GEO series
Absolute quantitative and base-resolution sequencing reveals comprehensive landscape of pseudouridine across the human transcriptome
GSE241849
Homo sapiens; Mus musculus
Other; Expression profiling by high throughput sequencing
54 samples
Submitted 2024/07/31
Platform GPL30173Platform GPL30172
Summary
Pseudouridine (Ψ) is one of the most abundant modifications in cellular RNA. However, its function remains elusive, mainly due to the lack of highly sensitive and accurate detection methods. To address this challenge, we introduced 2-bromoacrylamide-assisted cyclization sequencing (BACS) for quantitative profiling of Ψ at single-base resolution. Based on novel bromoacrylamide cyclization chemistry, BACS enables a Ψ-to-C transition. Compared to previous methods, BACS allowed the precise identification of Ψ positions, especially in densely modified Ψ regions and consecutive uridine sequences. BACS successfully detected all known Ψ sites in human rRNA and spliceosomal snRNAs and generated the first quantitative Ψ map of human snoRNA and tRNA. Furthermore, BACS simultaneously detected adenosine-to-inosine (A-to-I) editing sites and N1-methyladenosine (m1A). Depletion of three key pseudouridine synthases (PUS) enabled us to elucidate the targets and sequence motifs of TRUB1, PUS7, and PUS1 in HeLa cells. We further applied BACS to Epstein-Barr virus (EBV)-encoded small RNAs (EBERs) and identified a highly abundant Ψ114 site in EBER2. Surprisingly, applying BACS to a panel of RNA viruses demonstrated the absence of Ψ in their viral transcripts or genomes, shedding light on differences in pseudouridylation between virus families. We anticipate BACS to serve as a powerful tool to uncover the biological importance of Ψ in future studies.
Published in
Xu H, Kong L, Cheng J et al.
· Nature methods 2024
· PMID 39349603
· doi:10.1038/s41592-024-02439-8
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE241849_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 54 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1010332 and SRA study SRP457352. Searching any of these in the dataset finder brings you back here.
Study design
15 conditions, mostly in duplicate
TRUB1_BACS ×3
TRUB1_control ×3
HeLa_total_RNA_BACS ×2
HeLa_total_RNA_control ×2
HeLa_ribo–_BACS ×2
HeLa_ribo–_control ×2
HeLa_polyA+_BACS ×2
HeLa_polyA+_control ×2
+15 more
Supports a between-group comparison across 32 samples.
15 replicated groups read from the first 40 of 54 sample titles; they account for 32 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM7979758 HeLa_total_RNA_BACS_spike in_0%
- GSM7979759 HeLa_total_RNA_BACS_spike in_25%
- GSM7979760 HeLa_total_RNA_BACS_spike in_50%
- GSM7979761 HeLa_total_RNA_BACS_spike in_75%
- GSM7979762 HeLa_total_RNA_BACS_rep1
- GSM7979763 HeLa_total_RNA_BACS_rep2
- GSM7979764 HeLa_total_RNA_control_rep1
- GSM7979765 HeLa_total_RNA_control_rep2
- GSM7979766 HeLa_ribo–_BACS_rep3
- GSM7979767 HeLa_ribo–_BACS_rep4
- GSM7979768 HeLa_ribo–_control_rep3
- GSM7979769 HeLa_ribo–_control_rep4
- GSM7979770 HeLa_polyA+_BACS_rep1
- GSM7979771 HeLa_polyA+_BACS_rep2
- GSM7979772 HeLa_polyA+_control_rep1
- GSM7979773 HeLa_polyA+_control_rep2
- GSM7979774 IVT_BACS_rep1
- GSM7979775 IVT_BACS_rep2
- GSM7979776 PUS7_BACS_rep1
- GSM7979777 PUS7_BACS_rep2
- GSM7979778 PUS1_BACS_rep1
- GSM7979779 PUS1_BACS_rep2
- GSM7979780 PUS7_control_rep1
- GSM7979781 PUS7_control_rep2
- GSM7979782 PUS1_control_rep1
- GSM7979783 PUS1_control_rep2
- GSM7979784 TRUB1_BACS_rep1
- GSM7979785 TRUB1_BACS_rep2
- GSM7979786 TRUB1_BACS_rep3
- GSM7979787 TRUB1_control_rep1
- GSM7979788 TRUB1_control_rep2
- GSM7979789 TRUB1_control_rep3
- GSM7979790 C666.1_BACS_rep1
- GSM7979791 C666.1_BACS_rep2
- GSM7979792 C666.1_control_rep1
- GSM7979793 C666.1_control_rep2
- GSM7979794 Raji_BACS
- GSM7979795 Raji_control
- GSM7979796 Elijah_BACS
- GSM7979797 Elijah_control
+ 14 more — browse all 54 samples with per-sample file links →
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