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NuRNA™ Human Epitranscriptomics PCR Array AS-NM-003-1 384 (4x96)-well plate $435.00
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NuRNA™ Human Epitranscriptomics PCR Array (Roche Light Cycler 480) AS-NM-003-1-R 384 (4x96)-well plate $435.00
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Recent major breakthroughs in RNA modification mediated gene regulation have led to the emerging field of epitranscriptomics. mRNAs are internally and dynamically decorated with modifications such as N6-methyladenosine (m6A), 5-methylcytidine (m5C), inosine (I), pseudouridine (ψ), N1-methyladenosine (m1A) and 5-hydroxylmethylcytidine (hm5C), having regulatory impact on the functions and metabolism of the mRNAs [1] (Fig. 1). These epitranscriptomic marks are written, read and erased by enzymatic or protein factors/complexes. Their dysregulation and mutations are linked to a rapidly growing list of human diseases and disorders. Research in their epitranscriptomics is advancing rapidly (Table 1).

mRNA_modifications_and_proteins-1

Figure 1. mRNA modifications and their functions.

Table 1. Human mRNA modifier and reader proteins [1-4]

  m6A m5C I ψ m1A
Writers KIAA1429
METTL3
METTL4
METTL14
RBM15
RBM15B
WTAP
NSUN2
TRDMT1
ADAR
ADARB1
ADARB2
DKC1
PUS1
PUS3
PUS7
TRUB1
N.D.
Erasers ALKBH5
FTO
TET1
TET2
TET3
N.D. N.D. ALKBH1
ALKBH3
 
Readers YTH Family
eIF3 complex
HNRNPA2B1
HNRNPC        
SRSF2
N.D. N.D. N.D. N.D.

* N.D., Not determined

m6A is the most abundant internal mRNA modification in eukaryotes. It affects mRNA secondary structure, accessibility of binding-protein complexes, mRNA splicing events, mRNA maturation, nuclear export, translation, and sorting into a fast track for mRNA metabolism. m6A modification is catalyzed by a methyltransferase complex as the “writer”, which contains at least METTL3, METTL14 and WTAP. The installed m6A epitranscriptomic mark is recognized by multiple m6A-specific binding proteins such as YTHDF1 and YTHDF2 as the “readers”, which affect the functions and the metabolism of the m6A-marked mRNAs in various ways. m6A can be demethylated and removed by FTO and ALKBH5 as the “erasers”. The dynamic regulation of m6A is fundamentally important in the epitranscriptomic control of meiosis and pluripotency [5]. m6A is often elevated in cancer stem cells, which up-regulates key oncoproteins such as EGFR, confers a proliferative selection advantage, promotes neoplastic evolution and ultimately results in poorer cancer prognosis. Not surprisingly, m6A writer METTL3 [6] and erasers FTO [7] and ALKBH5 [8] are closely involved in cancer progression. Besides the regulatory roles in mammalian cells, m6A can also be installed on viral RNAs and influence viral infection and production. 

The dynamics of RNA modifications, their writers, readers and erasers is apparently critical, but still poorly understood, in gene regulation. To quickly and conveniently profile the expression of epitranscriptomic writers, readers and erasers, Arraystar has produced the first commercial PCR panel specially designed for profiling the epitranscriptional factors. The panel contains mRNA transcript expression qPCR assays for 89 enzymes or proteins validated or predicted in post-transcriptional mRNA modifications, compiled from research publications and authoritative databases including UniProt and Modomics. Each qPCR assay on the panel is rigorously validated across numerous tissues and cell lines. The included Spike-in control, Positive PCR Control, Genomic DNA Control and normalization references ensure the upmost data quality and accuracy.

Combined with data such as high-throughput LC-MS/MS modification profiling and next-gen sequencing modification mapping, the array helps to uncover the functional implications of epitranscriptomic marks in gene regulation and the link to biological processes and human diseases.

References

1. Gilbert, W. V., et al. (2016) Messenger RNA modifications: Form, distribution, and function. Science, 352(6292):1408-12 [PMID: 27313037]
2. Li, X., et al. (2016) Epitranscriptome sequencing technologies: decoding RNA modifications. Nat Methods, 14(1):23-31 [PMID: 28032622]
3. Li, X., et al. (2016) Pseudouridine: the fifth RNA nucleotide with renewed interests. Curr Opin Chem Biol, 33(108-16 [PMID: 27348156]
4. Machnicka, M. A., et al. (2013) MODOMICS: a database of RNA modification pathways--2013 update. Nucleic Acids Res, 41(Database issue):D262-7 [PMID: 23118484]
5. Klungland, A., et al. (2016) Reversible RNA modifications in meiosis and pluripotency. Nat Methods, 14(1):18-22 [PMID: 28032624]
6. Lin, S., et al. (2016) The m(6)A Methyltransferase METTL3 Promotes Translation in Human Cancer Cells. Mol Cell, 62(3):335-45 [PMID: 27117702]
7. Iles, M. M., et al. (2013) A variant in FTO shows association with melanoma risk not due to BMI. Nat Genet, 45(4):428-32, 432e1 [PMID: 23455637]
8. Zhang, C., et al. (2016) Hypoxia induces the breast cancer stem cell phenotype by HIF-dependent and ALKBH5-mediated m(6)A-demethylation of NANOG mRNA. Proc Natl Acad Sci U S A, 113(14):E2047-56 [PMID: 27001847]

89 Transcripts corresponding to Human mRNA Modification Enzymes/Proteins (identified or predicted)

m6A enzymes/proteins

Writers: KIAA1429, METTL14, METTL3, METTL4, RBM15, RBM15B, WTAP
Readers: DGCR8, EIF3A, EIF3B, ELAVL1, HNRNPA2, HNRNPB1, HNRNPC1, HNRNPC2, SRSF2, YTHDC1, YTHDC2, YTHDF1, YTHDF2, YTHDF3
Erasers: ALKBH5, FTO

m1A enzymes/proteins

Writers: HSD17B10, KIAA0391, TRMT10C, TRMT6, TRMT61A, TRMT61B
Erasers: ALKBH1, ALKBH3

m5C enzymes/proteins

Writers: DNMT1 , DNMT3A, DNMT3B, DNMT3L, NOP2, NSUN2, NSUN3, NSUN4, NSUN5, TRDMT1
Readers: MECP2, UHRF1
Erasers: TET1, TET2, TET3

hm5C enzymes/proteins

Writers: TET1, TET2, TET3
Readers: CHTOP, EGR1, ERH, HMCES, MEP50, MGME1, NEIL1, PRMT1, PRMT5, SMUG1, TDG, THYN1, WDR76, WT1

Inosine enzymes/proteins

Writers: ADAD1, ADAD2, ADAR, ADARB1, ADARB2, ADAT1, ADAT2, ADAT3

Pseudouridine enzymes/proteins

Writers: DKC1, GAR1, NAF1, NHP2, NOP10, PUS1, PUS10, PUS3, PUS7, PUS7L, PUSL1, RPUSD1, RPUSD2, RPUSD3, RPUSD4, TRUB1, TRUB2

Other modifications (m7G) enzymes/proteins

CMTR1, CMTR2, RNGTT, RNMT

• Epitranscriptomic regulation - An exciting new field of gene regulation extending beyond genomics, epigenomics and transcriptomics.
• Best contents – Comprehensively covers all the validated mRNA modification enzymes and protein factors in scientific publications, UniProt and Modomics.
• Representative transcript chosen – detect mRNA transcript that codes the canonical protein/subunit sequence in Uniprot.
• Comprehensive annotation – Connect mRNA transcripts to the corresponding genes and functional proteins or protein subunits by integrating genome/transcriptome data with protein UniProt annotations.
• Performance – All primer pairs and assays are highly optimized and rigorously validated for accurate and instant results. 
• Convenient – Easy-to-use plate format for common qPCR systems. Obtain results in hours.
 

 

AS-NM-003-overview-protocol

Compatible qPCR Instruments:

ABI ViiA™ 7
ABI 7500 & ABI 7500 FAST
ABI 7900HT
ABI QuantStudio™ 6 Flex Real-Time PCR system
ABI QuantStudio™ 7 Flex Real-Time PCR system
ABI QuantStudio™ 12K Flex Real-Time PCR System
Bio-Rad CFX384
Bio-Rad iCycler & iQ Real-Time PCR Systems
Eppendorf Realplex
QIAGEN Rotor Gene Q 100
Roche Light Cycler 480
Stratagene Mx3000
Roche Light Cycler 480