Uli-epic: profiling RNA modifications from ultra-low input samples
High-throughput sequencing with chemical labeling enables robust, transcriptome-wide detection of RNA modifications at single-nucleotide resolution. However, these methods typically require substantial RNA amounts due to harsh treatments. We introduce Uli-epic, an innovative library construction strategy that enables profiling epitranscriptomic modifications using 100 pg to 1 ng of RNA. Utilizing Uli-epic BID-seq, we investigate pseudouridine (Ψ) sites in neural stem cells and sperm RNA from wild-type and fetal growth restriction mice, using only 500 pg of rRNA-depleted RNA. Uli-epic GLORI quantifies m<sup>6</sup>A in sperm and neural stem cells from wild-type and fetal growth restriction mice, using 10 ng of rRNA-depleted RNA.
Authors
- Lulu Hu (ORCID: https://orcid.org/0000-0001-7246-1736)
- Yong Peng (ORCID: https://orcid.org/0000-0001-9562-4622)
- Weizhi He (ORCID: https://orcid.org/0000-0001-6869-4983)
- Shujuan Chang
- Wei‐Guo Zhu (ORCID: https://orcid.org/0000-0001-8385-6581)
- Jiang Xiao (ORCID: https://orcid.org/0000-0002-9519-0622)
- Jiuhong Kang (ORCID: https://orcid.org/0000-0001-7538-1889)
- Yu Wang (ORCID: https://orcid.org/0000-0001-7288-9150)
- Wen Chen (ORCID: https://orcid.org/0000-0001-7154-1750)
- Chu Xu
Institutions
- Shanghai Medical College of Fudan University (CN)
- Fudan University (CN)
- Fudan University Shanghai Cancer Center (CN)
- Shanghai FRP Research Institute (China) (CN)
- Shanghai First Maternity and Infant Hospital (CN)
- Chengdu University of Traditional Chinese Medicine (CN)
Publication Details
- Journal
- Genome biology
- Published
- 2025-11-11
- DOI
- https://doi.org/10.1186/s13059-025-03857-3
- Primary Topic
- RNA modifications and cancer
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Natural Science Foundation of China
- Fudan University
- Science and Technology Commission of Shanghai Municipality
- Shanghai Medical College, Fudan University