Uli-Epic: A cutting-edge library construction strategy for profiling ultra-limited RNA modifications [Uli-Epic GLORI]

RNA modifications have important function in nearly every aspect of RNA biology. Epitranscriptome RNA modifications detected by high-throughput sequencing technologies is critical for understanding the distribution, regularity, stoichiometry, function of RNA modifications. One of disadvantages about these high-throughput sequencing technologies is needing high-input RNA. Here we use poly(A) tailing, template switching by reverse transcription during DNA synthesis and in vitro transcription (IVT) to develop a cutting-edge library construction strategy for profiling ultra-limited RNA modifications (Uli-Epic). We apply Uli-Epic for RNA-seq using 100 pg of poly A+ RNA. We also apply Uli-Epic to combine with BID-seq to characterize dynamics of pseudouridine in neural stem cells (NSC) and sperm under normal and fetal growth restriction (FGR) mice using as low as 100 pg of rRNA-depleted RNA. In addition, we combined Uli-Epic and GLORI to quantify the m6A methylomes of sperm and NSC under normal and FGR mice using 10ng of rRNA-depleted RNA. Summary, Uli-Epic is a strand-specific, high throughput and low input RNA library construction strategy which is compatible with many RNA modifications detected technologies. Overall design: m6A detection by bulk GLORI and Uli-epic GLORI in HEK293T mRNA. m6A detection by Uli-epic GLORI in ribominus RNA of mouse sperm and NSC