Dynamic patterns of the translatome in a hybrid triplet show translational fractionation of the maize subgenomes

Heterosis,the phenomenon in which hybrids outperform their parents,has been utilized in maize(Zea mays L.)for over 100 years.To provide a more complete understanding of heterosis,we collected a comprehensive transcriptome and translatome dataset on seedling leaves for B73,Mo17,and their F1 hybrid,which provided a dynamic landscape of transcriptomic and translatomic variation in maize.Although additivity accounted for a large proportion of variation at two omics-levels,an elevated nonadditive effect was observed in the translatome,especially in the translated subgenome maize1 genes,and the genes that switched from additivity in the transcriptome to nonadditivity in the translatome were significantly enriched in the subgenome maize1.Many genes with allele-specific expression and translation show dramatic regulatory switches between the transcriptome and translatome,and partial genes with allele-specific translation underlying regulatory mechanism also exhibited subgenome bias.Interestingly,we found the translated isoforms show different expression patterns compared with transcriptome and more genes changed their dominant isoforms during the genetic flow from parents to the hybrid at the translatome level.The translated genes with switched dominant isoforms significantly biased to the subgenome maize2 while genes with conserved dominant isoforms significantly enriched in subgenome maize1.Together,the dynamic changed patterns in translatome across hybrid and parental lines show translational fractionation of the maize subgenomes,which may be associated with heterosis in maize and provides a potential theoretical basis for breeding.

Reproductive tissue-specific translatome of a rice thermo-sensitive genic male sterile line

Translational regulation,especially tissue-or cell type-specific gene regulation,plays essential roles in plant growth and development.Thermo-sensitive genic male sterile(TGMS)lines have been widely used for hybrid breeding in rice(Oryza sativa).However,little is known about translational regulation during reproductive stage in TGMS rice.Here,we use translating ribosome affinity purification(TRAP)combined with RNA sequencing to investigate the reproductive tissue-specific translatome of TGMS rice expressing FLAG-tagged ribosomal protein L18(RPL18)from the germline-specific promoter MEIOSIS ARRESTED AT LEPTOTENE1(MEL1).Differentially expressed genes at the transcriptional and translational levels are enriched in pollen and anther-related formation and development processes.These contain a number of genes reported to be involved in tapetum programmed cell death(PCD)and lipid metabolism during pollen development and anther dehiscence in rice,including several encoding transcription factors and key enzymes,as well as several long non-coding RNAs(lnc RNAs)that potentially affect tapetum and pollenrelated genes in male sterility.This study represents the comprehensive reproductive tissue-specific characterization of the translatome in TGMS rice.These results contribute to our understanding of the molecular basis of sterility in TGMS rice and will facilitate further genetic manipulation of TGMS rice in two-line breeding systems.

A hidden translatome in tumors——the coding lncRNAs

Long noncoding RNAs(lncRNAs)have been extensively identified in eukaryotic genomes and have been shown to play critical roles in the development of multiple cancers.Through the application and development of ribosome analysis and sequencing technologies,advanced studies have discovered the translation of lncRNAs.Although lncRNAs were originally defined as noncoding RNAs,many lncRNAs actually contain small open reading frames that are translated into peptides.This opens a broad area for the functional investigation of lncRNAs.Here,we introduce prospective methods and databases for screening lncRNAs with functional polypeptides.We also summarize the specific lncRNA-encoded proteins and their molecular mechanisms that promote or inhibit cancerous.Importantly,the role of lncRNA-encoded peptides/proteins holds promise in cancer research,but some potential challenges remain unresolved.This review includes reports on lncRNA-encoded peptides or proteins in cancer,aiming to provide theoretical basis and related references to facilitate the discovery of more functional peptides encoded by lncRNA,and to further develop new anti-cancer therapeutic targets as well as clinical biomarkers of diagnosis and prognosis.

Large-scale translatome profiling annotates the functional genome and reveals the key role of genic 30 untranslated regions in translatomic variation in plants

The translatome,a profile of the translational status of genetic information within cells,provides a new perspective on gene expression.Although many plant genomes have been sequenced,comprehensive translatomic annotations are not available for plants due to a lack of efficient translatome profiling techniques.Here,we developed a new technique termed 30 ribosome-profiling sequencing(30Ribo-seq)for reliable,robust translatomic profiling.30Ribo-seq combines polysome profiling and 30 selection with a barcoding and pooling strategy.Systematic translatome profiling of different tissues of Arabidopsis,rice,and maize using conventional ribosome profiling(Ribo-seq)and 30Ribo-seq revealed many novel translational genomic loci,thereby complementing functional genome annotation in plants.Using the low-cost,efficient 30Ribo-seq technique and genome-wide association mapping of translatome expression(eGWAS),we performed a population-level dissection of the translatomes of 159 diverse maize inbred lines and identified 1,777 translational expression quantitative trait loci(eQTLs).Notably,local eQTLs are significantly enriched in the 30 untranslated regions of genes.Detailed eQTL analysis suggested that sequence variation around the polyadenylation(polyA)signal motif plays a key role in translatomic variation.Our study provides a comprehensive translatome annotation of plant functional genomes and introduces 30Ribo-seq,which paves the way for deep translatomic analysis at the population level.

Combined analyses of translatome and transcriptome in Arabidopsis reveal new players responding to magnesium deficiency

Translational control of gene expression,including recruitment of ribosomes to messenger RNA(mRNA),is particularly important during the response to stress.Purification of ribosomeassociated mRNAs using translating ribosome affinity purification(TRAP)followed by RNAsequencing facilitates the study of mRNAs undergoing active transcription and better proxies the translatome,or protein response,to stimuli.To identify plant responses to Magnesium(Mg)deficiency at the translational level,we combined transcriptome and translatome analyses.Excitingly,we found 26 previously unreported Mg-responsive genes that were only regulated at the translational level and not the transcriptional level,during the early response to Mg deficiency.In addition,mutants of the transcription factor ELONGATED HYPOCOTYL 5(HY5),the H^(+)/CATION EXCHANGER 1 and 3(CAX1 and CAX3),and UBIQUITIN 11(UBQ11)exhibited early chlorosis phenotype under Mg deficiency,supporting their functional involvement in ion homeostasis.Overall,our study strongly supports that TRAP-seq combined with RNA-seq followed by phenotype screening could facilitate the identification of novel players during stress responses.

Effects and translatomics characteristics of a small-molecule inhibitor of METTL3 against non-small cell lung cancer

In non-small cell lung cancer(NSCLC),the heterogeneity promotes drug resistance,and the restricted expression of programmed death-ligand 1(PD-L1)limits the immunotherapy benefits.Based on the mechanisms related to translation regulation and the association with PD-L1 of methyltransferaselike 3(METTL3),the novel small-molecule inhibitor STM2457 is assumed to be useful for the treatment of NSCLC.We evaluated the efficacy of STM2457 in vivo and in vitro and confirmed the effects of its inhibition on disease progression.Next,we explored the effect of STM2457 on METTL3 and revealed its effects on the inhibition of catalytic activity and upregulation of METTL3 protein expression.Importantly,we described the genome-wide characteristics of multiple omics data acquired from RNA sequencing,ribosome profiling,and methylated RNA immunoprecipitation sequencing data under STM2457 treatment or METTL3 knockout.We also constructed a model for the regulation of the translation of METTL3 and PD-L1.Finally,we found PD-L1 upregulation by STM2457 in vivo and in vitro.In conclusion,STM2457 is a potential novel suppressor based on its inhibitory effect on tumor progression and may be able to overcome the heterogeneity based on its impact on the translatome.Furthermore,it can improve the immunotherapy outcomes based on PDL1 upregulation in NSCLC.