Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica

The Arabidopsis U1 snRNP regulates mRNA 3'-end processing

The removal of introns by the spliceosome is a key gene regulatory mechanism in eukaryotes, with the U1 snRNP subunit playing a crucial role in the early stages of splicing. Studies in metazoans show that the U1 snRNP also conducts splicing-independent functions, but the lack of genetic tools and knowledge about U1 snRNP-associated proteins have limited the study of such splicing-independent functions in plants. Here we describe an RNA-centric approach that identified more than 200 proteins associated with the Arabidopsis U1 snRNP and revealed a tight link to mRNA cleavage and polyadenylation factors. Interestingly, we found that the U1 snRNP protects mRNAs against premature cleavage and polyadenylation within introns-a mechanism known as telescripting in metazoans-while also influencing alternative polyadenylation site selection in 3'-UTRs. Overall, our work provides a comprehensive view of U1 snRNP interactors and reveals novel functions in regulating mRNA 3'-end processing in Arabidopsis, laying the groundwork for understanding non-canonical functions of plant U1 snRNPs.

Dynamics of alternative polyadenylation in single root cells of Arabidopsis thaliana

Introduction

Single-cell RNA-seq (scRNA-seq) technologies have been widely used to reveal the diversity and complexity of cells, and pioneering studies on scRNA-seq in plants began to emerge since 2019. However, existing studies on plants utilized scRNA-seq focused only on the gene expression regulation. As an essential post-transcriptional mechanism for regulating gene expression, alternative polyadenylation (APA) generates diverse mRNA isoforms with distinct 3' ends through the selective use of different polyadenylation sites in a gene. APA plays important roles in regulating multiple developmental processes in plants, such as flowering time and stress response.

Methods

In this study, we developed a pipeline to identify and integrate APA sites from different scRNA-seq data and analyze APA dynamics in single cells. First, high-confidence poly(A) sites in single root cells were identified and quantified. Second, three kinds of APA markers were identified for exploring APA dynamics in single cells, including differentially expressed poly(A) sites based on APA site expression, APA markers based on APA usages, and APA switching genes based on 3' UTR (untranslated region) length change. Moreover, cell type annotations of single root cells were refined by integrating both the APA information and the gene expression profile.

Results

We comprehensively compiled a single-cell APA atlas from five scRNA-seq studies, covering over 150,000 cells spanning four major tissue branches, twelve cell types, and three developmental stages. Moreover, we quantified the dynamic APA usages in single cells and identified APA markers across tissues and cell types. Further, we integrated complementary information of gene expression and APA profiles to annotate cell types and reveal subtle differences between cell types.

Discussion

This study reveals that APA provides an additional layer of information for determining cell identity and provides a landscape of APA dynamics during Arabidopsis root development.

Alternative polyadenylation profiles of susceptible and resistant rice (Oryza sativa L.) in response to bacterial leaf blight using RNA-seq

BACKGROUND

Alternative polyadenylation (APA) is an important pattern of post-transcriptional regulation of genes widely existing in eukaryotes, involving plant physiological and pathological processes. However, there is a dearth of studies investigating the role of APA profile in rice leaf blight.

RESULTS

In this study, we compared the APA profile of leaf blight-susceptible varieties (CT 9737-613P-M) and resistant varieties (NSIC RC154) following bacterial blight infection. Through gene enrichment analysis, we found that the genes of two varieties typically exhibited distal poly(A) (PA) sites that play different roles in two kinds of rice, indicating differential APA regulatory mechanisms. In this process, many disease-resistance genes displayed multiple transcripts via APA. Moreover, we also found five polyadenylation factors of similar expression patterns of rice, highlighting the critical roles of these five factors in rice response to leaf blight about PA locus diversity.

CONCLUSION

Notably, the present study provides the first dynamic changes of APA in rice in early response to biotic stresses and proposes a possible functional conjecture of APA in plant immune response, which lays the theoretical foundation for in-depth determination of the role of APA events in plant stress response and other life processes.

Natural variation in the plant polyadenylation complex

Messenger RNA polyadenylation, the process wherein the primary RNA polymerase II transcript is cleaved and a poly(A) tract added, is a key step in the expression of genes in plants. Moreover, it is a point at which gene expression may be regulated by determining the functionality of the mature mRNA. Polyadenylation is mediated by a complex (the polyadenylation complex, or PAC) that consists of between 15 and 20 subunits. While the general functioning of these subunits may be inferred by extending paradigms established in well-developed eukaryotic models, much remains to be learned about the roles of individual subunits in the regulation of polyadenylation in plants. To gain further insight into this, we conducted a survey of variability in the plant PAC. For this, we drew upon a database of naturally-occurring variation in numerous geographic isolates of Arabidopsis thaliana. For a subset of genes encoding PAC subunits, the patterns of variability included the occurrence of premature stop codons in some Arabidopsis accessions. These and other observations lead us to conclude that some genes purported to encode PAC subunits in Arabidopsis are actually pseudogenes, and that others may encode proteins with dispensable functions in the plant. Many subunits of the PAC showed patterns of variability that were consistent with their roles as essential proteins in the cell. Several other PAC subunits exhibit patterns of variability consistent with selection for new or altered function. We propose that these latter subunits participate in regulatory interactions important for differential usage of poly(A) sites.

Unravelling chilling-stress resistance mechanisms in endangered Mangrove plant Lumnitzera littorea (Jack) Voigt

Lumnitzera littorea (Jack) Voigt is one of the most endangered mangrove species in China. Previous studies have showed the impact of chilling stress on L. littorea and the repsonses at physiological and biochemical levels, but few attentions have been paid at molecular level. In this study, we conducted genome-wide investigation of transcriptional and post-transcriptional dynamics in L. littorea in response to chilling stress (8 °C day/5 °C night). In the seedlings of L. littorea, chilling sensing and signal transducing, photosystem II regeneration and peroxidase-mediated reactive oxygen species (ROS) scavenging were substantially enhanced to combat the adverse impact induced by chilling exposure. We further revealed that alternative polyadenylation (APA) events participated in chilling stress-responsive processes, including energy metabolism and steroid biosynthesis. Furthermore, APA-mediated miRNA regulations downregulated the expression of the genes involved in fatty acid biosynthesis and elongation, and protein phosphorylation, reflecting the important role of post-transcriptional regulation in modulating chilling tolerance in L. littorea. Our findings present a molecular view to the adaptive characteristics of L. littorea and shed light on the conservation genomic approaches of endangered mangrove species.

Stress responses of plants through transcriptome plasticity by mRNA alternative polyadenylation

The sessile nature of plants confines their responsiveness to changing environmental conditions. Gene expression regulation becomes a paramount mechanism for plants to adjust their physiological and morphological behaviors. Alternative polyadenylation (APA) is known for its capacity to augment transcriptome diversity and plasticity, thereby furnishing an additional set of tools for modulating gene expression. APA has also been demonstrated to exhibit intimate associations with plant stress responses. In this study, we review APA dynamic features and consequences in plants subjected to both biotic and abiotic stresses. These stresses include adverse environmental stresses, and pathogenic attacks, such as cadmium toxicity, high salt, hypoxia, oxidative stress, cold, heat shock, along with bacterial, fungal, and viral infections. We analyzed the overarching research framework employed to elucidate plant APA response and the alignment of polyadenylation site transitions with the modulation of gene expression levels within the ambit of each stress condition. We also proposed a general APA model where transacting factors, including poly(A) factors, epigenetic regulators, RNA m6A modification factors, and phase separation proteins, assume pivotal roles in APA related transcriptome plasticity during stress response in plants.

Genome-wide alternative polyadenylation dynamics underlying plant growth retardant-induced dwarfing of pomegranate

Dwarfed stature is a desired agronomic trait for pomegranate (Punica granatum L.), with its advantages such as lower cost and increased yield. A comprehensive understanding of regulatory mechanisms underlying the growth repression would provide a genetic foundation to molecular-assisted dwarfing cultivation of pomegranate. Our previous study induced dwarfed pomegranate seedlings via exogenous application of plant growth retardants (PGRs) and highlighted the important roles of differential expression of plant growth-related genes in eliciting the dwarfed phenotype of pomegranate. Alternative polyadenylation (APA) is an important post-transcriptional mechanism and has been demonstrated to act as a key regulator in plant growth and development. However, no attention has been paid to the role of APA in PGR-induced dwarfing in pomegranate. In this study, we characterized and compared APA-mediated regulation events underlying PGR-induced treatments and normal growth condition. Genome-wide alterations in the usage of poly(A) sites were elicited by PGR treatments, and these changes were involved in modulating the growth and development of pomegranate seedlings. Importantly, ample specificities were observed in APA dynamics among the different PGR treatments, which mirrors their distinct nature. Despite the asynchrony between APA events and differential gene expression, APA was found to regulate transcriptome via influencing microRNA (miRNA)-mediated mRNA cleavage or translation inhibition. A global preference for lengthening of 3' untranslated regions (3' UTRs) was observed under PGR treatments, which was likely to host more miRNA target sites in 3' UTRs and thus suppress the expression of the corresponding genes, especially those associated with developmental growth, lateral root branching, and maintenance of shoot apical meristem. Together, these results highlighted the key role of APA-mediated regulations in fine-tuning the PGR-induced dwarfed stature of pomegranate, which provides new insights into the genetic basis underlying the growth and development of pomegranate.

Alternative Polyadenylation Is a Novel Strategy for the Regulation of Gene Expression in Response to Stresses in Plants

Precursor message RNA requires processing to generate mature RNA. Cleavage and polyadenylation at the 3'-end in the maturation of mRNA is one of key processing steps in eukaryotes. The polyadenylation (poly(A)) tail of mRNA is an essential feature that is required to mediate its nuclear export, stability, translation efficiency, and subcellular localization. Most genes have at least two mRNA isoforms via alternative splicing (AS) or alternative polyadenylation (APA), which increases the diversity of transcriptome and proteome. However, most previous studies have focused on the role of alternative splicing on the regulation of gene expression. In this review, we summarize the recent advances concerning APA in the regulation of gene expression and in response to stresses in plants. We also discuss the mechanisms for the regulation of APA for plants in the adaptation to stress responses, and suggest that APA is a novel strategy for the adaptation to environmental changes and response to stresses in plants.

Coupling epigenetics and RNA polyadenylation: missing links

Precise regulation of gene expression is crucial for plant survival. As a cotranscriptional regulatory mechanism, pre-mRNA polyadenylation is essential for fine-tuning gene expression. Polyadenylation can be alternatively projected at various sites of a transcript, which contributes to transcriptome diversity. Epigenetic modification is another mechanism of transcriptional control. Recent studies have uncovered crosstalk between cotranscriptional polyadenylation processes and both epigenomic and epitranscriptomic markers. Genetic analyses have demonstrated that DNA methylation, histone modifications, and epitranscriptomic modification are involved in regulating polyadenylation in plants. Here we summarize current understanding of the links between epigenetics and polyadenylation and their novel biological efficacy for plant development and environmental responses. Unresolved issues and future directions are discussed to shed light on the field.

Novel Cyclized Derivatives of Ferulic Acid as Potential Antiviral Agents through Activation of Photosynthesis

To further develop new antiviral agents, several novel cyclized derivatives of ferulic acid were designed and synthesized. Their antiviral activities were evaluated against the cucumber mosaic virus (CMV), pepper mild mottle virus (PMMoV), and tomato spotted wilt virus (TSWV). The results showed that some ferulic acid derivatives exhibited desirable antiviral activities. Particularly, compound 5e exhibited excellent protective activities against CMV, PMMoV, and TSWV, with EC₅₀ values of 167.2, 102.5, and 145.8 μg mL^-1, respectively, which were superior to those obtained for trans-ferulic acid (581.7, 611.2, and 615.4 μg mL^-1), dufulin (312.6, 302.5, and 298.2 μg mL^-1), and ningnanmycin (264.3, 282.5, and 276.5 μg mL^-1). Thereafter, the protective mechanisms of 5e were evaluated through photosynthesis evaluation, transcriptome profiling, and proteomic analysis. The results indicated that 5e significantly activated the expression levels of photosynthesis-related regulatory genes and proteins in tobacco plants and promoted the accumulation of defense molecules to resist viral infection. Thus, the findings of this study indicated that novel cyclized ferulic acid derivatives are potential antiviral agents that act via regulating photosynthesis in the host.

Review: Mechanisms underlying alternative polyadenylation in plants - looking in the right places

Recent years have seen an explosion of interest in the subject of alternative polyadenylation in plants. Connections between the polyadenylation complex and numerous developmental and stress responses are well-established. However, those that link stimuli with the functioning of the polyadenylation complex are less well understood. To this end, it is imperative to clearly delineate the roles of the polyadenylation complex in both plant growth AND alternative polyadenylation. It is also necessary to understand the ways by which other molecular processes may contribute to alternative polyadenylation. This review discusses these issues, with a focus on instances that reveal mechanisms by which mRNA polyadenylation may be regulated. Insights from from characterizations of mutants affected in the polyadenylation complex are discussed, as are the limitations of such characterizations when it comes to teasing out cause and effect. These limitations encourage explorations to other processes that are beyond the core polyadenylation complex. Two such processes that sculpt the plant transcriptome - transcription termination and the epigenetic control of transposon activity - also contribute to regulated poly(A) site choice. These subjects define "the right places" - molecular mechanisms that contribute to the wide-ranging control of gene expression via mRNA polyadenylation.

Expanding the Coverage of Metabolic Landscape in Cultivated Rice with Integrated Computational Approaches

Genome-scale metabolomics analysis is increasingly used for pathway and function discovery in the post-genomics era. The great potential offered by developed mass spectrometry (MS)-based technologies has been hindered, since only a small portion of detected metabolites were identifiable so far. To address the critical issue of low identification coverage in metabolomics, we adopted a deep metabolomics analysis strategy by integrating advanced algorithms and expanded reference databases. The experimental reference spectra and in silico reference spectra were adopted to facilitate the structural annotation. To further characterize the structure of metabolites, two approaches were incorporated into our strategy, i.e., structural motif search combined with neutral loss scanning and metabolite association network. Untargeted metabolomics analysis was performed on 150 rice cultivars using ultra-performance liquid chromatography coupled with quadrupole-Orbitrap MS. Consequently, a total of 1939 out of 4491 metabolite features in the MS/MS spectral tag (MS2T) library were annotated, representing an extension of annotation coverage by an order of magnitude in rice. The differential accumulation patterns of flavonoids between indica and japonica cultivars were revealed, especially O-sulfated flavonoids. A series of closely-related flavonolignans were characterized, adding further evidence for the crucial role of tricin-oligolignols in lignification. Our study provides an important protocol for exploring phytochemical diversity in other plant species.

Comparative transcriptome analysis identifies genes associated with chlorophyll levels and reveals photosynthesis in green flesh of radish taproot

The flesh of the taproot of Raphanus sativus L. is rich in chlorophyll (Chl) throughout the developmental process, which is why the flesh is green. However, little is known about which genes are associated with Chl accumulation in this non-foliar, internal green tissue and whether the green flesh can perform photosynthesis. To determine these aspects, we measured the Chl content, examined Chl fluorescence, and carried out comparative transcriptome analyses of taproot flesh between green-fleshed "Cuishuai" and white-fleshed "Zhedachang" across five developmental stages. Numerous genes involved in the Chl metabolic pathway were identified. It was found that Chl accumulation in radish green flesh may be due to the low expression of Chl degradation genes and high expression of Chl biosynthesis genes, especially those associated with Part Ⅳ (from Protoporphyrin Ⅸ to Chl a). Bioinformatics analysis revealed that differentially expressed genes between "Cuishuai" and "Zhedachang" were significantly enriched in photosynthesis-related pathways, such as photosynthesis, antenna proteins, porphyrin and Chl metabolism, carbon fixation, and photorespiration. Twenty-five genes involved in the Calvin cycle were highly expressed in "Cuishuai". These findings suggested that photosynthesis occurred in the radish green flesh, which was also supported by the results of Chl fluorescence. Our study provides transcriptome data on radish taproots and provides new information on the formation and function of radish green flesh.

Gene Set Subtraction Reveals 633 Candidate Genes for Bamboo Culm Wall Thickening

Abundant research has been conducted on the physiological, biochemical, and anatomical aspects of bamboo culm wall thickening, but its molecular mechanism has not yet been investigated. In this study, we performed whole-genome resequencing of Phyllostachys edulis ‘Pachyloen’, Phyllostachys nidularia f. farcta, Phyllostachys heteroclada f. solida with significantly thicker culm walls, and Schizostachyum dumetorum var. xinwuense with extremely thin culm walls. Moreover, we pioneered the innovative use of gene set subtraction to explore candidate genes that regulate bamboo culm wall thickening. A candidate gene set, containing 633 genes, was obtained by eliminating shared genes that help maintain physiological processes after alignment with the P. edulis reference genome. Starch and sucrose, oxidative phosphorylation, and ribosome were the three most important pathways enriched by differentially expressed genes. Although it cannot be used for hyperfine localization of bamboo wall thickness-regulatory genes, gene set reduction narrows down the range of candidate genes at minimal cost and provides new clues for the application of bioinformatics in plant research.

scAPAtrap: identification and quantification of alternative polyadenylation sites from single-cell RNA-seq data

Alternative polyadenylation (APA) generates diverse mRNA isoforms, which contributes to transcriptome diversity and gene expression regulation by affecting mRNA stability, translation and localization in cells. The rapid development of 3' tag-based single-cell RNA-sequencing (scRNA-seq) technologies, such as CEL-seq and 10x Genomics, has led to the emergence of computational methods for identifying APA sites and profiling APA dynamics at single-cell resolution. However, existing methods fail to detect the precise location of poly(A) sites or sites with low read coverage. Moreover, they rely on priori genome annotation and can only detect poly(A) sites located within or near annotated genes. Here we proposed a tool called scAPAtrap for detecting poly(A) sites at the whole genome level in individual cells from 3' tag-based scRNA-seq data. scAPAtrap incorporates peak identification and poly(A) read anchoring, enabling the identification of the precise location of poly(A) sites, even for sites with low read coverage. Moreover, scAPAtrap can identify poly(A) sites without using priori genome annotation, which helps locate novel poly(A) sites in previously overlooked regions and improve genome annotation. We compared scAPAtrap with two latest methods, scAPA and Sierra, using scRNA-seq data from different experimental technologies and species. Results show that scAPAtrap identified poly(A) sites with higher accuracy and sensitivity than competing methods and could be used to explore APA dynamics among cell types or the heterogeneous APA isoform expression in individual cells. scAPAtrap is available at https://github.com/BMILAB/scAPAtrap.

Profiling Alternative 3' Untranslated Regions in Sorghum using RNA-seq Data

Sorghum is an important crop widely used for food, feed, and fuel. Transcriptome-wide studies of 3′ untranslated regions (3′UTR) using regular RNA-seq remain scarce in sorghum, while transcriptomes have been characterized extensively using Illumina short-read sequencing platforms for many sorghum varieties under various conditions or developmental contexts. 3′UTR is a critical regulatory component of genes, controlling the translation, transport, and stability of messenger RNAs. In the present study, we profiled the alternative 3′UTRs at the transcriptome level in three genetically related but phenotypically contrasting lines of sorghum: Rio, BTx406, and R9188. A total of 1,197 transcripts with alternative 3′UTRs were detected using RNA-seq data. Their categorization identified 612 high-confidence alternative 3′UTRs. Importantly, the high-confidence alternative 3′UTR genes significantly overlapped with the genesets that are associated with RNA N⁶-methyladenosine (m⁶A) modification, suggesting a clear indication between alternative 3′UTR and m⁶A methylation in sorghum. Moreover, taking advantage of sorghum genetics, we provided evidence of genotype specificity of alternative 3′UTR usage. In summary, our work exemplifies a transcriptome-wide profiling of alternative 3′UTRs using regular RNA-seq data in non-model crops and gains insights into alternative 3′UTRs and their genotype specificity.

The circadian clock shapes the Arabidopsis transcriptome by regulating alternative splicing and alternative polyadenylation

The circadian clock in plants temporally coordinates biological processes throughout the day, synchronizing gene expression with diurnal environmental changes. Circadian oscillator proteins are known to regulate the expression of clock-controlled plant genes by controlling their transcription. Here, using a high-throughput RNA-Seq approach, we examined genome-wide circadian and diurnal control of the Arabidopsis transcriptome, finding that the oscillation patterns of different transcripts of multitranscript genes can exhibit substantial differences and demonstrating that the circadian clock affects posttranscriptional regulation. In parallel, we found that two major posttranscriptional mechanisms, alternative splicing (AS; especially intron retention) and alternative polyadenylation (APA), display circadian rhythmicity resulting from oscillation in the genes involved in AS and APA. Moreover, AS-related genes exhibited rhythmic AS and APA regulation, adding another layer of complexity to circadian regulation of gene expression. We conclude that the Arabidopsis circadian clock not only controls transcription of genes but also affects their posttranscriptional regulation by influencing alternative splicing and alternative polyadenylation.

Genome-wide analysis identifies cis-acting elements regulating mRNA polyadenylation and translation during vertebrate oocyte maturation

Most cells change patterns of gene expression through transcriptional regulation. In contrast, oocytes are transcriptionally silent and regulate mRNA poly(A) tail length to control protein production. However, the genome-wide relationship of poly(A) tail changes to mRNA translation during vertebrate oocyte maturation is not known. We used Tail-seq and polyribosome analysis to measure poly(A) tail and translational changes during oocyte maturation in Xenopus laevis We identified large-scale poly(A) and translational changes during oocyte maturation, with poly(A) tail length changes preceding translational changes. Proteins important for completion of the meiotic divisions and early development exhibited increased polyadenylation and translation during oocyte maturation. A family of U-rich sequence elements was enriched near the polyadenylation signal of polyadenylated and translationally activated mRNAs. We propose that changes in mRNA polyadenylation are a conserved mechanism regulating protein expression during vertebrate oocyte maturation and that these changes are controlled by a spatial code of cis-acting sequence elements.

A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data

Alternative polyadenylation (APA) has been implicated to play an important role in post-transcriptional regulation by regulating mRNA abundance, stability, localization and translation, which contributes considerably to transcriptome diversity and gene expression regulation. RNA-seq has become a routine approach for transcriptome profiling, generating unprecedented data that could be used to identify and quantify APA site usage. A number of computational approaches for identifying APA sites and/or dynamic APA events from RNA-seq data have emerged in the literature, which provide valuable yet preliminary results that should be refined to yield credible guidelines for the scientific community. In this review, we provided a comprehensive overview of the status of currently available computational approaches. We also conducted objective benchmarking analysis using RNA-seq data sets from different species (human, mouse and Arabidopsis) and simulated data sets to present a systematic evaluation of 11 representative methods. Our benchmarking study showed that the overall performance of all tools investigated is moderate, reflecting that there is still lot of scope to improve the prediction of APA site or dynamic APA events from RNA-seq data. Particularly, prediction results from individual tools differ considerably, and only a limited number of predicted APA sites or genes are common among different tools. Accordingly, we attempted to give some advice on how to assess the reliability of the obtained results. We also proposed practical recommendations on the appropriate method applicable to diverse scenarios and discussed implications and future directions relevant to profiling APA from RNA-seq data.