Publications

The comment by Sánchez-Tójar et al. (2020, Ecol Lett) questioned the methodology, transparency and conclusion of our study (Ecol Lett, 22, 2019, 1976). The comment has overlooked important evolutionary assumptions in their reanalysis, and the issues raised were in fact dealt with through the peer-review process. Far from being biased, the key conclusion of our meta-analysis still stands; transgenerational effects are largely adaptive.

Eukaryotic histone deacetylation, critical for maintaining nucleosome structure and regulating gene expression, is mediated by histone deacetylases (HDACs). Although nucleosomes have been reported to regulate mRNA polyadenylation in humans, the role of HDACs in regulating polyadenylation has not been uncovered. Taking advantage of phenotypic studies on Arabidopsis, HDA6 (one of HDACs) was found to be a critical part of many biological processes. Here, we report that HDA6 affects mRNA polyadenylation in Arabidopsis Poly(A) sites of up-regulated transcripts are closer to the histone acetylation peaks in hda6 compared to the wild-type Col-0. HDA6 is required for the deacetylation of histones around DNA on nucleosomes, which solely coincides with up-regulated or uniquely presented poly(A) sites in hda6 Furthermore, defective HDA6 results in an overrepresentation of the canonical poly(A) signal (AAUAAA) usage. Chromatin loci for generating AAUAAA-type transcripts have a comparatively low H3K9K14ac around poly(A) sites when compared to other noncanonical poly(A) signal-containing transcripts. These results indicate that HDA6 regulates polyadenylation in a histone deacetylation-dependent manner in Arabidopsis.

Large amounts of wastewater are generated from stone processing, which are toxic and cause serious environmental and health risks. To quantify the content of stone processing wastewater and estimate its effects on plant growth, we collected water samples from sewage outfall of four stone processing factories and nearby water bodies. The concentration of potential toxic metals were much higher in the wastewater than background controls. Wastewater inhibited plant primary root elongation, lateral root formation, and growth of aerial part. Seedlings treated with the effluents were unhealthy with deep purple leaves and usually died before flowering. Chlorophyll a/b contents and chloroplast number were reduced in those abnormal mesophyll cells. Transcriptional levels were decreased for chloroplast formation genes, but increased for those participated in chloroplast degradation and catabolism. Six out of nine tested senescence-associated genes were up-regulated. Furthermore, our results show that endogenous toxic metal levels indeed increased after wastewater treatment. Altogether, these results indicated that the potential toxic metals rich wastewater had significant inhibition on plant growth and led to senescence-associated program cell death, which could be helpful for the government and enterprises to understand the environmental risks and formulate reasonable wastewater emission standards for the stone processing industry.

Pre-mRNA cleavage and polyadenylation is an essential step for almost all mRNA in eukaryotes. The cis-elements around the poly(A) sites, however, are very diverse among different organisms. We characterized the poly(A) signals of seven different species, and compared them with that of four well-studied organisms. We found that ciliates do not show any dominant poly(A) signal; a triplet (UAA) and tetramers (UAAA and GUAA) are dominant in diatoms and red alga, respectively; and green alga Ostreococcus uses UGUAA as its poly(A) signal. Spikemoss and moss use conserved AAUAAA signals that are similar to other land plants. Our analysis suggests that the first two bases (NN in NNUAAA) are likely degenerated whereas UAAA appears to be the core motif. Combined with other published results, it is suggested that the highly conserved poly(A) signal AAUAAA may be derived from UAA with an intermediate, putative UAAA, following a pathway of UAA→UAAA→AAUAAA.

Alternative polyadenylation (APA) is a widespread post-transcriptional mechanism that regulates gene expression through mRNA metabolism, playing a pivotal role in modulating phenotypic traits in rice (Oryza sativa L.). However, little is known about the APA-mediated regulation underlying the distinct characteristics between two major rice subspecies, indica and japonica. Using a poly(A)-tag sequencing approach, polyadenylation (poly(A)) site profiles were investigated and compared pairwise from germination to the mature stage between indica and japonica, and extensive differentiation in APA profiles was detected genome-wide. Genes with subspecies-specific poly(A) sites were found to contribute to subspecies characteristics, particularly in disease resistance of indica and cold-stress tolerance of japonica. In most tissues, differential usage of APA sites exhibited an apparent impact on the gene expression profiles between subspecies, and genes with those APA sites were significantly enriched in quantitative trait loci (QTL) related to yield traits, such as spikelet number and 1000-seed weight. In leaves of the booting stage, APA site-switching genes displayed global shortening of 3' untranslated regions with increased expression in indica compared with japonica, and they were overrepresented in the porphyrin and chlorophyll metabolism pathways. This phenomenon may lead to a higher chlorophyll content and photosynthesis in indica than in japonica, being associated with their differential growth rates and yield potentials. We further constructed an online resource for querying and visualizing the poly(A) atlas in these two rice subspecies. Our results suggest that APA may be largely involved in developmental differentiations between two rice subspecies, especially in leaf characteristics and the stress response, broadening our knowledge of the post-transcriptional genetic basis underlying the divergence of rice traits.

The post-transcriptional regulation involved in the responses of diatoms to silicon is poorly understood. Using a poly(A)-tag sequencing (PAT-seq) technique that interrogates only the junctions of 3'-untranslated region (UTR) and the poly(A) tails at the transcriptome level, a comprehensive comparison of alternative polyadenylation (APA) was performed to understand the role of post-transcriptional regulation in various silicon-related cellular responses for the marine diatom Thalassiosira pseudonana. In total, 23 701 poly(A) clusters and 6894 APA genes, treated with silicon starvation and replenishment, were identified at nine time points. Significant APA was found in numerous genes (e.g. five cingulin genes) closely associated with the silicon-starvation response, girdle bands and valve synthesis, suggesting that many genes participated in the responses to silicon availability and biosilica formation through changes in transcript isoforms. The poly(A) site usage profiles were distinct during various stages of silicon biomineralization responses. Moreover, a correlation between APA and expression levels of APA switching genes was also discovered. This is an interesting study that presents a genome-wide profile of transcript ends in diatoms, which is distinct from that of higher plants, animals and other microalgae. This work provides an important resource to understand a different aspect of cell-wall synthesis.

Alternative polyadenylation (APA) has been discovered to play regulatory roles in the development of many cancer cells through preferential addition of a poly(A) tail at specific sites of pre-mRNA. A recent study found that APA was involved in the mediation of acute myeloid leukaemia (AML). However, unlike gene expression heterogeneity, little attention has been directed toward variations in single-cell APA for different cell types during AML development. Here, we used single-cell RNA-seq data of a massive population of 16,843 bone marrow mononuclear cells (BMMCs) from healthy and AML patient samples to investigate dynamic APA usage in different cell types. Abnormalities of APA dynamics in the BMMCs from AML patient samples were uncovered compared to the stable APA dynamics in samples from healthy individuals, as well as lower APA diversity between eight cell types in AML patients. Genes with APA dynamics specific to the AML samples were significantly enriched in cellular signal transduction pathways that contribute to AML development. Moreover, many leukaemic cell marker genes such as NF-κB, GATA2 and IAP-Family genes exhibited APA dynamics that specifically affected abnormal proliferation and differentiation of leukemic BMMCs. Additionally, mature erythroid cells displayed greater APA dynamics and global 3' UTR shortening compared with other cell types. Our results revealed extensive involvement of APA regulation in leukemia development and erythropoiesis at the single-cell level, providing a high-resolution atlas to navigate cellular mRNA processing landscapes of differentiated cells in AML.

Transcriptional networks are tightly controlled in plant development and stress responses. Alternative polyadenylation (APA) has been found to regulate gene expression under abiotic stress by increasing the heterogeneity at mRNA 3'-ends. Heavy metals like cadmium pollute water and soil due to mining and industry applications. Understanding how plants cope with heavy metal stress remains an interesting question. The Arabidopsis root hair was chosen as a single cell model to investigate the functional role of APA in cadmium stress response. Primary root growth inhibition and defective root hair morphotypes were observed. Poly(A) tag (PAT) libraries from single cell types, i.e., root hair cells, non-hair epidermal cells, and whole root tip under cadmium stress were prepared and sequenced. Interestingly, a root hair cell type-specific gene expression under short term cadmium exposure, but not related to the prolonged treatment, was detected. Differentially expressed poly(A) sites were identified, which largely contributed to altered gene expression, and enriched in pentose and glucuronate interconversion pathways as well as phenylpropanoid biosynthesis pathways. Numerous genes with poly(A) site switching were found, particularly for functions in cell wall modification, root epidermal differentiation, and root hair tip growth. Our findings suggest that APA plays a functional role as a potential stress modulator in root hair cells under cadmium treatment.

Genetic admixture, the intraspecific hybridization among divergent introduced sources, can immediately facilitate colonization via hybrid vigor and profoundly enhance invasion via contributing novel genetic variation to adaption. As hybrid vigor is short-lived, provisioning adaptation is anticipated to be the dominant and long-term profit of genetic admixture, but the evidence for this is rare. We employed the 30 years' geographic-scale invasion of the salt marsh grass, Spartina alterniflora, as an evolutionary experiment and evaluated the consequences of genetic admixture by combining the reciprocal transplant experiment with quantitative and population genetic surveys. Consistent with the documentation, we found that the invasive populations in China had multiple origins from the southern Atlantic coast and the Gulf of Mexico in the US. Interbreeding among these multiple sources generated a "hybrid swarm" that spread throughout the coast of China. In the northern and mid-latitude China, natural selection greatly enhanced fecundity, plant height and shoot regeneration compared to the native populations. Furthermore, genetic admixture appeared to have broken the negative correlation between plant height and shoot regeneration, which was genetically-based in the native range, and have facilitated the evolution of super competitive genotypes in the invasive range. In contrast to the evolved northern and mid-latitude populations, the southern invasive populations showed slight increase of plant height and shoot regeneration compared to the native populations, possibly reflecting the heterotic effect of the intraspecific hybridization. Therefore, our study suggests a critical role of genetic admixture in accelerating the geographic invasion via provisioning rapid adaptive evolution.

A crucial step for mRNA polyadenylation is poly(A) signal recognition by trans-acting factors. The mammalian cleavage and polyadenylation specificity factor (CPSF) complex components CPSF30 and WD repeat-containing protein33 (WDR33) recognize the canonical AAUAAA for polyadenylation. In Arabidopsis (Arabidopsis thaliana), the flowering time regulator FY is the homolog of WDR33. However, its role in mRNA polyadenylation is poorly understood. Using poly(A) tag sequencing, we found that >50% of alternative polyadenylation (APA) events are altered in fy single mutants or double mutants with oxt6 (a null mutant of AtCPSF30), but mutation of the FY WD40-repeat has a stronger effect than deletion of the plant-unique Pro-Pro-Leu-Pro-Pro (PPLPP) domain. fy mutations disrupt AAUAAA or AAUAAA-like poly(A) signal recognition. Notably, A-rich signal usage is suppressed in the WD40-repeat mutation but promoted in PPLPP-domain deficiency. However, fy mutations do not aggravate the altered signal usage in oxt6 Furthermore, the WD40-repeat mutation shows a preference for 3' untranslated region shortening, but the PPLPP-domain deficiency shows a preference for lengthening. Interestingly, the WD40-repeat mutant exhibits shortened primary roots and late flowering with alteration of APA of related genes. Importantly, the long transcripts of two APA genes affected in fy are related to abiotic stress responses. These results reveal a conserved and specific role of FY in mRNA polyadenylation.