Print |

You have not viewed any products recently.


Small RNA Modifications

The Challenges and Solutions of Studying Modified Small RNAs



Small RNA Modifications: Integral to Functions and Diseases

Molecular Mechanisms of Small RNA Modifications

The Challenges and Solutions of Studying Modified Small RNAs


Profiling small RNA modifications is a key step in studying the increasingly important epitranscriptomics of the small RNA classes. However, not until recently, the methodologies and techniques were lacking or very limited in capabilities. With the new innovative array based technologies, the high throughput, sensitive, accurate, and modification stoichiometry capable small RNA profiling is now available to biological and clinical research labs to advance the new study of small RNA epitranscriptomics and clinical applications.


The challenges of profiling small RNA modifications

Although sequencing has been used for small RNA profiling, the influence of RNA modifications on the sequencing quantification has largely been ignored. Various RNA modifications, such as m1A, m3C and m1G, do interfere with the reverse transcription reaction during sequencing library construction, thereby making accurate quantification of small RNAs and especially their modifications impossible. For example, the presence of m1A in the TΨC loop blocks the proceeding of reverse transcriptase during cDNA synthesis. Most of the small RNA sequencing data were obtained using the library construction methods above. Consequently, the data could be misleading for modified small RNAs.

Also, small RNA profiling by small RNA-seq requires multiple PCR amplification steps, which incurs significant quantification bias/inaccuracies and therefore necessitates the use of independent, orthogonal methodologies.

In practice, most sequencing based method for modification studies requires large amount of input materials (> 100 ug total RNA), precluding many studies with only limited sample amounts.

Furthermore, small RNA-seq commonly uses Reads Per Million RNA reads (RPM) for normalization and to represent the relative RNA abundances in the sample. However, RPM depends on the composition of the small RNA population in a sample. A change in one small RNA’s RPM will adjust all the other small RNAs’ values even their actual absolute expression levels are not changed.

In order to identify and quantify the full spectrum of modified-small RNAs with high sensitivity and accurate stoichiometry, there is a need for overcoming the limitations of the sequencing-based approaches and developing non-sequencing-based methods.


Techniques to quantify small RNA post-transcriptional modifications

Arraystar small RNA modification profiling technology (Fig. 1) combines small RNA microarray with RNA immunoprecipitation (RIP) to simultaneously measure the modified and unmodified small RNA levels on the same array, providing the vital information to study regulatory impacts of the modification in small RNAs, including miRNA, pre-miRNA, and tsRNA (tRF and tiRNA) classes.


Figure 1. Arraystar small RNA modification profiling technology to identify and quantify small RNA post-transcriptional modifications, O8G, m7G, m6A, pseudouridine, and m5C respectively. Modified small RNAs are enriched by immunoprecipitation using a specific antibody, and then identified and quantified by using Arraystar small RNA modification microarray.


Related Service

Small RNA Modification Array Service


Back to news

Publications >>

Circular RNA Array
Zhong GL, et al. (2023) Molecular Cancer 

[PMID: 37004067] 

m6A Single Nucleotide Array
Yan W, et al. (2023) International Journal of Oral Science

[PMID: 36631441] 

LC-MS Based RNA Modification Analysis
 Li G, et al. (2023) Nature Microbiology 

[PMID: 37563288]


Promotions >>

NGS Promo: At Least 30% OFF 
microRNA Seq & RNA Seq
From Sample to Ready-to-publish Data

Save now>>


Brochures >> 

Arraystar Small RNA Array
miRNA, pre-miRNA, tRNA, tsRNA, snoRNA

The new way of sensitive, accurate, simultaneous profiling of major small RNA classes




Webinars >>

​​The Latest Highlights on CircRNA in Cancer


Watch video

New Discoveries in m6A Epitranscriptomics


Watch video

Raising the Bar of Multi-transcrptomic Profiling of Small RNAs


Watch video

Extrachromosomal Circular DNAs NEW!
- The extraordinary eccDNAs in cancer and diseases 


Watch video