Genome-Scale Computational Identification and Characterization of UTR Introns in Atalantia buxifolia

Accumulated evidence has shown that CDS introns (CIs) play important roles in regulating gene expression. However, research on UTR introns (UIs) is limited. In this study, UIs (including 5′UTR and 3′UTR introns (5UIs and 3UIs)) were identified from the Atalantia buxifolia genome. The length and nucleotide distribution characteristics of both 5UIs and 3UIs and the distributions of cis-acting elements and transcription factor binding sites (TFBSs) in 5UIs were investigated. Moreover, PageMan enrichment analysis was applied to show the possible roles of transcripts containing UIs (UI-Ts). In total, 1077 5UIs and 866 3UIs were identified from 897 5UI-Ts and 670 3UI-Ts, respectively. Among them, 765 (85.28%) 5UI-Ts and 527 (78.66%) 3UI-Ts contained only one UI, and 94 (6.38%) UI-Ts contained both 5UI and 3UI. The UI density was lower than that of CDS introns, but their mean and median intron sizes were ~2 times those of the CDS introns. The A. buxifolia 5UIs were rich in gene-expression-enhancement-related elements and contained many TFBSs for BBR-BPC, MIKC_MADS, AP2 and Dof TFs, indicating that 5UIs play a role in regulating or enhancing the expression of downstream genes. Enrichment analysis revealed that UI-Ts involved in ‘not assigned’ and ‘RNA’ pathways were significantly enriched. Noteworthily, 119 (85.61%) of the 3UI-Ts were genes encoding pentatricopeptide (PPR) repeat-containing proteins. These results will be helpful for the future study of the regulatory roles of UIs in A. buxifolia.

Methodological Investigation for Hydrogen Addition to Small Cage Carbon Fullerenes

Hydrogenated small fullerenes (Cn, n < 60) are of interest as potential astrochemical species, and as intermediates in hydrogen-catalysed fullerene growth. However, the computational identification of key stable species is difficult due to the vast configurationally space of structures. In this study, we explored routes to predict stable hydrogenated small fullerenes. We showed that neither local fullerene geometry nor local electronic structure analysis was able to correctly predict subsequent low-energy hydrogenation sites, and sequential stable addition searches also sometimes failed to identify most stable hydrogenated fullerene isomers. Of the empirical and semi-empirical methods tested, GFN2-xTB consistently gave highly accurate energy correlations (r > 0.99) to full DFT-LDA calculations at a fraction of the computational cost. This allowed identification of the most stable hydrogenated fullerenes up to 4H for four fullerenes, namely two isomers of C28 and C40, via “brute force” systematic testing of all symmetry-inequivalent combinations. The approach shows promise for wider systematic studies of smaller hydrogenated fullerenes.