Small RNA Modification Array Service

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Arraystar Small RNA Modification Array Service quantifies 8-oxoguanine (o8G), 7-methylguanosine (m7G), N6-methyladenosine (m6A), Pseudouridine (Ψ), or 5-methylcytidine (m5C) modifications in miRNAs, pre-miRNAs, and tRNA-derived small RNAs (tsRNAs, including tRFs and tiRNAs) on a single array.

Benefits

•  Capable of detecting and quantifying a variety of small RNA modifications, including o8G, m7G, m6A, Ψ, or m5C respectively

•  Coverage of multiple small RNA classes, including miRNAs, pre-miRNAs, and tsRNAs (tRFs and tiRNAs)

•  Gold standard for accurate quantification of modified small RNAs
The direct RNA end labeling ensures high fidelity of quantification. Bias-prone reverse transcription or PCR amplification are not required and eliminated. The array probe design fine tunes the probe–target hybridization Tm for optimal sensitivity and specificity. The quantification accuracy is unmatched by other methods.

•  High sensitivity for modified small RNAs at lower levels
Overcome the limitations of small RNA-seq based method, excellent analytical sensitivity for small RNAs at low levels of expression or modification.  

•  Low sample amount required, starting from as little as 1 µg total RNA.

Service NameSpeciesDescriptionFormatPrice
Small RNA Modification Array Service - m6A Human/Mouse Quantify m6A mod of miRNAs, pre-miRNAs, & tsRNAs 8 x 15K
Small RNA Modification Array Service - m7G Human/Mouse Quantify m7G mod of miRNAs, pre-miRNAs, & tsRNAs 8 x 15K
Small RNA Modification Array Service - o8G Human/Mouse Quantify o8G mod of miRNAs, pre-miRNAs, & tsRNAs 8 x 15K
Small RNA Modification Array Service - Ψ Human/Mouse Quantify Ψ mod of miRNAs, pre-miRNAs, & tsRNAs 8 x 15K
Small RNA Modification Array Service - m5C Human/Mouse Quantify m5C mod of miRNAs, pre-miRNAs, & tsRNAs 8 x 15K

Human Small RNA Modification Array V1.0

Total number of distinct probes 14,706
Probe design strategy Whole probe consisting of 5'-cap segment, small RNA specific, and 3'-linker sequences.
Probe-binding sites 5-p-miRNA and 5'tsRNA: 3'-region of the small RNA
3-p-miRNA and 3'tsRNA: 5'-region of the small RNA
Pre-miRNA: Loop region of the pre-miRNA
Probe specificity Small RNA specific
Coverage of miRNAs 2,628 (1,319 5-p-miRNAs and 1,309 3-p-miRNAs )
Coverage of pre-miRNAs 1,745
Coverage of tsRNAs 5,128
Small RNA sources miRNA: miRBase (v22)
pre-miRNA: miRBase (v22)
tsRNA: tRFdb, GtRNADb (Updated to 18.1 2019.08)
Literatures: Scientific publications up to 2019 [1-40]
Array Format 8 x 15K

 

Mouse Small RNA Modification Array V1.0

Total number of distinct probes 14,895
Probe design strategy Whole probe consisting of 5'-cap segment, small RNA specific, and 3'-linker sequences.
Probe-binding sites 5-p-miRNA and 5'tsRNA: 3'-region of the small RNA
3-p-miRNA and 3'tsRNA: 5'-region of the small RNA
Pre-miRNA: Loop region of the pre-miRNA
Probe specificity Small RNA specific
Coverage of miRNAs 1,949 (966 5-p-miRNAs and 983 3-p-miRNAs )
Coverage of pre-miRNAs 1,122
Coverage of TsRNAs 1,809
Small RNA sources miRNA: miRBase (v22)
pre-miRNA: miRBase (v22)
tsRNA: tRFdb, GtRNADb (Updated to 18.1 2019.08)
Literatures: Scientific publications up to 2019 [1-40]
Array Format 8 x 15K

 

References

1.    Guzzi N et al: Pseudouridylation of tRNA-Derived Fragments Steers Translational Control in Stem Cells. Cell 2018, 173(5):1204-1216 e1226.[PMID: 29628141]
2.    Keam SP et al: The human Piwi protein Hiwi2 associates with tRNA-derived piRNAs in somatic cells. Nucleic Acids Res 2014, 42(14):8984-8995.[PMID: 25038252]
3.    Keam SP, Sobala A, Ten Have S, Hutvagner G: tRNA-Derived RNA Fragments Associate with Human Multisynthetase Complex (MSC) and Modulate Ribosomal Protein Translation. J Proteome Res 2017, 16(2):413-420.[PMID: 27936807]
4.    Zhang X et al: IL-4 Inhibits the Biogenesis of an Epigenetically Suppressive PIWI-Interacting RNA To Upregulate CD1a Molecules on Monocytes/Dendritic Cells. J Immunol 2016, 196(4):1591-1603.[PMID: 26755820]
5.    Honda S et al: The biogenesis pathway of tRNA-derived piRNAs in Bombyx germ cells. Nucleic Acids Res 2017, 45(15):9108-9120.[PMID: 28645172]
6.    Cole C et al: Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA 2009, 15(12):2147-2160.[PMID: 19850906]
7.    Sobala A, Hutvagner G: Small RNAs derived from the 5' end of tRNA can inhibit protein translation in human cells. RNA Biol 2013, 10(4):553-563.[PMID: 23563448]
8.    Lee YS, Shibata Y, Malhotra A, Dutta A: A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev 2009, 23(22):2639-2649.[PMID: 19933153]
9.    Huang B et al: tRF/miR-1280 Suppresses Stem Cell-like Cells and Metastasis in Colorectal Cancer. Cancer Res 2017, 77(12):3194-3206.[PMID: 28446464]
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11.  Kim HK et al: A transfer-RNA-derived small RNA regulates ribosome biogenesis. Nature 2017, 552(7683):57-62.[PMID: 29186115]
12.  Kim HK et al: A tRNA-Derived Small RNA Regulates Ribosomal Protein S28 Protein Levels after Translation Initiation in Humans and Mice. Cell Rep 2019, 29(12):3816-3824 e3814.[PMID: 31851915]
13.  Yeung ML et al: Pyrosequencing of small non-coding RNAs in HIV-1 infected cells: evidence for the processing of a viral-cellular double-stranded RNA hybrid. Nucleic Acids Res 2009, 37(19):6575-6586.[PMID: 19729508]
14.  Schorn AJ, Gutbrod MJ, LeBlanc C, Martienssen R: LTR-Retrotransposon Control by tRNA-Derived Small RNAs. Cell 2017, 170(1):61-71 e11.[PMID: 28666125]
15.  Maute RL et al: tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma. Proc Natl Acad Sci U S A 2013, 110(4):1404-1409.[PMID: 23297232]
16.  Ruggero K et al: Small noncoding RNAs in cells transformed by human T-cell leukemia virus type 1: a role for a tRNA fragment as a primer for reverse transcriptase. J Virol 2014, 88(7):3612-3622.[PMID: 24403582]
17.  Falconi M et al: A novel 3'-tRNA(Glu)-derived fragment acts as a tumor-suppressor in breast cancer by targeting nucleolin. FASEB J 2019:fj201900382RR.[PMID: 31560576]
18.  Zhou K et al: A tRNA fragment, tRF5-Glu, regulates BCAR3 expression and proliferation in ovarian cancer cells. Oncotarget 2017, 8(56):95377-95391.[PMID: 29221134]
19.  Goodarzi H et al: Endogenous tRNA-Derived Fragments Suppress Breast Cancer Progression via YBX1 Displacement. Cell 2015, 161(4):790-802.[PMID: 25957686]
20.  Natt D et al: Human sperm displays rapid responses to diet. PLoS Biol 2019, 17(12):e3000559.[PMID: 31877125]
21.  Veneziano D et al: Dysregulation of different classes of tRNA fragments in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A 2019, 116(48):24252-24258.[PMID: 31723042]
22.  Haussecker D et al: Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA 2010, 16(4):673-695.[PMID: 20181738]
23.  Balatti V et al: tsRNA signatures in cancer. Proc Natl Acad Sci U S A 2017, 114(30):8071-8076.[PMID: 28696308]
24.  Cho H et al: Regulation of La/SSB-dependent viral gene expression by pre-tRNA 3' trailer-derived tRNA fragments. Nucleic Acids Res 2019, 47(18):9888-9901.[PMID: 31504775]
25.  Babiarz JE et al: Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev 2008, 22(20):2773-2785.[PMID: 18923076]
26.  Hasler D et al: The Lupus Autoantigen La Prevents Mis-channeling of tRNA Fragments into the Human MicroRNA Pathway. Mol Cell 2016, 63(1):110-124.[PMID: 27345152]
27.  Pekarsky Y et al: Dysregulation of a family of short noncoding RNAs, tsRNAs, in human cancer. Proc Natl Acad Sci U S A 2016, 113(18):5071-5076.[PMID: 27071132]
28.  Liao JY et al: Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex subcellular distribution of miRNAs and tRNA 3' trailers. PLoS One 2010, 5(5):e10563.[PMID: 20498841]
29.  La Ferlita A et al: Identification of tRNA-derived ncRNAs in TCGA and NCI-60 panel cell lines and development of the public database tRFexplorer. Database (Oxford) 2019, 2019.[PMID: 31735953]
30.  Honda S et al: Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers. Proc Natl Acad Sci U S A 2015, 112(29):E3816-3825.[PMID: 26124144]
31.  Donovan J, Rath S, Kolet-Mandrikov D, Korennykh A: Rapid RNase L-driven arrest of protein synthesis in the dsRNA response without degradation of translation machinery. RNA 2017, 23(11):1660-1671.[PMID: 28808124]
32.  Hanada T et al: CLP1 links tRNA metabolism to progressive motor-neuron loss. Nature 2013, 495(7442):474-480.[PMID: 23474986]
33.  Saikia M et al: Angiogenin-cleaved tRNA halves interact with cytochrome c, protecting cells from apoptosis during osmotic stress. Mol Cell Biol 2014, 34(13):2450-2463.[PMID: 24752898]
34.  Wang Q et al: Identification and functional characterization of tRNA-derived RNA fragments (tRFs) in respiratory syncytial virus infection. Mol Ther 2013, 21(2):368-379.[PMID: 23183536]
35.  Deng J et al: Respiratory Syncytial Virus Utilizes a tRNA Fragment to Suppress Antiviral Responses Through a Novel Targeting Mechanism. Mol Ther 2015, 23(10):1622-1629.[PMID: 26156244]
36.  Zhou J et al: Identification of two novel functional tRNA-derived fragments induced in response to respiratory syncytial virus infection. J Gen Virol 2017, 98(7):1600-1610.[PMID: 28708049]
37.  Yang X et al: 5-methylcytosine promotes mRNA export - NSUN2 as the methyltransferase and ALYREF as an m(5)C reader. Cell Res 2017, 27(5):606-625.[PMID: 28418038]
38.  Ivanov P et al: Angiogenin-induced tRNA fragments inhibit translation initiation. Mol Cell 2011, 43(4):613-623.[PMID: 21855800]
39.  Ivanov P et al: G-quadruplex structures contribute to the neuroprotective effects of angiogenin-induced tRNA fragments. Proc Natl Acad Sci U S A 2014, 111(51):18201-18206.[PMID: 25404306]
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The data analysis includes ready-to-use key measurements, useful annotations and publication quality graphics.

Differentially Modified miRNAs, pre-miRNAs, and tsRNAs (tRFs and tiRNAs)

Bioinfo-differential

MatureID:  miRBase ID for the mature miRNA.

Group m7G miRNA level (normalized, log2):  Group averaged, log2 transformed, normalized m7G modified miRNA level, based on the Cy5 signal intensities of the m7G-IP RNA in the sample group.

Treated, Control:  The “treated” and “Control” sample groups.

FC:  The fold change comparing the sample groups.

P:  p-value by t-test, for the statistical significance of the difference.

Regulation: Up- or down-regulation by comparing the sample groups.

Group m7G %modified miRNA: Group averaged percentage of m7G modified miRNA for the sample group. miRNA_family: miRNA family members having the same seed sequence.

m7G_motif: “RAm7GGT” motif sequence of the m7G site, where R represents G or A.

 

Hierarchical clustering heatmap of differentially modified miRNAs, pre-miRNAs, and tsRNAs (tRFs and tiRNAs)

bioinfo-Hierarchical_clustering

Figure 1. Hierarchical clustering heatmap of differentially modified small RNAs. The modified RNA levels are represented by red-blue color scale referenced in the color key on the top left. The top dendrogram shows the relative closeness of the modification profiles among the samples. The sample group membership is indicated by the color bars above the heat map.