Role of FY in polyadenylation

APA是存在于真核生物中一种重要的基因表达调控机制，其关键步骤是mRNA前体的核苷酸序列的识别，直接决定了成熟mRNA转录本的序列。本项目研究人员全面探讨了FY不同结构域在poly(A)位点使用中的作用，同时阐明FY与AtCPSF30在polyA信号识别过程中的关系。进一步研究发现FY的WD40结构域的突变与PPLPP结构域的缺失对3’UTR区间polyA位点选择和信号使用有着相反的影响。该论文揭示了拟南芥开花因子FY在选择性多聚腺苷化（Alternative PolyAdenylation, APA）过程中的功能，为植物复杂的多聚腺苷化（polyA）信号识别机制提供遗传学证据，完善了植物polyA过程的分子机制，同时为深入理解通过APA调控植物生长发育和植物对环境响应的分子机制奠定基础。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 WDR33 recognize the canonical AAUAAA signal for efficient polyadenylation. In Arabidopsis thaliana, the flowering time regulator FY is the homologue of WDR33. However, its role in mRNA polyadenylation is poorly understood. Using poly(A) tag sequencing, we found that over 50% of alternative polyadenylation (APA) events are altered in fy single mutants or double mutants with Atcpsf30, but mutation of the FY WD40-repeat has a stronger effect than deletion of the plant-unique 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 Pro-Pro-Leu-Pro-Pro (PPLPP)-domain deficiency. However, fy mutations do not aggravate the alteration of signal usage in the Atcpsf30 null mutant. Furthermore, the WD40-repeat mutation shows a preference for 3'UTR 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.This work was supported in part by a grant from the National Key R&D Project of China (2016YFE0108800), a grant from the U.S. NSF (IOS-154173), both to QQL, and grants (2017M620274, 2018T110649) from China Postdoctoral Science Foundation to JL

Predictive modeling of plant messenger RNA polyadenylation sites

BACKGROUND: One of the essential processing events during pre-mRNA maturation is the post-transcriptional addition of a polyadenine [poly(A)] tail. The 3'-end poly(A) track protects mRNA from unregulated degradation, and indicates the integrity of mRNA through recognition by mRNA export and translation machinery. The position of a poly(A) site is predetermined by signals in the pre-mRNA sequence that are recognized by a complex of polyadenylation factors. These signals are generally tri-part sequence patterns around the cleavage site that serves as the future poly(A) site. In plants, there is little sequence conservation among these signal elements, which makes it difficult to develop an accurate algorithm to predict the poly(A) site of a given gene. We attempted to solve this problem. RESULTS: Based on our current working model and the profile of nucleotide sequence distribution of the poly(A) signals and around poly(A) sites in Arabidopsis, we have devised a Generalized Hidden Markov Model based algorithm to predict potential poly(A) sites. The high specificity and sensitivity of the algorithm were demonstrated by testing several datasets, and at the best combinations, both reach 97%. The accuracy of the program, called poly(A) site sleuth or PASS, has been demonstrated by the prediction of many validated poly(A) sites. PASS also predicted the changes of poly(A) site efficiency in poly(A) signal mutants that were constructed and characterized by traditional genetic experiments. The efficacy of PASS was demonstrated by predicting poly(A) sites within long genomic sequences. CONCLUSION: Based on the features of plant poly(A) signals, a computational model was built to effectively predict the poly(A) sites in Arabidopsis genes. The algorithm will be useful in gene annotation because a poly(A) site signifies the end of the transcript. This algorithm can also be used to predict alternative poly(A) sites in known genes, and will be useful in the design of transgenes for crop genetic engineering by predicting and eliminating undesirable poly(A) sites

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms ( SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds ( a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines - in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases

A Restricted Role for FcγR in the Regulation of Adaptive Immunity.

By their interaction with IgG immune complexes, FcγR and complement link innate and adaptive immunity, showing functional redundancy. In complement-deficient mice, IgG downstream effector functions are often impaired, as well as adaptive immunity. Based on a variety of model systems using FcγR-knockout mice, it has been concluded that FcγRs are also key regulators of innate and adaptive immunity; however, several of the model systems underpinning these conclusions suffer from flawed experimental design. To address this issue, we generated a novel mouse model deficient for all FcγRs (FcγRI/II/III/IV-/- mice). These mice displayed normal development and lymphoid and myeloid ontogeny. Although IgG effector pathways were impaired, adaptive immune responses to a variety of challenges, including bacterial infection and IgG immune complexes, were not. Like FcγRIIb-deficient mice, FcγRI/II/III/IV-/- mice developed higher Ab titers but no autoantibodies. These observations indicate a redundant role for activating FcγRs in the modulation of the adaptive immune response in vivo. We conclude that FcγRs are downstream IgG effector molecules with a restricted role in the ontogeny and maintenance of the immune system, as well as the regulation of adaptive immunity

Microglia-containing cerebral organoids derived from induced pluripotent stem cells for the study of neurological diseases

Summary: 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

Anti-CD11b antibody treatment suppresses the osteoclast generation, inflammatory cell infiltration, and autoantibody production in arthritis-prone FcγRIIB-deficient mice

Abstract Background Previously we established an arthritis-prone FcγRIIB-deficient mouse strain (designated KO1). Anti-mouse CD11b mAb (5C6) has been reported to inhibit the recruitment of peripheral CD11b+ myelomonocytic cells from the blood to the inflammatory site. These cells include neutrophils and monocytes, both of which play important roles in the development of arthritis. Here we treated KO1 mice with 5C6 mAb in order to study its effect on arthritis development. Methods To evaluate the disease-preventive effect of 5C6, 4-month-old preclinical KO1 mice were divided into three groups: the first treated with 5C6 for 6 months, the second treated with normal rat IgG for 6 months, as a control, and the third left untreated. Arthritis severity and immunological abnormalities were compared among the groups, along with transcriptional levels of several important arthritis-related factors in ankle joints, spleen, and peripheral blood cells. Results The 5C6 treatment ameliorated arthritis in KO1 mice, showing decreases in inflammatory cell infiltration and osteoclast formation. Analysis of transcriptional levels in ankle joints revealed that compared with the two control groups, the 5C6-treated group showed downregulated expression of RANK, RANKL, MCP-1, RANTES, TNFα, and IL-6, and at the same time showed significantly up-regulated expression of the decoy receptor for RANKL, i.e. osteoprotegerin. In addition, the disease suppression was associated with the lower serum levels of autoantibodies, and the decreased frequencies of activated B cells and plasma cells. The expression levels of B cell activation/differentiation-related cytokines were suppressed in spleen and peripheral leukocytes of the 5C6-treated mice. Intriguingly, while untreated KO1 mice spontaneously developed marked monocytosis, the 5C6-treated mice showed the significantly down-regulated frequency of monocytes. Conclusions The outcome of 5C6 treatment was complex, in which the 5C6-mediated disease-preventive effect is likely due on one hand to the decrease in the recruitment of inflammatory cells and osteoclast precursor monocytes from the periphery into the joints, and on the other hand to the suppression of B cell activation/maturation and of autoantibody production via the suppression of B cell stimulating cytokine production. The lower levels of these cytokines may be the secondary effect of the lower frequency of monocytes, since monocytes/macrophages are the major producers of these cytokines

多种环境条件下的亲本效应均惠及后代：基于动植物数据的元分析研究

在生物界，当上代生存环境恶劣时，是否一定会带给后代一个消极、负面的影响?环境与生态学院李庆顺教授课题组就此展开了大数据元分析研究，综合分析了从上世纪90年代至今的大量相关研究数据,从关键词索引得到的1000余篇论文中，筛选出139篇研究论文，这些论文涉及112个物种，包括不同的亲代环境处理、不同的子世代等。结果发现，对那些世代周期短、活动能力受限的一年生植物和无脊椎动物（如昆虫），无论上一代经历的是优质环境还是恶劣环境，这些经历总能使子代受益。但是，对于脊椎动物如老鼠和人等，只有上代经历优质环境才能使其子代受益。这一“源头”上的机制发现或为今后快速改良农作物，使其更有效应对干旱、升温、虫害等不良影响提供一种思路和方向。The adaptive value of transgenerational effects (the ancestor environmental effects on offspring) in changing environments has received much attention in recent years, but the related empirical evidence remains equivocal. Here, we conducted a meta‐analysis summarising 139 experimental studies in plants and animals with 1170 effect sizes to investigate the generality of transgenerational effects across taxa, traits, and environmental contexts. It was found that transgenerational effects generally enhanced offspring performance in response to both stressful and benign conditions. The strongest effects are in annual plants and invertebrates, whereas vertebrates appear to benefit mostly under benign conditions, and perennial plants show hardly any transgenerational responses at all. These differences among taxonomic/life‐history groups possibly reflect that vertebrates can avoid stressful conditions through their mobility, and longer‐lived plants have alternative strategies. In addition to environmental contexts and taxonomic/life‐history groups, transgenerational effects also varied among traits and developmental stages of ancestors and offspring, but the effects were similarly strong across three generations of offspring. By way of a more comprehensive data set and a different effect size, our results differ from those of a recent meta‐analysis, suggesting that transgenerational effects are widespread, strong and persistent and can substantially impact the responses of plants and animals to changing environments.This study is supported by the National Natural Science Foundation of China (grant No. 31600291 to Y‐YZ) and the Fundamental Research Funds for the Central Universities in China (grant No. 20720170074 to Y‐YZ)