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Series GSE121927 Query DataSets for GSE121927
Status Public on Oct 30, 2018
Title Detection of internal N7-methylguanosine (m7G) RNA modifications by mutational profiling sequencing
Organisms Escherichia coli; Arabidopsis thaliana; Saccharomyces cerevisiae; Homo sapiens
Experiment type Other
Summary Methylation of guanosine on position N7 (m7G) on internal RNA positions have been found in all domains of life and have been implicated in human disease, but m7G modifications has so far only been mapped in a limited number of RNA molecules. Here, we present m7G Mutational Profiling sequencing (m7G-MaP-seq), which allows high throughput detection of m7G modifications. In our method, m7G modified positions are converted to abasic sites by mild reduction, recorded as cDNA mutations through reverse transcription, sequenced and subsequently detected by identification of positions with increased mutation rates in the reduced sample compared to the control. We show that m7G-MaP-seq efficiently detects m7G modifications in rRNA, including a previously uncharacterised rRNA modification in Arabidopsis thaliana. Furthermore, we identify m7G tRNA modifications in budding yeast, human and arabidopsis tRNA and show that m7G modification occurs before tRNA splicing. We do not find any evidence for internal m7G modifications being present in other small RNA, such as miRNA, snoRNA and sRNA. Likewise, high coverage m7G-MaP-seq analysis of mRNA from E. coli or yeast cells failed to identify any internal m7G modifications.
Overall design RNA from E. coli (strain BW25113 and RsmG KO), Saccharomyces cerevisiae (BY4741), HeLa, Arabidopsis Thaliana Columbia-0 . The RNA was treated with NaBH4 or mock-treated, then reverse transcribed.
Contributor(s) Enroth C, Poulsen LD, Iversen S, Albrechtsen A, Vinther J
Citation(s) 31504776
Submission date Oct 29, 2018
Last update date Mar 11, 2021
Contact name Jeppe Vinther
Organization name University of Copenhagen
Department Biology
Lab Vinther Lab
Street address Ole Maaloes Vej 5
City Copenhagen N
ZIP/Postal code DK-2200
Country Denmark
Platforms (7)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13222 Illumina HiSeq 2000 (Arabidopsis thaliana)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
Samples (44)
GSM3450047 E. coli-WT-untreated-total RNA
GSM3450048 E. coli-WT-NaBH4 treated-total RNA
GSM3450049 E. coli-RsmG KO-untreated-total RNA
BioProject PRJNA499084
SRA SRP167149

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE121927_ara_wt_rrna_out.txt.gz 248.8 Kb (ftp)(http) TXT
GSE121927_arabidopsis_tRNA_out.txt.gz 567.0 Kb (ftp)(http) TXT
GSE121927_coli_mrna_rrna_out.txt.gz 53.9 Mb (ftp)(http) TXT
GSE121927_hela_wt_rrna_out.txt.gz 243.6 Kb (ftp)(http) TXT
GSE121927_human_tRNA_out.txt.gz 750.6 Kb (ftp)(http) TXT
GSE121927_srsmg_coli_out.txt.gz 8.4 Mb (ftp)(http) TXT
GSE121927_swt_coli_out.txt.gz 9.1 Mb (ftp)(http) TXT
GSE121927_yeast_mrna_rrna_out.txt.gz 106.1 Mb (ftp)(http) TXT
GSE121927_yeast_tRNA_out.txt.gz 273.1 Kb (ftp)(http) TXT
GSE121927_yeast_wt_rrna_out.txt.gz 377.1 Kb (ftp)(http) TXT
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