Publications

BACKGROUND: The architecture of inflorescence in crops is a key agronomic feature determining grain yield and thus has been a major target trait of cereal domestication.

RESULTS: In this study, we show that a simple spreading panicle change in rice panicle shape, controlled by the Spreading Panicle 9 (SPR9) locus, also has a significant impact on the resistance to rice false smut (RFS). Meanwhile, we mapped a novel spr9 mutant gene between markers Indel5-18 and Indel5-22 encompassing a genomic region of 43-kb with six candidate genes. Through gene prediction and cDNA sequencing, we confirmed that LOC_Os05g38520 is the target gene in the spr9 mutant, which encodes 60 S ribosomal protein L36-2. Further analysis showed that the spr9 mutant is caused by a 1 bp deletion in the first exon that resulted in premature termination. Knockout experiments showed that the SPR9 gene is responsible for the spreading panicle phenotype of the spr9 mutant. Interestingly, the spr9 mutant was found to improve resistance to RFS without affecting major agronomic traits. Taken together, our results revealed that the spr9 allele has good application prospects in rice breeding for disease resistance and panicle improvement.

CONCLUSIONS: We report the map-based cloning and functional characterization of SPR9, which encodes a 60 S ribosomal protein that regulates spreading panicles and affects the resistance to false smut in rice.

Microglia play an important role in neuroinflammation and neurodegeneration. Here, we report an approach for generating microglia-containing cerebral organoids derived from human pluripotent stem cells involving the supplementation of growth factors (FGF, EGF, heparin) and 10% CO2 culture conditions. Using this platform, Western Pacific Amyotrophic Lateral Sclerosis and Parkinsonism-Dementia Complex (ALS-PDC) cerebral organoids were generated from patient-derived induced pluripotent stem cells (iPSCs). These ALS-PDC-affected organoids had more reactive astrocytes and M1 microglia, and had fewer M2 microglia than their unaffected counterparts, leading to impaired microglia-mediated phagocytosis. RNA-seq analysis of ALS-PDC and control organoids indicated that the most significant changes were microglia- and astrocyte-related genes (IFITM1/2, TGF-β, and GFAP). The most significantly downregulated pathway was type I interferon signaling. Interferon-gamma supplementation increased IFITM expression, enhanced microglia-mediated phagocytosis, and reduced beta-amyloid accumulation in ALS-PDC-affected network. The results demonstrated the feasibility of using microglia-containing organoids for the study of neurodegenerative diseases.

Cleavage and polyadenylation specificity factor (CPSF) is a protein complex that plays an essential biochemical role in mRNA 3'-end formation, including poly(A) signal recognition and cleavage at the poly(A) site. However, its biological functions at the organismal level are mostly unknown in multicellular eukaryotes. The study of plant CPSF73 has been hampered by the lethality of Arabidopsis (Arabidopsis thaliana) homozygous mutants of AtCPSF73-I and AtCPSF73-II. Here, we used poly(A) tag sequencing to investigate the roles of AtCPSF73-I and AtCPSF73-II in Arabidopsis treated with AN3661, an antimalarial drug with specificity for parasite CPSF73 that is homologous to plant CPSF73. Direct seed germination on an AN3661-containing medium was lethal; however, 7-d-old seedlings treated with AN3661 survived. AN3661 targeted AtCPSF73-I and AtCPSF73-II, inhibiting growth through coordinating gene expression and poly(A) site choice. Functional enrichment analysis revealed that the accumulation of ethylene and auxin jointly inhibited primary root growth. AN3661 affected poly(A) signal recognition, resulted in lower U-rich signal usage, caused transcriptional readthrough, and increased the distal poly(A) site usage. Many microRNA targets were found in the 3' untranslated region lengthened transcripts; these miRNAs may indirectly regulate the expression of these targets. Overall, this work demonstrates that AtCPSF73 plays important part in co-transcriptional regulation, affecting growth, and development in Arabidopsis.

Because allohexaploid wheat genome contains ABD subgenomes, how the expression of homoeologous genes is coordinated remains largely unknown, particularly at the co-transcriptional level. Alternative polyadenylation (APA) is an important part of co-transcriptional regulation, which is crucial in developmental processes and stress responses. Drought stress is a major threat to the stable yield of wheat. Focusing on APA, we used poly(A) tag sequencing to track poly(A) site dynamics in wheat under drought stress. The results showed that drought stress led to extensive APA involving 37-47% of differentially expressed genes in wheat. Significant poly(A) site switching was found in stress-responsive genes. Interestingly, homoeologous genes exhibit unequal numbers of poly(A) sites, divergent APA patterns with tissue specificity and time-course dynamics, and distinct 3'-UTR length changes. Moreover, differentially expressed transcripts in leaves and roots used different poly(A) signals, the up- and downregulated isoforms had distinct preferences for non-canonical poly(A) sites. Genes that encode key polyadenylation factors showed differential expression patterns under drought stress. In summary, poly(A) signals and the changes in core poly(A) factors may widely affect the selection of poly(A) sites and gene expression levels during the response to drought stress, and divergent APA patterns among homoeologous genes add extensive plasticity to this responsive network. These results not only reveal the significant role of APA in drought stress response, but also provide a fresh perspective on how homoeologous genes contribute to adaptability through transcriptome diversity. In addition, this work provides information about the ends of transcripts for a better annotation of the wheat genome.

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.

Salt stress threatens plant growth, development and crop yields, and has become a critical global environmental issue. Increasing evidence has suggested that the epigenetic mechanism such as DNA methylation can mediate plant response to salt stress through transcriptional regulation and transposable element (TE) silencing. However, studies exploring genome-wide methylation dynamics under salt stress remain limited, in particular, for studies on multiple genotypes. Here, we adopted four natural accessions of the model species Arabidopsis thaliana and investigated the phenotypic and genome-wide methylation responses to salt stress through whole-genome bisulfite sequencing (WGBS). We found that salt stress significantly changed plant phenotypes, including plant height, rosette diameter, fruit number, and aboveground biomass, and the change in biomass tended to depend on accessions. Methylation analysis revealed that genome-wide methylation patterns depended primarily on accessions, and salt stress caused significant methylation changes in ∼ 0.1% cytosines over the genomes. About 33.5% of these salt-induced differential methylated cytosines (DMCs) were located to transposable elements (TEs). These salt-induced DMCs were mainly hypermethylated and accession-specific. TEs annotated to have DMCs (DMC-TEs) across accessions were found mostly belonged to the superfamily of Gypsy, a type II transposon, indicating a convergent DMC dynamic on TEs across different genetic backgrounds. Moreover, 8.0% of salt-induced DMCs were located in gene bodies and their proximal regulatory regions. These DMCs were also accession-specific, and genes annotated to have DMCs (DMC-genes) appeared to be more accession-specific than DMC-TEs. Intriguingly, both accession-specific DMC-genes and DMC-genes shared by multiple accessions were enriched in similar functions, including methylation, gene silencing, chemical homeostasis, polysaccharide catabolic process, and pathways relating to shifts between vegetative growth and reproduction. These results indicate that, across different genetic backgrounds, methylation changes may have convergent functions in post-transcriptional, physiological, and phenotypic modulation under salt stress. These convergent methylation dynamics across accession may be autonomous from genetic variation or due to convergent genetic changes, which requires further exploration. Our study provides a more comprehensive picture of genome-wide methylation dynamics under salt stress, and highlights the importance of exploring stress response mechanisms from diverse genetic backgrounds.

Salt tolerance is an important mechanism by which plants can adapt to a saline environment. To understand the process of salt tolerance, we performed global analyses of mRNA alternative polyadenylation (APA), an important regulatory mechanism during eukaryotic gene expression, in Arabidopsis thaliana and its halophytic relative Eutrema salsugineum with regard to their responses to salt stress. Analyses showed that while APA occurs commonly in both Arabidopsis and Eutrema, Eutrema possesses fewer APA genes than Arabidopsis (47% vs. 54%). However, the proportion of APA genes was significantly increased in Arabidopsis under salt stress but not in Eutrema. This indicated that Arabidopsis is more sensitive to salt stress and that Eutrema exhibits an innate response to such conditions. Both species utilized distal poly(A) sites under salt stress; however, only eight genes were found to overlap when their 3' untranslated region (UTR) lengthen genes were compared, thus revealing their distinct responses to salt stress. In Arabidopsis, genes that use distal poly(A) sites were enriched in response to salt stress. However, in Eutrema, the use of poly(A) sites was less affected and fewer genes were enriched. The transcripts with upregulated poly(A) sites in Arabidopsis showed enriched pathways in plant hormone signal transduction, starch and sucrose metabolism, and fatty acid elongation; in Eutrema, biosynthetic pathways (stilbenoid, diarylheptanoid, and gingerol) and metabolic pathways (arginine and proline) showed enrichment. APA was associated with 42% and 29% of the differentially expressed genes (DE genes) in Arabidopsis and Eutrema experiencing salt stress, respectively. Salt specific poly(A) sites and salt-inducible APA events were identified in both species; notably, some salt tolerance-related genes and transcription factor genes exhibited differential APA patterns, such as CIPK21 and LEA4-5. Our results suggest that adapted species exhibit more orderly response at the RNA maturation step under salt stress, while more salt-specific poly(A) sites were activated in Arabidopsis to cope with salinity conditions. Collectively, our findings not only highlight the importance of APA in the regulation of gene expression in response to salt stress, but also provide a new perspective on how salt-sensitive and salt-tolerant species perform differently under stress conditions through transcriptome diversity.

Alternative polyadenylation (APA) of pre-mRNA is an important co-transcriptional mechanism that modulates gene expression, leading to transcriptomic and functional diversities. The role of APA in Arabidopsis leaf development, however, remains elusive. We applied a poly(A)-tag sequencing (PAT-seq) technique to characterize APA-mediated regulation events in cotyledon and in five stages of true leaf development. Over 60% APA was identified in genes expressed in leaves, consistent with the results in previous publications. However, a reduced APA level was detected in younger leaves, reaching 44% in the 18th true leaf. Importantly, we also found that >70% of the poly(A) site usages were altered in the second true leaf relative to the cotyledon. Compared with the cotyledon, more genes in the second true leaf tended to use the distal site of 3'UTR, but this was not found in pairwise comparison among other true leaves. In addition, a significant APA gene was found to be decreased in a pairwise comparison among true leaves, including differentially expressed genes. The APA genes identified herein were associated with specific biological processes, including metabolic and cellular processes and response to stimuli and hormones. These results provide a new insight into the regulation of Arabidopsis leaf development through APA.

Aquaporins (AQPs) play important roles in plant growth, development and tolerance to environmental stresses. To understand the role of AQPs in the mangrove plant Kandelia obovata, which has the ability to acquire water from seawater, we identified 34 AQPs in the K. obovata genome and analysed their structural features. Phylogenetic analysis revealed that KoAQPs are homologous to AQPs of Populus and Arabidopsis, which are evolutionarily conserved. The key amino acid residues were used to assess water-transport ability. Analysis of cis-acting elements in the promoters indicated that KoAQPs may be stress- and hormone-responsive. Subcellular localization of KoAQPs in yeast showed most KoAQPs function in the membrane system. That transgenic yeast with increased cell volume showed that some KoAQPs have significant water-transport activity, and the substrate sensitivity assay indicates that some KoAQPs can transport H2 O2 . The transcriptome data were used to analyze the expression patterns of KoAQPs in different tissues and developing fruits of K. obovata. In addition, real-time quantitative PCR analyses combined transcriptome data showed that KoAQPs have complex responses to environmental factors, including salinity, flooding and cold. Collectively, the transport of water and solutes by KoAQPs contributed to the adaptation of K. obovata to the coastal intertidal environment.

The process of plastids developing into chloroplasts is critical for plants to survive. However, this process in woody plants is less understood. Kandelia obovata Sheue, Liu & Yong is a viviparous mangrove species; the seeds germinate on the maternal tree, and the hypocotyls continue to develop into mature propagules. We identified rare albino propagules through field observation among normal green and brown ones. Toward unveiling the propagule plastid development mechanism, albino propagule leaves only have etioplasts, low photosynthesis rates, and drastically reduced chlorophyll a/b and carotenoid contents, but with increased superoxide dismutase activities. To identify candidate genes controlling propagule plastid development, a genome-wide association study (GWAS) was performed between the albino and green propagules. Twenty-five significant single nucleotide polymorphisms (SNPs) were associated with albino propagule plastid development, the most significant SNPs being located on chromosomes 1 and 5. Significant differentially expressed genes were identified in porphyrin and chlorophyll metabolisms, carotenoid and flavonoid biosynthesis by combining transcriptome and GWAS data. In particular, KoDELLAs, encoding a transcription factor and KoCHS, encoding chalcone synthase, may be essential to regulate the albino propagules plastid development through weakened chlorophyll and flavonoid biosynthesis pathways while promoting chlorophyll degradation. Our results provide insights into genetic mechanisms regulating propagule plastid development in woody plants.