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Series GSE196043 Query DataSets for GSE196043
Status Public on Dec 12, 2022
Title mRNA aging shapes the Cap2 methylome in mammalian mRNA
Organisms Caenorhabditis elegans; Drosophila melanogaster; Danio rerio; Homo sapiens; Mus musculus
Experiment type Other
Expression profiling by high throughput sequencing
Summary The mRNA cap structure is a major site of dynamic mRNA methylation. mRNA caps exist in either the Cap1 or Cap2 form, depending on the presence of 2’-O-methylation on the first, or both the first and second transcribed nucleotide, respectively. However, the identity of Cap2-containing mRNAs and the function of Cap2 are unclear. Here we describe CLAM-Cap-Seq, a method for transcriptome-wide mapping and quantification of Cap2. We find that unlike other epitranscriptomic modifications, Cap2 can occur on all mRNAs. Cap2 is formed through a slow continuous conversion of mRNAs from Cap1 to Cap2 as mRNAs age in the cytosol. As a result, Cap2 is enriched on long-lived mRNAs. We find that large increases in the abundance of Cap1 leads to activation of RIG-I, especially in conditions where RIG-I expression is increased. The methylation of Cap1 to Cap2 markedly reduces the ability of RNAs to bind and activate RIG-I. We find that the slow Cap2 methylation rate allows Cap2 to accumulate on host mRNAs yet ensures that low Cap2 levels occur on newly expressed viral RNAs. Overall, these results reveal an immunostimulatory role for Cap1, and that Cap2 functions to reduce activation of the innate immune response.
 
Overall design We developed next-generation sequencing methods for quantification of Cap2 methylation in bulk mRNA (CapTag-seq), as well as in individual mRNAs in a transcriptome-wide manner (CLAM-Cap-seq). Furthermore, we developed tools for measuring translation and stability of transcript-start nucleotide (TSN) mRNA isoforms by combining polysome profiling and actinomycin D treatment with TSS-seq (transcription start site-sequencing).
 
Contributor(s) Despic V, Jaffrey SR
Citation(s) 36725932
Submission date Feb 03, 2022
Last update date Feb 10, 2023
Contact name Vladimir Despic
E-mail(s) vld2002@med.cornell.edu
Organization name Weill Cornell Medicine
Department Pharmacology
Street address 1300 York Ave
City New York
State/province New York
ZIP/Postal code 10044
Country USA
 
Platforms (8)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL17275 Illumina HiSeq 2500 (Drosophila melanogaster)
Samples (95)
GSM5858477 WT ActD-TSS-seq _0 hrs 1
GSM5858478 WT ActD-TSS-seq _0 hrs 2
GSM5858479 WT ActD-TSS-seq _2 hrs 1
Relations
BioProject PRJNA803151

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
GSE196043_A549_CTS1.xlsx 13.3 Kb (ftp)(http) XLSX
GSE196043_A549_CTS2.xlsx 13.3 Kb (ftp)(http) XLSX
GSE196043_Brain_CTS1.xlsx 13.3 Kb (ftp)(http) XLSX
GSE196043_Brain_CTS2.xlsx 13.2 Kb (ftp)(http) XLSX
GSE196043_CMTR2KO-HEK293T_CCS.xlsx 880.0 Kb (ftp)(http) XLSX
GSE196043_CMTR2KO-HEK293T_CTS1.xlsx 13.3 Kb (ftp)(http) XLSX
GSE196043_CMTR2KO-HEK293T_CTS2.xlsx 13.3 Kb (ftp)(http) XLSX
GSE196043_CMTR2KO-HEK293T_HalfLives.xlsx 1.0 Mb (ftp)(http) XLSX
GSE196043_CMTR2KO-HEK293T_MRL.xlsx 1.5 Mb (ftp)(http) XLSX
GSE196043_CMTR2WT-HEK293T_CCS.xlsx 1.0 Mb (ftp)(http) XLSX
GSE196043_CMTR2WT-HEK293T_CTS1.xlsx 13.2 Kb (ftp)(http) XLSX
GSE196043_CMTR2WT-HEK293T_CTS2.xlsx 13.4 Kb (ftp)(http) XLSX
GSE196043_CMTR2WT-HEK293T_HalfLives.xlsx 1016.7 Kb (ftp)(http) XLSX
GSE196043_CMTR2WT-HEK293T_MRL.xlsx 1.4 Mb (ftp)(http) XLSX
GSE196043_CMTR2WT-HEK293T_nodecapping_CTS1.xlsx 10.7 Kb (ftp)(http) XLSX
GSE196043_CMTR2WT-HEK293T_nodecapping_CTS2.xlsx 10.6 Kb (ftp)(http) XLSX
GSE196043_Fruitfly_CTS1.xlsx 13.3 Kb (ftp)(http) XLSX
GSE196043_Fruitfly_CTS2.xlsx 13.3 Kb (ftp)(http) XLSX
GSE196043_HEK293T_TSNmRNAisoforms.xlsx 1.1 Mb (ftp)(http) XLSX
GSE196043_Heart_CTS1.xlsx 13.3 Kb (ftp)(http) XLSX
GSE196043_Heart_CTS2.xlsx 13.3 Kb (ftp)(http) XLSX
GSE196043_Kidney_CTS1.xlsx 13.3 Kb (ftp)(http) XLSX
GSE196043_Kidney_CTS2.xlsx 13.2 Kb (ftp)(http) XLSX
GSE196043_Liver_CTS1.xlsx 13.3 Kb (ftp)(http) XLSX
GSE196043_Liver_CTS2.xlsx 13.2 Kb (ftp)(http) XLSX
GSE196043_Lung_CTS1.xlsx 13.3 Kb (ftp)(http) XLSX
GSE196043_Lung_CTS2.xlsx 13.2 Kb (ftp)(http) XLSX
GSE196043_MCF-7_CCS.xlsx 696.4 Kb (ftp)(http) XLSX
GSE196043_MCF-7_CTS1.xlsx 13.2 Kb (ftp)(http) XLSX
GSE196043_MCF-7_CTS2.xlsx 13.2 Kb (ftp)(http) XLSX
GSE196043_MCF-7_TSNmRNAisoforms.xlsx 957.6 Kb (ftp)(http) XLSX
GSE196043_RAW.tar 6.1 Mb (http)(custom) TAR (of XLSX)
GSE196043_RNA-seq-WTandCMTR2KO-counts.xlsx 1.1 Mb (ftp)(http) XLSX
GSE196043_RNA-seq_differential-analysis.xlsx 1.0 Mb (ftp)(http) XLSX
GSE196043_Spleen_CTS1.xlsx 13.3 Kb (ftp)(http) XLSX
GSE196043_Spleen_CTS2.xlsx 13.2 Kb (ftp)(http) XLSX
GSE196043_Worm_CTS1.xlsx 12.9 Kb (ftp)(http) XLSX
GSE196043_Worm_CTS2.xlsx 12.7 Kb (ftp)(http) XLSX
GSE196043_Zebrafish_CTS1.xlsx 13.3 Kb (ftp)(http) XLSX
GSE196043_Zebrafish_CTS2.xlsx 13.4 Kb (ftp)(http) XLSX
GSE196043_mESC_CCS.xlsx 819.8 Kb (ftp)(http) XLSX
GSE196043_mESC_CTS1.xlsx 13.2 Kb (ftp)(http) XLSX
GSE196043_mESC_CTS2.xlsx 13.2 Kb (ftp)(http) XLSX
GSE196043_mESC_TSNmRNAisoforms.xlsx 1.1 Mb (ftp)(http) XLSX
GSE196043_readme.xlsx 11.1 Kb (ftp)(http) XLSX
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