Datasets

Title	Ribosome profiling in DDX3X degron cell lines and covering variants
Organism
Number of Samples	8
Release Date	2020/08/28 00:00
Sequencing Types
Protocol Details

Title
Authors	Calviello L,Venkataramanan S,Rogowski KJ,Wyler E,Wilkins K,Tejura M,Thai B,Krol J,Filipowicz W,Landthaler M,Floor SN
Journal	Nucleic acids research
Publication Date	2021 May 21
Abstract	DDX3 is an RNA chaperone of the DEAD-box family that regulates translation. Ded1, the yeast ortholog of DDX3, is a global regulator of translation, whereas DDX3 is thought to preferentially affect a subset of mRNAs. However, the set of mRNAs that are regulated by DDX3 are unknown, along with the relationship between DDX3 binding and activity. Here, we use ribosome profiling, RNA-seq, and PAR-CLIP to define the set of mRNAs that are regulated by DDX3 in human cells. We find that while DDX3 binds highly expressed mRNAs, depletion of DDX3 particularly affects the translation of a small subset of the transcriptome. We further find that DDX3 binds a site on helix 16 of the human ribosomal rRNA, placing it immediately adjacent to the mRNA entry channel. Translation changes caused by depleting DDX3 levels or expressing an inactive point mutation are different, consistent with different association of these genetic variant types with disease. Taken together, this work defines the subset of the transcriptome that is responsive to DDX3 inhibition, with relevance for basic biology and disease states where DDX3 is altered. © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
PMC	PMC8136831
PMID	33905506
DOI

Calviello et al. 2020 (PRJNA660002)