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Nanopore full length cDNA analysis of Cmtr1 cKO activated CD4 T cells

ABSTRACT: We investigated the role of CMTR1 in T cells using a Cmtr1 conditional knockout mouse model. We demonstrate that CMTR1 has gene-specific impacts in T cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE284393 | GEO | 2025/10/16

REPOSITORIES: GEO

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TMT proteomics of Cmtr1 cKO activated CD4 T cells

Project description:We aim to find the gene-specific effects of Cmtr1 KO in mouse CD4 T cells. TMT proteomics datasets were generated to find out which proteins are dependent on CMTR1 for their expression.

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Cmtr1 regulates the activated CD4 T cell transcriptome [GEO_Cmtr1_act]

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Project description:We investigated the role of CMTR1 in T cells using an Cmtr1 conditional knockout mouse model. We report that the cap-specific RNA (nucleoside-2'-O-)-methyltransferase, CMTR1, supports naïve T cell survival and activation-induced proliferation. We demonstrate that CMTR1 has gene-specific impacts in T cells. These RNAseq experiments investigate the effect of Cmtr1 cKO on the naïve CD4 T cell transcriptome.

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Improved Nanopore full-length cDNA sequencing by PCR-suppression.

Project description:Full-length transcript sequencing remains a main goal of RNA sequencing. However, even the application of long-read sequencing technologies such as Oxford Nanopore Technologies still fail to yield full-length transcript sequencing for a significant portion of sequenced reads. Since these technologies can sequence reads that are far longer than the longest known processed transcripts, the lack of efficiency to obtain full-length transcripts from good quality RNAs stems from library preparation inefficiency rather than the presence of degraded RNA molecules. It has previously been shown that addition of inverted terminal repeats in cDNA during reverse transcription followed by single-primer PCR creates a PCR suppression effect that prevents amplification of short molecules thus enriching the library for longer transcripts. We adapted this method for Nanopore cDNA library preparation and show that not only is PCR efficiency increased but gene body coverage is dramatically improved. The results show that implementation of this simple strategy will result in better quality full-length RNA sequencing data and make full-length transcript sequencing possible for most of sequenced reads.

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DHX15 regulates CMTR1-dependent gene expression and cell proliferation

Project description:We discovered that the RNA helicase DHX15 is a regulator of the methyltransferase CMTR1. To determine the biological consequences of this interaction we overexpressed CMTR1 or a mutated CMTR1 (2LA)that does not bind DHX15, in the human breast cancer cell line HCC1806. To assess the effects of the DHX15-CMTR1 interaction on translation, polysomes were separated on a sucrose gradient and sequencing libraries generated from the polysomal and input RNA. We found that the DHX15-CMTR1 interaction controls ribosome loading of a subset of mRNAs and impacts on cell proliferation.

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Project description:We investigated influence of CMTR1 phosphorylation by CK2 on RNA expression. In this experiment, we added wild-type and phosphorylation deficient mutant of CMTR1 and knocked out the endogenous CMTR1. We demonstrated that lack of phosphorylation of CMTR1 affects only small but specific group of genes.

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