Journal
CELL DISCOVERY
Volume 7, Issue 1, Pages -Publisher
SPRINGERNATURE
DOI: 10.1038/s41421-021-00265-2
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Funding
- Ministry of Science and Technology of China (MoST) [2019YFA0801501, 2016YFA0100500]
- National Natural Science Foundation of China [31970687, 31571509, 31522038]
- Shanghai Sailing Plan for the Young Scientific Talents [19YF1434000]
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High-throughput sequencing was used to analyze the landscape of small noncoding RNAs, revealing a large number of previously undetected sRNAs. The study also reported extensive tissue-specific differences in sRNAs by comparing sRNomes from nine mouse tissues. Additionally, the researchers observed changes in sRNomes during hepatic reprogramming, and found that knockdown of a certain type of sRNA promoted this reprogramming process.
High-throughput sequencing reveals the complex landscape of small noncoding RNAs (sRNAs). However, it is limited by requiring 5 '-monophosphate and 3 '-hydroxyl in RNAs for adapter ligation and hindered by methylated nucleosides that interfere with reverse transcription. Here we develop Cap-Clip acid pyrophosphatase (Cap-Clip), T4 polynucleotide kinase (PNK) and AlkB/AlkB(D135S)-facilitated small ncRNA sequencing (CPA-seq) to detect and quantify sRNAs with terminus multiplicities and nucleoside methylations. CPA-seq identified a large number of previously undetected sRNAs. Comparison of sRNAs with or without AlkB/AlkB(D135S) treatment reveals nucleoside methylations on sRNAs. Using CPA-seq, we profiled the sRNA transcriptomes (sRNomes) of nine mouse tissues and reported the extensive tissue-specific differences of sRNAs. We also observed the transition of sRNomes during hepatic reprogramming. Knockdown of mesenchymal stem cell-enriched U1-5 ' snsRNA promoted hepatic reprogramming. CPA-seq is a powerful tool with high sensitivity and specificity for profiling sRNAs with methylated nucleosides and diverse termini.
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