Ribosome profiling reveals the translational landscape and allele-specific translational efficiency in rice

Translational regulation is a critical step in the process of gene expression and governs the synthesis of proteins from mRNAs.Many studies have revealed translational regulation in plants in response to various environmental stimuli.However,there have been no studies documenting the comprehensive landscape of translational regulation and allele-specific translational efficiency in multiple plant tissues,especially those of rice,a main staple crop that feeds nearly half of the world’s population.Here we used RNA sequencing and ribosome profiling data to analyze the transcriptome and translatome of an elite hybrid rice,Shanyou 63(SY63),and its parental varieties Zhenshan 97 and Minghui 63.The results revealed that gene expression patterns varied more among tissues than among varieties at the transcriptional and translational levels.We identified 3392 upstream open reading frames(uORFs),and the uORF-containing genes were enriched in transcription factors.Only 668 of 13492 long non-coding RNAs could be translated into peptides.Finally,we discovered numerous genes with allele-specific translational efficiency in SY63 and demonstrated that some cis-regulatory elements may contribute to allelic divergence in translational efficiency.Overall,these findings may improve our understanding of translational regulation in rice and provide information for molecular breeding research.

Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues

Although the function of tRNAs in the translational process is well established,it remains controversial whether tRNA abundance is tightly associated with translational efficiency(TE)in mammals.Moreover,how critically the expression of tRNAs contributes to the establishment of tissue-specific proteomes in mammals has not been well addressed.Here,we measured both tRNA expression using demethylase-tRNA sequencing(DM-tRNA-seq)and TE of mRNAs using ribosome-tagging sequencing(RiboTag-seq)in the brain,heart,and testis of mice.Remarkable variation in the expression of tRNA isodecoders was observed among different tissues.When the statistical effect of isodecoder-grouping on reducing variations is considered through permutating the anticodons,we observed an expected reduction in the variation of anticodon expression across all samples,an unexpected smaller variation of anticodon usage bias,and an unexpected larger variation of tRNA isotype expression at amino acid level.Regardless of whether or not they share the same anticodons,the isodecoders encoding the same amino acids are co-expressed across different tissues.Based on the expression of tRNAs and the TE of mRNAs,we find that the tRNA adaptation index(tAI)and TE are significantly correlated in the same tissues but not between tissues;and tRNA expression and the amino acid composition of translating peptides are positively correlated in the same tissues but not between tissues.We therefore hypothesize that the tissue-specific expression of tRNAs might be due to post-transcriptional mechanisms.This study provides a resource for tRNA and translation studies,as well as novel insights into the dynamics of tRNAs and their roles in translational regulation.

Prediction of the next highly pathogenic avian influenza pandemic that can cause illness in humans

Background:In recent years,avian influenza viruses(AIVs)have seriously threatened human health.Questions such as:why do AIVs infect humans?,how quickly can an AIV become pandemic?,and which virus is the most dangerous?cannot be sufficiently answered using current bioinformatic studies.Method:Secondary structures and energies of representative 5′-untranslated region(UTR)of the HA gene were calculated.Then their secondary structures and energies were re-calculated after one or two nucleotide substitutions were introduced into the HA 5′-UTR.Phylogenetic trees on the basis of hemagglutinin(HA)and polymerase basic protein 2(PB2)amino acid sequences and HA 5′-UTR nucleotide sequences were constructed.The connection between the energy and translation efficiency of 5′-UTR was confirmed by in vitro coupled transcription/translation assay.Results:The simplicity of the secondary structure of the 5′-UTR of the HA gene determines the overall virus replication rate and transmission potential.Point mutation assays show that the 5′-UTR sequences of the HA gene in the influenza subtypes H2N2,H3N2,and H7N9 have greater variation potentials than other virus subtypes.Conclusion:Some high-virulent strains of avian influenza might emerge in the next two to three years.The H2N2 subtype,once disappeared in humans,may stage a comeback.The current outbreak of H7N9 may become pandemic and cause even more deaths,if one or two bases are substituted in the 5′-UTR sequence of the HA gene.