Project description:Improper regulation of translation initiation, a vital check-point of protein synthesis in the cell, has been linked to a number of cancers. Overexpression of protein subunits of eukaryotic translation initiation factor 3 (eIF3) has been associated with increased translation of mRNAs involved in cell proliferation. In addition to playing a major role in general translation initiation by serving as a scaffold for the assembly of translation initiation complexes, eIF3 regulates translation of specific cellular mRNAs and viral RNAs. Mutations in the N-terminal Helix-Loop-Helix (HLH) RNA-binding motif of the EIF3A subunit in eIF3 interfere with Hepatitis C Virus Internal Ribosome Entry Site (IRES) mediated translation initiation in vitro. Here we use RNA-seq and ribosome profiling of engineered lentiviral HEK293T cells to show that the EIF3A HLH motif controls translation of a small set of cellular transcripts enriched in oncogenic mRNAs, including MYC.
Project description:A cascade of basic helix-loop-helix transcription factors guide tapetal cell development in maize anthers, using proteins conserved in Arabidopsis and rice but deployed with a distinctive timing. Anthers were dissected and staged to be 1500 μm in length (+/- 100 μm) and samples were compared between mutants and fertile siblings on an Agilent 4x44 custom microarray. Analysis included MS32 which is another basic helix-loop-helix factor that acts later during tapetal differentiation.
Project description:Supporting .raw data for "Functional conservation and divergence of the helix-turn-helix motif of E2 ubiquitin-conjugating enzymes", DOI: 10.15252/embj.2021108823
Related to Figure 1E and EV1A.
Project description:Immediate early genes (IEGs) are useful markers of neuronal activation and essential components of neuronal response. While studies of gastropods have provided many insights into the basic learning and memory mechanisms, the genome-wide assessment of IEGs has been mainly restricted to vertebrates. In this study we identified IEGs in the terrestrial snail Helix lucorum. In the absence of the genome, we conducted de novo transcriptome assembly using reads with short and intermediate lengths cumulatively covering more than 98 billion nucleotides. Based on this assembly, we identified 37 proteins corresponding to contigs differentially expressed in either the parietal ganglia or two giant interneurons located within the parietal ganglia of the snail in response to the neuronal stimulation. These proteins included homologues of well-known mammalian IEGs, such as c-jun/jund, C/EBP, c-fos/fosl2 and Egr1, as well as homologues of genes not yet implicated in the neuronal response.
