Computational protocol: The N6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of normal and leukemia cells

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Protocol publication

[…] Metagenes were constructed for the called m6 A sites using MetaPlotR. In brief, DRACH sites were mapped to different RNA features (5′ UTR, CDS and 3′ UTR) of the human genome (hg19). The position of the sites was normalized to the median feature length of the transcripts to which the sites mapped. A frequency distribution plot was generated by counting the number of sites in contiguous bins on a virtual mRNA transcript, sites whose feature lengths represent the median feature lengths of transcripts under analysis. A Gaussian estimate of kernel density was then plotted as a metagene. Analysis of motif enrichment was performed on the sense DNA sequence ±2 nucleotides up- and down-stream of the called truncation sites using the MEME suite. […]

Pipeline specifications

Software tools MetaPlotR, AME, MEME Suite
Application ChIP-seq analysis
Organisms Mus musculus, Homo sapiens
Diseases Leukemia, Leukemia, Myeloid, Neoplasms, Leukemia, Myeloid, Acute
Chemicals Nucleotides