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The effects of WTAP on m6A mRNA modification in the heart [meRIP-seq]

ABSTRACT: The effects of WTAP on m6A mRNA modification in the heart [meRIP-seq]

PROVIDER: PRJNA943506 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23822363_1.fastq.gz	Fastqsanger.gz
	SRR23822363_2.fastq.gz	Fastqsanger.gz
	SRR23822364_1.fastq.gz	Fastqsanger.gz
	SRR23822364_2.fastq.gz	Fastqsanger.gz
	SRR23822365_1.fastq.gz	Fastqsanger.gz

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The effects of WTAP on m6A mRNA modification in the heart [meRIP-seq]

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m6A Modification Regulates Planarian Regeneration [MeRIP-seq]

Project description:The fundamental of regeneration process of invertebrates involves the renewal, differentiation and reprogramming of stem cell in an orchestrated manner. It has been known that N6-methyladenosine (m6A) regulates stem cell renewal and differentiation. It is still unclear if m6A is crucial for the regeneration at whole-organism level. Here, we demonstrate that wtap knockdown mediated m6A depletion impairs planarian regeneration upon amputation. The cell cycle related genes displayed decreased m6A while increased expression levels in response to wtap knockdown. The m6A depletion induced phenotypes can be rescued by double-knocking down these genes together with wtap, suggesting that m6A-mediated cell cycle controls planarian regeneration. Further analysis combining the single-cell sequencing unveils a unique neuronal progenitor-like cell type, named NCC and characterized by specific expression of grn, which is indispensable for neuroregeneration. Overall, our study uncovered an essential role of wtap-mediated m6A modification in regulating stem cell population dynamics and homeostasis in terms of general-body regeneration.

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Analysis of m6A methylome in CHAPIR overexpressed heart [MeRIP]

Project description:To elucidate the molecular mechanism by which cardiac-hypertrophy-associated piRNA (CHAPIR) regulates m6A modification, we performed m6A methylated RNA immunoprecipitation sequencing (MeRIP-seq) in control or CHAPIR-overexpressing mice heart. The sequential analysis of m6A peaks showed that RGACH motif was highly enriched within m6A sites in heart and that is aligning with the classical consensus sequence of mammals ‘RGACH’, where ‘R’ indicates purine (A/G) and ‘H’ indicates non-guanine base (A/C/U). In CHAPIR treated heart, m6A mostly occurred in mRNAs (89.5%) and only about 10.5% were identified in non-coding RNAs. The majority of mRNAs contain one or two m6A peaks (89.2%) and 10.8% mRNA contain >2 m6A peaks . M6A peaks were predominantly distributed in coding sequences (CDSs), 3’ untranslated regions (3’UTRs) and near stop codon.

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TTC22 increasing total m6A RNA level and colon cancer metastasis via RPL4-WTAP-YTHDF1 axis

Project description:WTAP is an essential component of the RNA N-6-methyladenosine (m6A) modification complexes that guides METLL3-METLL14 heteroduplexes to target RNAs in the nucleus of mammalian cells. Through mining the genotype-tissue expression (GTEx) datasets, we initially found that TTC22 expression was highly correlated with WTAP and FTO in many normal human tissues. Our experimental results indicate that TTC22 could directly capture RNA binding protein RPL4, induce the binding between RPL4 and WTAP mRNA in the cytoplasm, which increased the m6A level, induced alterative splicing, enhanced the stability and translation efficiency of WTAP mRNA, and consequently upregulated the level of total m6A RNA. These results indicate that WTAP mRNA is a m6A target and there is a positive feedback loop between total m6A and WTAP expression. YTHDF1 was found to be an essential m6A WTAP mRNA binding protein. Downregulation of RPL4, WTAP, or YTHDF1 expression could reverse TTC22-enhanced total m6A RNA level. m6A-specific antibody immunoprecipitated RNA-sequencing (meRIP-seq) demonstrated that TTC22 caused dramatic expression changes of genes related to metabolic pathways, ribosome biogenesis, and RNA spliceosome. Furthermore, we also found that TTC22 upregulated the expression of epithelial-mesenchymal transition (EMT)-related gene SNAI1 via m6A, and promoted metastasis of colon cancer in vitro and in mice. In conclusion, our study illustrates that WTAP mRNA is a m6A target using YTHDF1 as the binding protein. TTC22 could upregulate the levels of WTAP expression and total m6A RNA through the PRL4 binding. The m6A-mediated upregulation of SNAI1 expression may contribute to TTC22-enhanced colon cancer metastasis.

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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.

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