迈向长链非编码RNA的结构分类
Towards structural classification of long non-coding RNAs.
作者信息
Sanbonmatsu Karissa Y
机构信息
Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
出版信息
Biochim Biophys Acta. 2016 Jan;1859(1):41-5. doi: 10.1016/j.bbagrm.2015.09.011. Epub 2015 Oct 30.
Abstract
While long non-coding RNAs play key roles in disease and development, few structural studies have been performed to date for this emerging class of RNAs. Previous structural studies are reviewed, and a pipeline is presented to determine secondary structures of long non-coding RNAs. Similar to riboswitches, experimentally determined secondary structures of long non-coding RNAs for one species, may be used to improve sequence/structure alignments for other species. As riboswitches have been classified according to their secondary structure, a similar scheme could be used to classify long non-coding RNAs. This article is part of a Special Issue titled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
摘要
虽然长链非编码RNA在疾病和发育过程中发挥着关键作用，但迄今为止针对这类新兴RNA的结构研究却很少。本文回顾了以往的结构研究，并提出了一种确定长链非编码RNA二级结构的流程。与核糖开关类似，某一物种的长链非编码RNA通过实验确定的二级结构，可用于改进其他物种的序列/结构比对。由于核糖开关已根据其二级结构进行了分类，因此类似的方案可用于对长链非编码RNA进行分类。本文是由广濑哲郎博士和中川真一博士编辑的名为《长链非编码RNA分类线索》特刊的一部分。
相似文献
1
Towards structural classification of long non-coding RNAs.迈向长链非编码RNA的结构分类
Biochim Biophys Acta. 2016 Jan;1859(1):41-5. doi: 10.1016/j.bbagrm.2015.09.011. Epub 2015 Oct 30.
2
Bioinformatics tools for lncRNA research.用于长链非编码RNA研究的生物信息学工具。
Biochim Biophys Acta. 2016 Jan;1859(1):23-30. doi: 10.1016/j.bbagrm.2015.07.014. Epub 2015 Aug 10.
3
The ins and outs of lncRNA structure: How, why and what comes next?长链非编码RNA结构的来龙去脉：方式、原因及后续发展？
Biochim Biophys Acta. 2016 Jan;1859(1):46-58. doi: 10.1016/j.bbagrm.2015.08.009. Epub 2015 Aug 29.
4
Circular RNAs: Identification, biogenesis and function.环状RNA：鉴定、生物发生及功能
Biochim Biophys Acta. 2016 Jan;1859(1):163-8. doi: 10.1016/j.bbagrm.2015.07.007. Epub 2015 Jul 11.
5
The long non-coding RNA world in yeasts.酵母中的长链非编码RNA世界
Biochim Biophys Acta. 2016 Jan;1859(1):147-54. doi: 10.1016/j.bbagrm.2015.08.003. Epub 2015 Aug 8.
6
Methods for distinguishing between protein-coding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs.区分蛋白质编码RNA和长链非编码RNA的方法以及长链非编码RNA翻译难以捉摸的生物学目的。
Biochim Biophys Acta. 2016 Jan;1859(1):31-40. doi: 10.1016/j.bbagrm.2015.07.017. Epub 2015 Aug 8.
7
Functions of plants long non-coding RNAs.植物长链非编码RNA的功能。
Biochim Biophys Acta. 2016 Jan;1859(1):155-62. doi: 10.1016/j.bbagrm.2015.06.009. Epub 2015 Jun 22.
8
MALAT1 long non-coding RNA in cancer.癌症中的MALAT1长链非编码RNA
Biochim Biophys Acta. 2016 Jan;1859(1):192-9. doi: 10.1016/j.bbagrm.2015.09.012. Epub 2015 Oct 3.
9
Architectural RNAs (arcRNAs): A class of long noncoding RNAs that function as the scaffold of nuclear bodies.结构RNA（arcRNA）：一类作为核体支架发挥作用的长链非编码RNA。
Biochim Biophys Acta. 2016 Jan;1859(1):139-46. doi: 10.1016/j.bbagrm.2015.05.007. Epub 2015 Jun 3.
10
lncRNAs and microRNAs with a role in cancer development.在癌症发展中起作用的长链非编码RNA和微小RNA。
Biochim Biophys Acta. 2016 Jan;1859(1):169-76. doi: 10.1016/j.bbagrm.2015.06.015. Epub 2015 Jul 4.
引用本文的文献
1
LncRNA SChLAP1 promotes cancer cell proliferation and invasion via its distinct structural domains and conserved regions.长链非编码RNA SChLAP1通过其独特的结构域和保守区域促进癌细胞增殖和侵袭。
bioRxiv. 2025 Jan 28:2025.01.28.635288. doi: 10.1101/2025.01.28.635288.
2
MicroRNA Targets PAP1 to Mediate Melanization in (Linnaeus) Infected by .miRNA 靶向 PAP1 介导 （Linnaeus） 感染 后黑化
Int J Mol Sci. 2024 Jan 17;25(2):1140. doi: 10.3390/ijms25021140.
3
LncRNA H19 Regulates BMP2-Induced Hypertrophic Differentiation of Mesenchymal Stem Cells by Promoting Runx2 Phosphorylation.长链非编码RNA H19通过促进Runx2磷酸化来调节骨形态发生蛋白2诱导的间充质干细胞肥大分化。
Front Cell Dev Biol. 2020 Jul 29;8:580. doi: 10.3389/fcell.2020.00580. eCollection 2020.
4
Long non‑coding RNA PRNCR1 exerts oncogenic effects in tongue squamous cell carcinoma in vitro and in vivo by sponging microRNA‑944 and thereby increasing HOXB5 expression.长链非编码 RNA PRNCR1 通过海绵吸附 microRNA-944 并增加 HOXB5 表达，从而在体外和体内发挥致癌作用。
Int J Mol Med. 2020 Jul;46(1):119-130. doi: 10.3892/ijmm.2020.4581. Epub 2020 Apr 16.
5
Long non-coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution.长非编码亚基因组 flavivirus RNA 具有扩展的 3D 结构，在溶液中具有柔韧性。
EMBO Rep. 2019 Nov 5;20(11):e47016. doi: 10.15252/embr.201847016. Epub 2019 Sep 10.
6
Understanding the mechanistic basis of non-coding RNA through molecular dynamics simulations.通过分子动力学模拟理解非编码 RNA 的机制基础。
J Struct Biol. 2019 Jun 1;206(3):267-279. doi: 10.1016/j.jsb.2019.03.004. Epub 2019 Mar 15.
7
New Insights Into the Long Non-coding RNA SRA: Physiological Functions and Mechanisms of Action.长链非编码RNA SRA的新见解：生理功能及作用机制
Front Med (Lausanne). 2018 Sep 6;5:244. doi: 10.3389/fmed.2018.00244. eCollection 2018.
8
Long non-coding regulatory RNAs in sponges and insights into the origin of animal multicellularity.海绵动物中的长非编码调控 RNA 及其对动物多细胞性起源的启示。
RNA Biol. 2018;15(6):696-702. doi: 10.1080/15476286.2018.1460166. Epub 2018 May 25.
9
RNA secondary structure profiling in zebrafish reveals unique regulatory features.在斑马鱼中进行 RNA 二级结构分析揭示了独特的调控特征。
BMC Genomics. 2018 Feb 15;19(1):147. doi: 10.1186/s12864-018-4497-0.
10
nextPARS: parallel probing of RNA structures in Illumina.nextPARS：Illumina 中 RNA 结构的并行探测。
RNA. 2018 Apr;24(4):609-619. doi: 10.1261/rna.063073.117. Epub 2018 Jan 22.
本文引用的文献
1
HOTAIR forms an intricate and modular secondary structure.HOTAIR形成一种复杂且模块化的二级结构。
Mol Cell. 2015 Apr 16;58(2):353-61. doi: 10.1016/j.molcel.2015.03.006. Epub 2015 Apr 9.
2
Systematic discovery of Xist RNA binding proteins.Xist RNA结合蛋白的系统性发现。
Cell. 2015 Apr 9;161(2):404-16. doi: 10.1016/j.cell.2015.03.025. Epub 2015 Apr 2.
3
Structural imprints in vivo decode RNA regulatory mechanisms.体内的结构印记可解码RNA调控机制。
Nature. 2015 Mar 26;519(7544):486-90. doi: 10.1038/nature14263. Epub 2015 Mar 18.
4
Toward a consensus on the binding specificity and promiscuity of PRC2 for RNA.关于PRC2与RNA结合特异性和多特异性达成共识。
Mol Cell. 2015 Feb 5;57(3):552-8. doi: 10.1016/j.molcel.2014.12.017. Epub 2015 Jan 15.
5
Physiological roles of long noncoding RNAs: insight from knockout mice.长链非编码RNA的生理作用：来自基因敲除小鼠的见解
Trends Cell Biol. 2014 Oct;24(10):594-602. doi: 10.1016/j.tcb.2014.06.003. Epub 2014 Jul 9.
6
Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix.双部分三螺旋稳定 MALAT1 非编码 RNA 的结构见解。
Nat Struct Mol Biol. 2014 Jul;21(7):633-40. doi: 10.1038/nsmb.2844. Epub 2014 Jun 22.
7
The crystal structure of the Split End protein SHARP adds a new layer of complexity to proteins containing RNA recognition motifs.剪接末端蛋白SHARP的晶体结构为含有RNA识别基序的蛋白质增添了新的复杂层面。
Nucleic Acids Res. 2014 Jun;42(10):6742-52. doi: 10.1093/nar/gku277. Epub 2014 Apr 19.
8
Steroid receptor RNA activator (SRA) modification by the human pseudouridine synthase 1 (hPus1p): RNA binding, activity, and atomic model.人假尿苷合酶1（hPus1p）对类固醇受体RNA激活剂（SRA）的修饰：RNA结合、活性及原子模型
PLoS One. 2014 Apr 10;9(4):e94610. doi: 10.1371/journal.pone.0094610. eCollection 2014.
9
The noncoding RNA revolution-trashing old rules to forge new ones.非编码 RNA 革命——打破旧规则，开创新局面。
Cell. 2014 Mar 27;157(1):77-94. doi: 10.1016/j.cell.2014.03.008.
10
Structure and function of steroid receptor RNA activator protein, the proposed partner of SRA noncoding RNA.甾体激素受体 RNA 激活蛋白的结构与功能，SRA 非编码 RNA 的假定伴侣。
J Mol Biol. 2014 Apr 17;426(8):1766-1785. doi: 10.1016/j.jmb.2014.01.006. Epub 2014 Jan 30.
Zotero 插件