通过高通量测序发现细菌小RNA
Discovery of bacterial sRNAs by high-throughput sequencing.
作者信息
Liu Jane M, Camilli Andrew
机构信息
Howard Hughes Medical Institute and Tufts University School of Medicine, Boston, MA, USA.
出版信息
Methods Mol Biol. 2011;733:63-79. doi: 10.1007/978-1-61779-089-8_5.
Abstract
sRNA-Seq is an unbiased method that allows for the discovery of small noncoding RNAs in bacterial transcriptomes through direct cloning and massively parallel sequencing by synthesis. Small bacterial transcripts are enriched from a total RNA preparation and modified with 5' and 3' linkers that allow for downstream amplification and sequencing. This protocol includes a treatment that depletes small RNA fractions of tRNAs and 5S rRNA, thereby enriching the starting pool for non-tRNA/rRNA sequences. This protocol can be readily modified to target different RNA species for depletion or to change the size range of RNAs to be sequenced. Thus, sRNA-Seq represents a comprehensive, versatile cloning protocol that may be applicable to the cloning of small RNAs of any size range from any organisms.
摘要
小RNA测序是一种无偏差的方法，可通过直接克隆和大规模平行合成测序在细菌转录组中发现小非编码RNA。从小RNA制备物中富集细菌小转录本，并用5'和3'接头进行修饰，以便进行下游扩增和测序。该方案包括一种去除tRNA和5S rRNA小RNA组分的处理，从而富集非tRNA/rRNA序列的起始文库。该方案可以很容易地进行修改，以靶向不同的RNA种类进行去除，或改变要测序的RNA的大小范围。因此，小RNA测序代表了一种全面、通用的克隆方案，可能适用于克隆来自任何生物体的任何大小范围的小RNA。
相似文献
1
Discovery of bacterial sRNAs by high-throughput sequencing.通过高通量测序发现细菌小RNA
Methods Mol Biol. 2011;733:63-79. doi: 10.1007/978-1-61779-089-8_5.
2
Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing.通过直接克隆、5S/tRNA 去除和平行测序对霍乱弧菌中小RNA的实验发现
Nucleic Acids Res. 2009 Apr;37(6):e46. doi: 10.1093/nar/gkp080. Epub 2009 Feb 17.
3
SPORTS1.0: A Tool for Annotating and Profiling Non-coding RNAs Optimized for rRNA- and tRNA-derived Small RNAs.SPORTS1.0：一种针对 rRNA 和 tRNA 衍生的小 RNA 进行注释和分析的非编码 RNA 工具。
Genomics Proteomics Bioinformatics. 2018 Apr;16(2):144-151. doi: 10.1016/j.gpb.2018.04.004. Epub 2018 May 3.
4
APERO: a genome-wide approach for identifying bacterial small RNAs from RNA-Seq data.APERO：一种从 RNA-Seq 数据中识别细菌小 RNA 的全基因组方法。
Nucleic Acids Res. 2019 Sep 5;47(15):e88. doi: 10.1093/nar/gkz485.
5
Disentangling sRNA-Seq data to study RNA communication between species.解析 sRNA-Seq 数据以研究物种间的 RNA 通讯。
Nucleic Acids Res. 2020 Feb 28;48(4):e21. doi: 10.1093/nar/gkz1198.
6
Mapping the small RNA interactome in bacteria using RIL-seq.利用 RIL-seq 绘制细菌中的小 RNA 相互作用组。
Nat Protoc. 2018 Jan;13(1):1-33. doi: 10.1038/nprot.2017.115. Epub 2017 Dec 7.
7
Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies.利用新技术加速小分子 RNA 的发现和功能分析。
Annu Rev Genet. 2015;49:367-94. doi: 10.1146/annurev-genet-112414-054804. Epub 2015 Oct 14.
8
Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data.通过 RNA 测序数据分析的生物信息学分析鉴定链球菌的小 RNA 作为 RNase III 的潜在靶标。
BMC Bioinformatics. 2017 Dec 28;18(Suppl 14):540. doi: 10.1186/s12859-017-1897-0.
9
Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032.谷氨酸棒杆菌ATCC 13032中小RNA的全面发现与表征
BMC Genomics. 2013 Oct 19;14(1):714. doi: 10.1186/1471-2164-14-714.
10
Identification of unknown RNA partners using MAPS.使用MAPS鉴定未知RNA伴侣。
Methods. 2017 Mar 15;117:28-34. doi: 10.1016/j.ymeth.2016.11.011. Epub 2016 Nov 19.
引用本文的文献
1
Devising Isolation Forest-Based Method to Investigate the sRNAome of Using sRNA-seq Data.设计基于孤立森林的方法以利用小RNA测序数据研究小RNA组。
Bioinform Biol Insights. 2024 Jul 30;18:11779322241263674. doi: 10.1177/11779322241263674. eCollection 2024.
2
Genome-wide screen and functional analysis in Xanthomonas reveal a large number of mRNA-derived sRNAs, including the novel RsmA-sequester RsmU.在黄单胞菌中进行全基因组筛选和功能分析，揭示了大量的 mRNA 衍生的小 RNA，包括新型 RsmA 结合物 RsmU。
Mol Plant Pathol. 2020 Dec;21(12):1573-1590. doi: 10.1111/mpp.12997. Epub 2020 Sep 23.
3
Prevalence of small base-pairing RNAs derived from diverse genomic loci.来源于不同基因组位置的小碱基配对 RNA 的流行。
Biochim Biophys Acta Gene Regul Mech. 2020 Jul;1863(7):194524. doi: 10.1016/j.bbagrm.2020.194524. Epub 2020 Mar 5.
4
Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032.谷氨酸棒杆菌ATCC 13032中小RNA的全面发现与表征
BMC Genomics. 2013 Oct 19;14(1):714. doi: 10.1186/1471-2164-14-714.
5
A systematic comparison and evaluation of high density exon arrays and RNA-seq technology used to unravel the peripheral blood transcriptome of sickle cell disease.系统比较和评价高密度外显子芯片和 RNA-seq 技术用于揭示镰状细胞病外周血转录组。
BMC Med Genomics. 2012 Jun 29;5:28. doi: 10.1186/1755-8794-5-28.
本文引用的文献
1
Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing.通过直接克隆、5S/tRNA 去除和平行测序对霍乱弧菌中小RNA的实验发现
Nucleic Acids Res. 2009 Apr;37(6):e46. doi: 10.1093/nar/gkp080. Epub 2009 Feb 17.
2
Small toxic proteins and the antisense RNAs that repress them.小毒性蛋白以及抑制它们的反义RNA。
Microbiol Mol Biol Rev. 2008 Dec;72(4):579-89, Table of Contents. doi: 10.1128/MMBR.00025-08.
3
Noncoding RNA control of the making and breaking of sugars.非编码RNA对糖类合成与分解的调控
Genes Dev. 2008 Nov 1;22(21):2914-25. doi: 10.1101/gad.1717808.
4
Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence.鼠伤寒沙门氏菌基因岛编码的小RNA表现出宿主诱导表达及其在毒力中的作用。
Nucleic Acids Res. 2008 Apr;36(6):1913-27. doi: 10.1093/nar/gkn050. Epub 2008 Feb 11.
5
Mechanism of RNA silencing by Hfq-binding small RNAs.Hfq结合小RNA介导的RNA沉默机制。
Curr Opin Microbiol. 2007 Apr;10(2):134-9. doi: 10.1016/j.mib.2007.03.010. Epub 2007 Mar 26.
6
Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans.大规模测序揭示了秀丽隐杆线虫中的21U-RNA以及其他微小RNA和内源性小干扰RNA。
Cell. 2006 Dec 15;127(6):1193-207. doi: 10.1016/j.cell.2006.10.040.
7
The role of RNAs in the regulation of virulence-gene expression.RNA在毒力基因表达调控中的作用。
Curr Opin Microbiol. 2006 Apr;9(2):229-36. doi: 10.1016/j.mib.2006.02.005. Epub 2006 Mar 10.
8
Micros for microbes: non-coding regulatory RNAs in bacteria.微生物的微型分子：细菌中的非编码调控RNA
Trends Genet. 2005 Jul;21(7):399-404. doi: 10.1016/j.tig.2005.05.008.
9
Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli.大肠杆菌中5'-和3'-非翻译区衍生的小RNA和顺式编码反义RNA的检测
Nucleic Acids Res. 2005 Feb 17;33(3):1040-50. doi: 10.1093/nar/gki256. Print 2005.
10
6S RNA regulates E. coli RNA polymerase activity.6S RNA调节大肠杆菌RNA聚合酶的活性。
Cell. 2000 Jun 9;101(6):613-23. doi: 10.1016/s0092-8674(00)80873-9.
Zotero 插件