• Create Time: 2022-06-17
• Update Time: 2022-06-17

Abstract

RNA is often altered post-transcriptionally by the covalent modification of particular nucleotides; these modifications are known to modulate the structure and activity of their host RNAs. The recent discovery that an RNA methyl-6 adenosine demethylase (FTO) is a risk gene in obesity has brought to light the significance of RNA modifications to human biology. These noncanonical nucleotides, when converted to cDNA in the course of RNA sequencing, can produce sequence patterns that are distinguishable from simple base-calling errors. To determine whether these modifications can be detected in RNA sequencing data, we developed a method that can not only locate these modifications transcriptome-wide with single nucleotide resolution, but can also differentiate between different classes of modifications. Using small RNA-seq data we were able to detect 92% of all known human tRNA modification sites that are predicted to affect RT activity. We also found that different modifications produce distinct patterns of cDNA sequence, allowing us to differentiate between two classes of adenosine and two classes of guanine modifications with 98% and 79% accuracy, respectively. To show the robustness of this method to sample preparation and sequencing methods, as well as to organismal diversity, we applied it to a publicly available yeast data set and achieved similar levels of accuracy. We also experimentally validated two novel and one known 3-methylcytosine (3mC) sites predicted by HAMR in human tRNAs. Researchers can now use our method to identify and characterize RNA modifications using only RNA-seq data, both retrospectively and when asking questions specifically about modified RNA.

收获

1. 知道了Ternary Plot到底怎么看。

2. 文章中的结果其实也可以跟参考文献，就是一些很普遍的结果，可以提到这个和什么之前的研究相符。

3. 当出现假阳性的结果，还用CNV的数据库来进行了说明。

4. 提供了一些detectable的modifications，我们可以根据这个list来做后续的研究。

感想

这篇文章算是很老的了，但是我仍旧觉得有必要读一下，因为最近也想做一个类似的东西出来，所以还是要找一些相关的文献进行了解。不知道是什么原因，文章中的结果都是tRNA的结果，虽说也用到了whole-transcriptome RNA-seq的数据，但是仍旧是针对与small-RNA来做的研究。

按理说，这个软件应该可以针对于whole-transcriptome来做计算的，所以我打算用这个HAMR来试一下，看看能不能在whole-transcriptome上做计算。

新词