Control of gene expression mRNA N6-methyladenosine in pro-B cells
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE151071 | GEO | 2020/06/22
REPOSITORIES: GEO
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Project description:N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNA (mRNA). Recent conceptual and technological advances have sparked extensive research interests in the functions of m6A, which led to the discovery of its writers, erasers and readers; as well as its regulatory roles in a number of biological processes. However, the physiological roles of mRNA m6A in B cells remained unknown. Here, we report that loss of Mettl14, the core component of the m6A writer complex, severely blocked B cell development in mice. In the bone marrow, deletion of Mettl14 in B lineage cells impaired key processes of B lymphopoiesis, including the recombination of immunoglobulin heavy chain (IgH), the IL-7-induced pro-B cell proliferation, and the transition from the large cycling pre-B stage to the small pre-B stage. Associated with these broad biological effects, Mettl14 deficiency in developing B cells dramatically decreased m6A levels in over 40% transcripts of the whole transcriptome. Global gene expression analysis in Mettl14 KO B cells showed extensive abnormalities in gene expression programs important for B cell development. To further characterize the underlying molecular mechanisms, we investigated the role of two m6A reader proteins YTHDF2 and YTHDF1. Loss of Ythdf2 impaired the IgH recombination and IL-7-induced proliferation of pro-B cells but did not affect the large pre-B-to-small pre-B cell transition. In contrast, Ythdf1 deficiency did not cause any significant defects in B cell development. These data highlighted the complexity of reader proteins that may have distinct, overlapping, or synergistic roles. Altogether, our data demonstrate that mRNA m6A modification represents a novel regulatory mechanism in early B cell development.
2020-06-22 | GSE112022 | GEO
Project description:N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNA (mRNA). Recent conceptual and technological advances have sparked extensive research interests in the functions of m6A, which led to the discovery of its writers, erasers and readers; as well as its regulatory roles in a number of biological processes. However, the physiological roles of mRNA m6A in B cells remained unknown. Here, we report that loss of Mettl14, the core component of the m6A writer complex, severely blocked B cell development in mice. In the bone marrow, deletion of Mettl14 in B lineage cells impaired key processes of B lymphopoiesis, including the recombination of immunoglobulin heavy chain (IgH), the IL-7-induced pro-B cell proliferation, and the transition from the large cycling pre-B stage to the small pre-B stage. Associated with these broad biological effects, Mettl14 deficiency in developing B cells dramatically decreased m6A levels in over 40% transcripts of the whole transcriptome. Global gene expression analysis in Mettl14 KO B cells showed extensive abnormalities in gene expression programs important for B cell development. To further characterize the underlying molecular mechanisms, we investigated the role of two m6A reader proteins YTHDF2 and YTHDF1. Loss of Ythdf2 impaired the IgH recombination and IL-7-induced proliferation of pro-B cells but did not affect the large pre-B-to-small pre-B cell transition. In contrast, Ythdf1 deficiency did not cause any significant defects in B cell development. These data highlighted the complexity of reader proteins that may have distinct, overlapping, or synergistic roles. Altogether, our data demonstrate that mRNA m6A modification represents a novel regulatory mechanism in early B cell development.
2020-06-23 | GSE136419 | GEO
Project description:SUMOylation affects many aspects of target proteins such as activity, stability, localization and protein-protein interactions. We have found that SUMOylation of YTHDF2 increased its binding activity with m6A-RNAs by using different experimental approaches. To confiremd this conclusion,the analysis of RIP-seq, MeRIP-seq and RNA-seq in H1299-shYTHDF2 cells re-expressing YTHDF2-WT and YTHDF2-K571R was performed. MeRIP+RIP targets showed lower binding affinities in the mutant YTHDF2-K571R when compared with YTHDF2-WT. Compared to the control group, the binding capacities of YTHDF2 to RIP targets in treated group with either 2-D08 or GA were decreased, especially to MeRIP+RIP targets. Moreover, SUMOylated YTHDF2 promoted m6A-RNAs degradation. Combined analysis of RNA-seq, RIP-seq and MeRIP-seq showed that the mRNA levels were up-regulated in shYTHDF2 stable cells re-expressing YTHDF2-K571R compared with those in re-expressing YTHDF2-WT.
2021-01-26 | GSE164917 | GEO
Project description:Modification of RNAs with N6-methadenosine (m6A) has gained attention in recent years as a general mechanism of gene regulation. In the liver, m6A and its associated machinery has been studied as a potential biomarker of disease and cancer, with impacts on metabolism, cell cycle regulation, and pro-cancer state signaling. In vivo studies have begun to explore the effects of m6A in the liver, but differences in outcome of deletion of m6A writers Mettl3 and Mettl14 have not been thoroughly described or explained. Similarly, in vivo studies of the effects of m6A readers such as Ythdf1 and Ythdf2 have not been extended to characterize impacts of dysregulation of these reader proteins in the liver. To understand Mettl14 function, as well as Ythdf1 and Ythdf2, we developed mouse models and found a Mettl14 deletion specific phenotype of progressive liver injury characterized by nuclear heterotypia, with studies highlighting changes in mRNA splicing, processing and export leading to increases in mRNA surveillance and recycling.
2024-06-18 | GSE265879 | GEO
Project description:In order to obtain a stringent m6A methylome in Drosophila adults, we performed m6A-RIP-seq in yw control (male and female), Mettl3 (male), Mettl14 (male) and Hakai (male) mutant flies. We find that the effective m6A modification, which depends on the writer complex, is mostly distributed in 5’ UTR and near start codon in Drosophila, in contrast to the mammalian system. We define a set of high-confident m6A methylation sites shared by Mettl3, Mettl14 and Hakai, indicating that Hakai is a core component of the m6A writer complex. We also find differential methylation pattern in certain loci between male and female flies.
2021-03-01 | GSE155662 | GEO
Project description:N6-methyladenosine (m6A) is the most prevalent internal modification present in the mRNA of all higher eukaryotes. Here we present that m6A is selectively recognized by human YTH domain family (YTHDF2) protein to regulate mRNA degradation. By using crosslinking and immunoprecipitation, we have identified over 4000 substrate RNA of YTHDF2 with conserved core motif of G(m6A)C. We further estabilshed the role of YTHDF2 in RNA metabolism by a combination of ribosome profiling, RNA sequencing, m6A level quantification and cell-based imaging: the C-terminal domain of YTHDF2 selectively binds to m6A of mRNA and the N-terminal domain is responsive for localizing mRNA from translatable pool to processing body where mRNA decay occurs. PAR-CLIP and RIP was used to identify YTHDF2 binding sites followed by ribosome profling and RNA seq to assess the consequences of YTHDF2 siRNA knock-down
2013-11-29 | E-GEOD-49339 | biostudies-arrayexpress
Project description:The mRNA m6A reader YTHDF2 is overexpressed in a broad spectrum of human acute myeloid leukemias (AML). To understand the role of YTHDF2 in AML, we generated m6A meRIP-seq libraries form Ythdf2fl/fl (Ythdf2CTL) pre-leukemic cells.
2019-04-05 | E-MTAB-6791 | biostudies-arrayexpress
Project description:The mRNA m6A reader YTHDF2 is overexpressed in a broad spectrum of human acute myeloid leukemias (AML). To understand the role of YTHDF2 in AML, we generated m6A meRIP-seq libraries form Ythdf2fl/fl; Vav-iCre (Ythdf2CKO) pre-leukemic cells.
2019-04-05 | E-MTAB-7783 | biostudies-arrayexpress
Project description:N6-methyladenosine (m6A) modification is the most abundant internal RNA modification in eukaryotes. Recent studies have shown that the dynamic and reversible regulation of m6A modifications in mRNAs or non-coding RNAs plays critical roles in tissue development, stem cell self-renewal and differentiation, control of heat shock response, and circadian clock controlling, as well as in RNA metabolism and processing. METTL14 is a major m6A writer which together with METTL3 forms the core of the methyltransferase complex that catalyzes the conversion of adenosine (A) to m6A. To investigate the effect of METTL14 on m6A modfication, we performed m6A-seq in HepG2 cells with stably expressed shRNAs against METTL14 (shMETTL14) or non-specific control shRNA (shNS).
2018-03-26 | GSE90642 | GEO
Project description:N6-methyladenosine (m6A) is the most prevalent and reversible internal modification of mammalian messenger and noncoding RNAs mediated by specificm6A writer, reader, and eraser proteins. As an m6A writer, the methyltransferase-like 3-methyltransferase–like 14 (METTL14)–Wilms tumor 1–associated protein complex dynamically regulates m6A modification and plays important roles in diverse biologic processes. However, our knowledge about the complete functions of this RNA methyltransferase complex, the contributions of each componenttothemethylation, andtheir effects on different biologicpathways are still limited. By using both in vivo and in vitro models, we here report that METTL14 is indispensable for postimplantation embryonic development by facilitating the conversion from naive to primed state of the epiblast. Depletion of Mettl14 leads to conspicuous embryonic growth retardation from embryonic d 6.5, mainly as a result of resistanceto differentiation, which further leads to embryonic lethality early in gestation. Our data highlight the critical function of METTL14 as an m6A modification regulator in orchestrating early mouse embryogenesis.
2020-12-10 | GSE162906 | GEO