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Series GSE112276 Query DataSets for GSE112276
Status Public on Apr 26, 2019
Title Transcriptome Mapping of Internal N7-methylguanosine Methylome in Mammalian mRNA
Organisms Homo sapiens; Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary N7-methylguanosine (m7G) is a positively charged, essential modification at the 5′ cap of eukaryotic mRNA, regulating mRNA export, translation, and splicing. m7G also occurs internally within tRNA and rRNA, but its existence and distribution within eukaryotic mRNA remain to be investigated. Here, we show the presence of internal m7G sites within mammalian mRNA. We then performed transcriptome-wide profiling of internal m7G methylome using m7G-MeRIP sequencing (MeRIP-seq). To map this modification at base resolution, we developed a chemical-assisted sequencing approach that selectively converts internal m7G sites into abasic sites, inducing misincorporation at these sites during reverse transcription. This base-resolution m7G-seq enabled transcriptome-wide mapping of m7G in human tRNA and mRNA, revealing distribution features of the internal m7G methylome in human cells. We also identified METTL1 as a methyltransferase that installs a subset of m7G within mRNA and showed that internal m7G methylation could affect mRNA translation.
Overall design [dataset 1] 12 samples. Duplicates for PAR-CLIP of METTL1 and WDR4 in HeLa cell line. Duplicates for PAR-CLIP of eIF4E, RNMT, METTL1 and WDR4 in HEK293T cell line.
[dataset 2] 8 samples. Duplicates for Ribo-Seq samples, mRNA input and ribosome-bound RNA of siControl vs siMETTL1 in HeLa cell.
[dataset 3] 46 samples. Duplicates for m7G-seq of small RNA (<200 nt) and mRNA samples, including three sections of RNA input, before_pulldown, and pulldown in HeLa, HepG2, and HEK293T cell lines.
[dataset 4] 38 samples. Duplicates for m7G-MeRIP-seq (anti-m7G antibody, MBL) of cell mRNA samples, including two sections of RNA input and IP in HeLa, HepG2, HEK293T, MEF and mESC wild-type cell lines; also in HeLa cell siControl vs siMETTL1, and HepG2 cell shControl vs shMETTL1.
Contributor(s) Zhang L, Liu C, He C
Citation(s) 31031084
NIH grant(s)
Grant ID Grant title Affiliation Name
RM1 HG008935 Center for dynamic RNA epitranscriptomes UNIVERSITY OF CHICAGO CHUAN HE
Submission date Mar 23, 2018
Last update date Mar 16, 2023
Contact name Li-Sheng Zhang
Phone (852) 3469 2392
Organization name The University of Chicago
Department Department of Chemistry
Lab Prof. Chuan He Lab
Street address 929 E 57th St Rm E313
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
Platforms (3)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (104)
GSM3069536 HEK293T-eIF4E-PARCLIP1 (dataset 1)
GSM3069537 HEK293T-eIF4E-PARCLIP2 (dataset 1)
GSM3069538 HEK293T-RNMT-PARCLIP1 (dataset 1)
BioProject PRJNA445453
SRA SRP136352

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

Supplementary file Size Download File type/resource
GSE112276_22_sites_of_internal_m7G_in_tRNAs.xlsx 106.3 Kb (ftp)(http) XLSX
GSE112276_49_sites_of_internal_m7G_in_mRNA_with_high_estimated_methylation_status.xlsx 13.8 Kb (ftp)(http) XLSX
GSE112276_HEK293T_HighFC.txt.gz 176.1 Kb (ftp)(http) TXT
GSE112276_HeLa_HighFC.txt.gz 169.1 Kb (ftp)(http) TXT
GSE112276_HeLa_HighFC_m6A.txt.gz 326.7 Kb (ftp)(http) TXT
GSE112276_HeLa_OverallFC.txt.gz 431.1 Kb (ftp)(http) TXT
GSE112276_HeLa_siMETTL1_ConsistentDiff_peak.txt.gz 72.3 Kb (ftp)(http) TXT
GSE112276_HepG2_HighFC.txt.gz 196.3 Kb (ftp)(http) TXT
GSE112276_HepG2_OverallFC.txt.gz 451.0 Kb (ftp)(http) TXT
GSE112276_HepG2_shMETTL1_ConsistentDiff_peak.txt.gz 188.4 Kb (ftp)(http) TXT
GSE112276_M13.reliableMutations.pipeclip.bed.gz 157.0 Kb (ftp)(http) BED
GSE112276_M14.reliableMutations.pipeclip.bed.gz 129.4 Kb (ftp)(http) BED
GSE112276_M15.reliableMutations.pipeclip.bed.gz 143.4 Kb (ftp)(http) BED
GSE112276_M16.reliableMutations.pipeclip.bed.gz 147.7 Kb (ftp)(http) BED
GSE112276_MEF_HighFC.txt.gz 89.0 Kb (ftp)(http) TXT
GSE112276_P5.reliableMutations.pipeclip.bed.gz 896.5 Kb (ftp)(http) BED
GSE112276_P6.reliableMutations.pipeclip.bed.gz 933.6 Kb (ftp)(http) BED
GSE112276_P7.reliableMutations.pipeclip.bed.gz 292.4 Kb (ftp)(http) BED
GSE112276_P8.reliableMutations.pipeclip.bed.gz 318.3 Kb (ftp)(http) BED
GSE112276_R1.fpkm_tracking.gz 900.2 Kb (ftp)(http) FPKM_TRACKING
GSE112276_R2.fpkm_tracking.gz 905.3 Kb (ftp)(http) FPKM_TRACKING
GSE112276_R3.fpkm_tracking.gz 906.4 Kb (ftp)(http) FPKM_TRACKING
GSE112276_R4.fpkm_tracking.gz 900.2 Kb (ftp)(http) FPKM_TRACKING
GSE112276_R5.fpkm_tracking.gz 856.5 Kb (ftp)(http) FPKM_TRACKING
GSE112276_R6.fpkm_tracking.gz 863.3 Kb (ftp)(http) FPKM_TRACKING
GSE112276_R7.fpkm_tracking.gz 847.5 Kb (ftp)(http) FPKM_TRACKING
GSE112276_R8.fpkm_tracking.gz 847.7 Kb (ftp)(http) FPKM_TRACKING
GSE112276_W13.reliableMutations.pipeclip.bed.gz 885.0 Kb (ftp)(http) BED
GSE112276_W14.reliableMutations.pipeclip.bed.gz 966.3 Kb (ftp)(http) BED
GSE112276_W15.reliableMutations.pipeclip.bed.gz 7.1 Mb (ftp)(http) BED
GSE112276_W16.reliableMutations.pipeclip.bed.gz 6.3 Mb (ftp)(http) BED
GSE112276_mESC_HighFC.txt.gz 96.2 Kb (ftp)(http) TXT
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