Identification of novel conserved peptide uORF homology groups in Arabidopsis and rice reveals ancient eukaryotic origin of select groups and preferential association with transcription factor-encoding genes

Abstract Background Upstream open reading frames (uORFs) can mediate translational control over the largest, or major ORF (mORF) in response to starvation, polyamine concentrations, and sucrose concentrations. One plant uORF with conserved peptide sequences has been shown to exert this control in an amino acid sequence-dependent manner but generally it is not clear what kinds of genes are regulated, or how extensively this mechanism is invoked in a given genome. Results By comparing full-length cDNA sequences from Arabidopsis and rice we identified 26 distinct homology groups of conserved peptide uORFs, only three of which have been reported previously. Pairwise Ka/Ks analysis showed that purifying selection had acted on nearly all conserved peptide uORFs and their associated mORFs. Functions of predicted mORF proteins could be inferred for 16 homology groups and many of these proteins appear to have a regulatory function, including 6 transcription factors, 5 signal transduction factors, 3 developmental signal molecules, a homolog of translation initiation factor eIF5, and a RING finger protein. Transcription factors are clearly overrepresented in this data set when compared to the frequency calculated for the entire genome (p = 1.2 × 10-7). Duplicate gene pairs arising from a whole genome duplication (ohnologs) with a conserved uORF are much more likely to have been retained in Arabidopsis (Arabidopsis thaliana) than are ohnologs of other genes (39% vs 14% of ancestral genes, p = 5 × 10-3). Two uORF groups were found in animals, indicating an ancient origin of these putative regulatory elements. Conclusion Conservation of uORF amino acid sequence, association with homologous mORFs over long evolutionary time periods, preferential retention after whole genome duplications, and preferential association with mORFs coding for transcription factors suggest that the conserved peptide uORFs identified in this study are strong candidates for translational controllers of regulatory genes.</p

Searching for low-mass dark matter via the Migdal effect in COSINE-100

We report on the search for weakly interacting massive particle (WIMP) dark matter candidates in the galactic halo that interact with sodium and iodine nuclei in the COSINE-100 experiment and produce energetic electrons that accompany recoil nuclei via the the Migdal effect. The WIMP mass sensitivity of previous COSINE-100 searches that relied on the detection of ionization signals produced by target nuclei recoiling from elastic WIMP-nucleus scattering was restricted to WIMP masses above ∼5 GeV/c2 by the detectors' 1 keVee energy-electron-equivalent threshold. The search reported here looks for recoil signals enhanced by the Migdal electrons that are ejected during the scattering process. This is particularly effective for the detection of low-mass WIMP scattering from the crystals' sodium nuclei in which a relatively larger fraction of the WIMP's energy is transferred to the nucleus recoil energy and the excitation of its orbital electrons. In this analysis, the low-mass WIMP search window of the COSINE-100 experiment is extended to WIMP mass down to 200 MeV/c2. The low-mass WIMP sensitivity will be further improved by lowering the analysis threshold based on a multivariable analysis technique. We consider the influence of these improvements and recent developments in detector performance to re-evaluate sensitivities for the future COSINE-200 experiment. With a 0.2 keVee analysis threshold and high light-yield NaI(Tl) detectors (22 photoelectrons/keVee), the COSINE-200 experiment can explore low-mass WIMPs down to 20 MeV/c2 and probe previously unexplored regions of parameter space

Searching for low-mass dark matter via Migdal effect in COSINE-100 [preprint]

We report on the search for weakly interacting massive particle (WIMP) dark matter candidates in the galactic halo that interact with sodium and iodine nuclei in the COSINE-100 experiment and produce energetic electrons that accompany recoil nuclei via the the Migdal effect. The WIMP mass sensitivity of previous COSINE-100 searches that relied on the detection of ionization signals produced by target nuclei recoiling from elastic WIMP-nucleus scattering was restricted to WIMP masses above $\sim$5 GeV/$c^2$ by the detectors' 1 keVee energy-electron-equivalent threshold. The search reported here looks for recoil signals enhanced by the Migdal electrons that are ejected during the scattering process. This is particularly effective for the detection of low-mass WIMP scattering from the crystals' sodium nuclei in which a relatively larger fraction of the WIMP's energy is transferred to the nucleus recoil energy and the excitation of its orbital electrons. In this analysis, the low-mass WIMP search window of the COSINE-100 experiment is extended to WIMP mass down to 200 MeV/c. The low-mass WIMP sensitivity will be further improved by lowering the analysis threshold based on a multivariable analysis technique. We consider the influence of these improvements and recent developments in detector performance to re-evaluate sensitivities for the future COSINE-200 experiment. With a 0.2 keVee analysis threshold and high light-yield NaI(Tl) detectors (22photoelectrons/keVee), the COSINE-200 experiment can explore low-mass WIMPs down to 20 MeV/c2 and probe previously unexplored regions of parameter space