Tag: uORF

Novel protein products encoded by upstream open reading frames of the MYCN gene in pediatric embryonal tumors

The MYCC and MYCN loci are each associated with two upstream open reading frames (uORFs) potentially encoding small proteins (9-21 kDa). We previously demonstrated that uORFs mrtl and MYCHEX1 of MYCC are translated, and their protein products may function to regulate the expression of the “parent” oncogene. We hypothesized that…

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Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi

Global identification of 3′ ends Initial computational predictions of open reading frames (ORFs) in B. burgdorferi38 overlooked elements such as mRNA boundaries, sRNA genes, and translation initiation from non-canonical start codons. B. burgdorferi transcription start sites (TSSs) and 5′ processed RNA ends were previously detected using 5′RNA-seq37. Here we sought…

Continue Reading Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi

Amplifying gene expression with RNA-targeted therapeutics

RNA-targeted NBTs that are currently being used to upregulate gene expression address both transcriptional and translational mechanisms and can be roughly divided into two groups: (1) NBTs that increase mRNA abundance by enhancing transcription or increasing mRNA stability (Fig. 3) and (2) NBTs that optimize translation (Fig. 4). Strategies in the first…

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Scientists develop predictable method to downregulate gene translation in plants

Breeding plants with a predicted phenotype by engineering uORFs. Credit: IGDB Gao Caixia’s group from the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences (CAS) has developed a new method of downregulating gene translation to a predictable and desired level in plants by precisely engineering upstream…

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error making Txdb from GTF and fasta files

Hello, I would like to use ORFik to map Ribo-reads to different ORFs in the maize genome. The latest version of the genome is Zm-B73-REFERENCE-NAM-5.0.fa. The annotation file is a GFF3. I have the genome fasta file, the fasta fai file, and the GFF3 file. The ORFik package uses GTF…

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[SOLVED] Special .bed to .fa conversion (GenomicCoordinates/DNAsequence) ~ Linux Fixes

My aim is to create a custom protein sequence reference file (protein.fa) from genomic coordinates (origin.bed). (origin.bed; with Chromosome, start, end, TranscriptID, strand, GeneID) chr1 109202569 109202584 ENST00000370031.1_uORF_0 – ENSG00000162639.11 chr1 109203584 109203617 ENST00000370031.1_uORF_0 – ENSG00000162639.11 chr11 102188276 102188302 ENST00000263464.3_uORF_0 + ENSG00000023445.9 chr11 10830291 10830306 ENST00000530211.1_uORF_1 – ENSG00000110321.11 chr11 10830400…

Continue Reading [SOLVED] Special .bed to .fa conversion (GenomicCoordinates/DNAsequence) ~ Linux Fixes