a hypothesis, based on codon distribution statistics in genes, and its implications.真核生物内含子的起源：基于基因中密码子分布统计的一种假说及其影响。
Proc Natl Acad Sci U S A. 1986 Apr;83(7):2133-7. doi: 10.1073/pnas.83.7.2133.
8
Possible evolution of splice-junction signals in eukaryotic genes from stop codons.真核基因中剪接连接信号可能从终止密码子演变而来。
Proc Natl Acad Sci U S A. 1988 Feb;85(4):1129-33. doi: 10.1073/pnas.85.4.1129.
9
Unusual branch point selection in processing of human growth hormone pre-mRNA.人类生长激素前体信使核糖核酸加工过程中异常的分支点选择
Mol Cell Biol. 1988 May;8(5):2011-20. doi: 10.1128/mcb.8.5.2011-2020.1988.
10
Pre-mRNA splicing.前体信使核糖核酸剪接
Annu Rev Genet. 1986;20:671-708. doi: 10.1146/annurev.ge.20.120186.003323.
Zotero 插件