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Tenascin C Deletion Impairs Tendon Healing and Functional Recovery After Rotator Cuff Repair Tenascin C缺失会影响肩袖修复后的肌腱愈合和功能恢复
Pub Date : 2024-09-15 DOI: 10.1101/2024.09.11.612543
ROBERT TASHJIAN, Jared Zitnay, Nikolas Kazmers, Shivakumar Veerabhadraiah, Antonio Zelada, Matthew Honeggar, Matthew Smith, Peter Chalmers, Heath Henninger, Michael Jurynec
The biological factors that affect healing after rotator cuff repair (RCR) are not well understood. Genetic variants in the extracellular matrix protein Tenascin C (TNC) are associated with impaired tendon healing and it is expressed in rotator cuff tendon tissue after injury, suggesting it may have a role in the repair process. The purpose of the current study was to determine the role of TNC on tendon healing after RCR in a murine model. The supraspinatus tendon was transected and repaired on the left shoulder of Wild-Type (WT-RCR), Tenascin C null (Tnc--RCR) and Tnc heterozygous (Tnc+/--RCR) mice. Controls included the unoperated, contralateral shoulder of WT-RCR, Tnc-RCR, Tnc+/--RCR mice and unoperated shoulders from age and genotype matched controls. We performed histologic, activity testing, RNA-seq, and biomechanical analyses. At 8-weeks post-RCR, Tnc- and Tnc+/- mice had severe bone and tendon defects following rotator cuff repair. Tnc--RCR mice had reduced activity after rotator cuff repair including reduced wheel rotations, wheel duration, and wheel episode average velocity compared with WT-RCR. Loss of Tnc following RCR altered gene expression in the shoulder, including upregulation of sex hormone and WNT pathways and a downregulation of inflammation and cell cycle pathways. Tnc- mice had similar biomechanical properties after repair as WT. Further research is required to evaluate tissue specific alterations of Tnc, the interactions of Tnc and sex hormone and inflammation pathways as well as possible adjuvants to improve enthesis healing in the setting of reduced TNC function.
影响肩袖修复术(RCR)后愈合的生物学因素尚不十分清楚。细胞外基质蛋白Tenascin C(TNC)的基因变异与肌腱愈合受损有关,它在损伤后的肩袖肌腱组织中表达,表明它可能在修复过程中发挥作用。本研究的目的是在小鼠模型中确定 TNC 对 RCR 后肌腱愈合的作用。对野生型(WT-RCR)、Tenascin C无效型(Tnc--RCR)和Tnc杂合型(Tnc+/-RCR)小鼠的左肩冈上肌腱进行横断和修复。对照组包括 WT-RCR、Tnc-RCR、Tnc+/-RCR 小鼠未手术的对侧肩部,以及年龄和基因型匹配的对照组未手术的肩部。我们进行了组织学、活动测试、RNA-seq 和生物力学分析。在肩袖修复术后8周,Tnc-和Tnc+/-小鼠在肩袖修复后出现了严重的骨和肌腱缺损。与WT-RCR相比,Tnc--RCR小鼠在肩袖修复后活动减少,包括车轮旋转次数、车轮持续时间和车轮发作平均速度减少。RCR后Tnc的缺失改变了肩部的基因表达,包括性激素和WNT通路的上调以及炎症和细胞周期通路的下调。Tnc-小鼠修复后的生物力学特性与WT小鼠相似。还需要进一步研究,以评估Tnc的组织特异性改变、Tnc与性激素和炎症途径的相互作用,以及在TNC功能降低的情况下改善内骨愈合的可能佐剂。
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引用次数: 0
Solanum pan-genomics and pan-genetics reveal paralogs as contingencies in crop engineering 茄科植物泛基因组学和泛遗传学揭示了作物工程中的旁系亲缘关系
Pub Date : 2024-09-14 DOI: 10.1101/2024.09.10.612244
Matthias Benoit, Katharine M Jenike, James W Satterlee, Srividya Ramakrishnan, Iacopo Gentile, Anat Hendelman, Michael J Passalacqua, Hamsini Suresh, Hagai Shohat, Gina M Robitaille, Blaine Fitzgerald, Michael M Alonge, Xingang Wang, Ryan Santos, Jia He, Shujun Ou, Hezi Golan, Yumi Green, Kerry Swartwood, Gina P Sierra, Andres Orejuela, Federico Fornaguera, Sara Goodwin, William Richard McCombie, Elizabeth Balyejusa Kizito, Edeline Gagnon, Sandra Knapp, Tiina Sarkinen, Amy Frary, Jesse Gillis, Joyce Van Eck, Michael C Schatz, Zachary B Lippman
Pan-genomics and genome editing technologies are revolutionizing the breeding of globally cultivated crops. A transformative opportunity lies in the reciprocal exchange of genotype-to-phenotype knowledge of agricultural traits between these major crops and hundreds of locally cultivated indigenous crops, thereby enhancing the diversity and resilience of our food system. However, species-specific genetic variants and their interactions with desired natural or engineered mutations pose barriers to achieving predictable phenotypic effects, even between closely related crops or genotypes. Here, by establishing a pan-genome of the crop-rich genus Solanum and integrating functional genomics and genetics, we show that gene duplication and subsequent paralog diversification are a major obstacle to genotype-phenotype predictability. Despite broad conservation of gene macrosynteny among chromosome-scale references for 22 species, including 13 indigenous crops, hundreds of global and lineage-specific gene duplications exhibited dynamic evolutionary trajectories in paralog sequence, expression, and function, including among members of key domestication gene families. Extending our pan-genome with 10 cultivars of African eggplant and leveraging quantitative genetics and genome editing, we uncovered an intricate history of paralog emergence and evolution within this indigenous crop. The loss of an ancient redundant paralog of the classical regulator of stem cell proliferation and fruit organ number, CLAVATA3 (CLV3), was compensated by a lineage-specific tandem duplication. Subsequent pseudogenization of the derived copy followed by a cultivar-specific structural variant resulted in a single fused functional copy of CLV3 that modifies locule number alongside a newly identified gene controlling the same trait. Our findings demonstrate that paralog diversifications over short evolutionary periods are critical yet underexplored contingencies in trait evolvability and independent crop domestication histories. Unraveling these contingencies is crucial for translating genotype-to-phenotype relationships across related species.
泛基因组学和基因组编辑技术正在彻底改变全球栽培作物的育种。这些主要作物与数百种当地栽培的土著作物之间可以相互交流农业性状的基因型到表型知识,从而提高我们粮食系统的多样性和复原力,这是一个变革性的机遇。然而,物种特有的基因变异及其与所需的自然或工程突变之间的相互作用,对实现可预测的表型效应构成了障碍,即使在亲缘关系很近的作物或基因型之间也是如此。在这里,通过建立作物丰富的茄属的泛基因组并整合功能基因组学和遗传学,我们表明基因复制和随后的旁系多样化是基因型-表型可预测性的主要障碍。尽管包括 13 种本土作物在内的 22 个物种的染色体尺度参考文献中的基因大合成得到了广泛的保护,但数百个全球性和品系特异性基因重复在旁系序列、表达和功能方面表现出动态的进化轨迹,包括关键驯化基因家族成员之间的进化轨迹。通过对非洲茄子的 10 个栽培品种进行泛基因组扩展,并利用定量遗传学和基因组编辑技术,我们发现了这种本土作物中旁系亲属出现和进化的复杂历史。干细胞增殖和果实器官数量的经典调控因子CLAVATA3(CLV3)的一个古老冗余旁系亲属的缺失被一个特定品系的串联重复所弥补。随后对衍生拷贝进行假基因化,再加上栽培品种特异性结构变异,形成了 CLV3 的单个融合功能拷贝,它与新发现的控制相同性状的基因一起改变了子房室数。我们的研究结果表明,短进化时期的旁系变异是性状可进化性和独立作物驯化历史中至关重要但却未被充分探索的偶然因素。揭示这些偶然性对于在相关物种间转换基因型到表型的关系至关重要。
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引用次数: 0
SCAMPI: A scalable statistical framework for genome-wide interaction testing harnessing cross-trait correlations SCAMPI:利用跨性状相关性进行全基因组交互作用测试的可扩展统计框架
Pub Date : 2024-09-14 DOI: 10.1101/2024.09.10.612314
Shijia Bian, Andrew J. Bass, Yue Liu, Aliza P. Wingo, Thomas Wingo, David J. Cutler, Michael P. Epstein
Family-based heritability estimates of complex traits are often considerably larger than their single-nucleotide polymorphism (SNP) heritability estimates. This discrepancy may be due to non-additive effects of genetic variation, including variation that interacts with other genes or environmental factors to influence the trait. Variance-based procedures provide a computationally efficient strategy to screen for SNPs with potential interaction effects without requiring the specification of the interacting variable. While valuable, such variance-based tests consider only a single trait and ignore likely pleiotropy among related traits that, if present, could improve power to detect such interaction effects. To fill this gap, we propose SCAMPI (Scalable Cauchy Aggregate test using Multiple Phenotypes to test Interactions), which screens for variants with interaction effects across multiple traits. SCAMPI is motivated by the observation that SNPs with pleiotropic interaction effects induce genotypic differences in the patterns of correlation among traits. By studying such patterns across genotype categories among multiple traits, we show that SCAMPI has improved performance over traditional univariate variance-based methods. Like those traditional variance-based tests, SCAMPI permits the screening of interaction effects without requiring the specification of the interaction variable and is further computationally scalable to biobank data. We employed SCAMPI to screen for interacting SNPs associated with four lipid-related traits in the UK Biobank and identified multiple gene regions missed by existing univariate variance-based tests. SCAMPI is implemented in software for public use.
基于家系的复杂性状遗传率估计值往往大大高于其单核苷酸多态性(SNP)遗传率估计值。造成这种差异的原因可能是遗传变异的非加成效应,包括与其他基因或环境因素相互作用影响性状的变异。基于方差的程序提供了一种计算效率高的策略,用于筛选具有潜在交互效应的 SNP,而无需说明交互变量。虽然这种基于方差的检验很有价值,但它只考虑了单一性状,而忽略了相关性状之间可能存在的多效性。为了填补这一空白,我们提出了 SCAMPI(使用多表型测试交互作用的可扩展考奇聚合检验),它可以筛选出在多个性状中具有交互作用的变异体。SCAMPI 的原理是观察到具有多向交互效应的 SNPs 会导致性状间相关模式的基因型差异。通过研究多个性状间不同基因型类别的这种模式,我们发现 SCAMPI 比传统的基于单变量方差的方法有更好的表现。与那些传统的基于方差的检验方法一样,SCAMPI 允许筛选交互效应,而不需要指定交互变量,而且在计算上可进一步扩展到生物库数据。我们利用 SCAMPI 筛选了英国生物库中与四种脂质相关性状有关的互作 SNPs,并发现了现有基于单变量方差检验所遗漏的多个基因区域。SCAMPI 已在软件中实现,供公众使用。
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引用次数: 0
EBAX-1/ZSWIM8 destabilizes miRNAs resulting in transgenerational memory of a predatory trait EBAX-1/ZSWIM8会破坏miRNA的稳定性,导致掠夺性性状的世代记忆
Pub Date : 2024-09-14 DOI: 10.1101/2024.09.10.612280
Shiela Pearl Quiobe, Ata Kalirad, Waltraud Roeseler, Hanh Witte, Yinan Wang, Christian Roedelsperger, Ralf J. Sommer
Environmental influences on traits and associated transgenerational epigenetic inheritance have widespread implications, but remain controversial and underlying mechanisms poorly understood. We introduce long-term environmental induction experiments on alternative diets in Pristionchus pacificus, a nematode exhibiting mouth-form plasticity including predation, by propagating 110 isogenic lines for 101 generations with associated food-reversal experiments. We found dietary induction and subsequent transgenerational memory of the predatory morph and identified a role of ubiquitin ligase EBAX-1/ZSWIM8 in this process. Ppa-ebax-1 mutants have no memory and Ppa-EBAX-1 destabilizes the clustered microRNA family miR-2235a/miR-35. Deletions of a cluster of 44 identical miR-2235a copies resulted in precocious and extended transgenerational inheritance of the predatory morph. These findings indicate that EBAX-1/ZSWIM8 destabilizes miRNAs resulting in transgenerational memory, suggesting a role for target-directed miRNA degradation.
环境对性状的影响以及相关的跨代表观遗传具有广泛的影响,但仍然存在争议,而且对其潜在的机制了解甚少。我们通过将 110 个同源品系繁殖 101 代,并进行相关的食物反转实验,在 Pristionchus pacificus(一种表现出包括捕食在内的口形可塑性的线虫)中引入了替代饮食的长期环境诱导实验。我们发现了捕食形态的饮食诱导和随后的跨代记忆,并确定了泛素连接酶 EBAX-1/ZSWIM8 在这一过程中的作用。Ppa-ebax-1突变体没有记忆,而Ppa-EBAX-1会破坏成簇的microRNA家族miR-2235a/miR-35的稳定性。44个相同的miR-2235a拷贝集群的缺失导致捕食性形态的早熟和延长的跨代遗传。这些研究结果表明,EBAX-1/ZSWIM8会破坏miRNA的稳定性,从而导致转基因记忆,这表明靶向miRNA降解的作用。
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引用次数: 0
Pushing the limits of single molecule transcript sequencing to uncover the largest disease-associated transcript isoforms in the human neural retina 突破单分子转录本测序的极限,发现人类神经视网膜中最大的疾病相关转录本同工形式
Pub Date : 2024-09-14 DOI: 10.1101/2024.09.10.612265
Merel Stemerdink, Tabea Riepe, Nick Zomer, Renee Salz, Michael Kwint, Raoul Timmermans, Barbara Ferrari, Stefano Ferrari, Alfredo Duenas Rey, Emma Delanote, Suzanne E de Bruijn, Hannie Kremer, Susanne Roosing, Frauke Coppieters, Alexander Hoischen, Frans P.M. Cremers, Peter A.C. 't Hoen, Erwin van Wijk, Erik de Vrieze
Sequencing technologies have long limited the comprehensive investigation of large transcripts associated with inherited retinal diseases (IRDs) like Usher syndrome, which involves 11 associated genes with transcripts up to 19.6 kb. To address this, we used PacBio long-read mRNA isoform sequencing (Iso-Seq) following standard library preparation and an optimized workflow to enrich for long transcripts in the human neural retina. While our workflow achieved sequencing of transcripts up to 15 kb, this was insufficient for Usher syndrome-associated genes USH2A and ADGRV1, with transcripts of 18.9 kb and 19.6 kb, respectively. To overcome this, we employed the Samplix Xdrop System for indirect target enrichment of cDNA, a technique typically used for genomic DNA capture. This method facilitated the successful capture and sequencing of ADGRV1 transcripts as well as the full-length 18.9 kb USH2A transcripts. By combining algorithmic analysis with detailed manual curation of sequenced reads, we identified novel isoforms and alternative splicing events across the 11 Usher syndrome-associated genes, with implications for diagnostics and therapy development. Our findings demonstrate the Xdrop systems adaptability for cDNA capture and the advantages of integrating computational and manual transcript analyses. The full neural retina sequencing dataset is available via EGA under identifier EGAD50000000720.
长期以来,测序技术一直限制着对与遗传性视网膜疾病(IRD)相关的大转录本的全面研究,如Usher综合征,它涉及11个相关基因,转录本长达19.6 kb。为了解决这个问题,我们使用 PacBio 长读程 mRNA 同工酶测序(Iso-Seq),采用标准文库制备和优化的工作流程来富集人类神经视网膜中的长转录本。虽然我们的工作流程能对长达 15 kb 的转录本进行测序,但这对于乌谢尔综合征相关基因 USH2A 和 ADGRV1 来说是不够的,这两个基因的转录本分别为 18.9 kb 和 19.6 kb。为了克服这一问题,我们采用了 Samplix Xdrop 系统对 cDNA 进行间接目标富集,这是一种通常用于基因组 DNA 捕获的技术。这种方法有助于成功捕获 ADGRV1 转录本和全长 18.9 kb 的 USH2A 转录本并进行测序。通过将算法分析与对测序读数的详细手工整理相结合,我们发现了 11 个乌谢尔综合征相关基因中的新型同工酶和替代剪接事件,这对诊断和治疗开发具有重要意义。我们的研究结果证明了Xdrop系统对cDNA捕获的适应性,以及将计算和人工转录本分析相结合的优势。完整的神经视网膜测序数据集可通过 EGA 获得,标识符为 EGAD50000000720。
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引用次数: 0
Comparative transcriptome and variant analyses of the pancreatic islets of a rat model of obese type 2 diabetes identifies a frequently distributed nonsense mutation in the lipocalin 2 gene 对肥胖型 2 型糖尿病大鼠模型的胰岛进行转录组和变异比较分析,发现脂联素 2 基因中存在一种频繁分布的无义突变
Pub Date : 2024-09-14 DOI: 10.1101/2024.09.13.609843
Norihide Yokoi, Naoki Adachi, Tomoki Hirokoji, Kenta Nakano, Minako Yoshihara, Saki Shigenaka, Ryuya Urakawa, Yukio Taniguchi, Yusaku Yoshida, Shigeo Yokose, Mikita Suyama, Tadashi Okamura
We have recently established the Zucker fatty diabetes mellitus (ZFDM) rat as a novel model of obese type 2 diabetes (T2D), originating from the obese Zucker fatty (ZF) rat harboring a missense mutation in the leptin receptor gene. Pathogenesis of dysfunction of the pancreatic islets and genetic factors of T2D in ZFDM rats remain unknown. Here, we perform comparative transcriptome and variant analyses of the pancreatic islets between the two strains. Among differentially expressed genes irrespective of obesity and glucose intolerance states, we identify a nonsense mutation, c.409C>T (p.Gln137X), in the lipocalin 2 (Lcn2) gene which encodes a secreted protein called neutrophil gelatinase-associated lipocalin, a well-known biomarker for inflammation. Interestingly, we find that the Lcn2 mutation is distributed widely in rat species, such as commonly used DA and F344 strains. We examine the Lcn2 mutation as a strong candidate gene for T2D in ZFDM rats by using genome editing of ZFDM rats in which the nonsense mutation is replaced with a wild-type nucleotide. We find that the genome editing well works but also observe that there is no significant difference in the development of T2D between genome-edited and original ZFDM rats. Finally, we perform a genetic linkage analysis by using backcross progeny between ZF and ZFDM rats and confirm that the Lcn2 mutation exhibits no significant association with the onset of T2D. Our data indicate that several rat strains would serve as Lcn2 deficient models, contributing to elucidate pathophysiological roles of Lcn2 in a wide variety of phenotypes.
我们最近建立了扎克脂肪性糖尿病(ZFDM)大鼠作为肥胖型 2 型糖尿病(T2D)的新型模型,该模型源自瘦素受体基因发生错义突变的肥胖扎克脂肪性(ZF)大鼠。ZFDM大鼠胰岛功能障碍的发病机制和T2D的遗传因素仍不清楚。在这里,我们对两个品系的胰岛进行了转录组和变异分析。在与肥胖和葡萄糖不耐受状态无关的差异表达基因中,我们在脂联素 2(Lcn2)基因中发现了一个无义突变,即 c.409C>T(p.Gln137X),该基因编码一种叫做中性粒细胞明胶酶相关脂联素的分泌蛋白,它是一种众所周知的炎症生物标志物。有趣的是,我们发现 Lcn2 基因突变广泛分布于大鼠物种中,如常用的 DA 和 F344 品系。我们通过对 ZFDM 大鼠进行基因组编辑,将无义突变替换为野生型核苷酸,将 Lcn2 突变作为 ZFDM 大鼠 T2D 的强候选基因进行研究。我们发现基因组编辑的效果很好,但也观察到基因组编辑后的 ZFDM 大鼠与原始 ZFDM 大鼠在 T2D 的发病率上没有显著差异。最后,我们利用 ZF 大鼠和 ZFDM 大鼠之间的回交后代进行了遗传关联分析,证实 Lcn2 突变与 T2D 的发病无明显关联。我们的数据表明,多个大鼠品系可作为 Lcn2 缺陷模型,有助于阐明 Lcn2 在多种表型中的病理生理作用。
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引用次数: 0
Somatic evolution of cancer genes in sex chromosomes 性染色体中癌症基因的体细胞进化
Pub Date : 2024-09-13 DOI: 10.1101/2024.09.11.612525
Antonio Marco, Amarachi C Akachukwu, Jasmine Samantha Ratcliff
Genes on sex chromosomes have higher evolutionary rates than those on autosomes. However, this does not necessarily apply to somatic evolution in cancer. Many dominant mutations have been described in the so-called proto-oncogenes (OGs), while recessive mutations are typically described in tumor-suppressor genes (TSGs). Evidence indicates that mutations in X-chromosome TSGs are more likely to contribute to cancer than those in autosomal TSGs. Here, we formalize this in several dynamic models and predict, as expected, that mutations spread faster in TSGs located on the X chromosome than on autosomes (faster-X effect). Conversely, mutations in OGs spread faster on autosomes than on the X chromosome, but under high selective pressure, this difference is negligible. Published genomic screenings of cancer samples show evidence of the faster-X effect in TSGs. This pattern is observed in both sexes, suggesting that the maintenance of X-chromosome inactivation during cancer progression plays an important role in the evolution of TSGs. Strikingly, the relative mutation incidence in X-linked TSGs among females across individual studies is bimodal, with one group of studies showing a faster-X effect and another group showing similar incidences for X-linked and autosomal TSGs. This differentiation between cancer samples is not associated with the specific type of cancer or the tissue of origin. This may indicate that X-chromosome inactivation plays a differential role in the involvement of X-linked TSGs across individual cancers.
性染色体上的基因比常染色体上的基因有更高的进化率。然而,这并不一定适用于癌症的体细胞进化。在所谓的原癌基因(OGs)中出现了许多显性突变,而隐性突变通常出现在抑癌基因(TSGs)中。有证据表明,X 染色体 TSG 基因突变比常染色体 TSG 基因突变更有可能导致癌症。在这里,我们用几个动态模型正式说明了这一点,并预测,与常染色体相比,位于 X 染色体上的 TSG 中的突变传播速度更快(更快-X 效应)。相反,OGs 中的突变在常染色体上比在 X 染色体上传播得更快,但在高选择压力下,这种差异可以忽略不计。已发表的癌症样本基因组筛查结果显示,TSGs 中存在较快的 X 效应。这种模式在男女两性中均可观察到,这表明在癌症进展过程中维持 X 染色体失活在 TSG 的进化过程中起着重要作用。令人震惊的是,在各项研究中,女性 X 连锁 TSG 的相对突变发生率呈双峰分布,一组研究显示了较快的 X 效应,另一组研究显示 X 连锁 TSG 和常染色体 TSG 的发生率相似。癌症样本之间的这种差异与癌症的具体类型或原发组织无关。这可能表明,X 染色体失活在不同癌症的 X 连锁 TSG 参与中起着不同的作用。
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引用次数: 0
Stabilising selection enriches the tails of complex traits with rare alleles of large effect 稳定选择使复杂性状的尾部富含具有较大效应的稀有等位基因
Pub Date : 2024-09-12 DOI: 10.1101/2024.09.12.612687
Anil PS Ori, Carla Giner-Delgado, Clive Julian Hoggart, Paul F O'Reilly
Establishing the relative contribution of common and rare variants to complex trait heritability is a key goal of biomedical research. Recent statistical genetics inference suggests that common variants explain most complex trait heritability, but little is known about how genetic architecture varies across the trait continuum. If rare variants make a small contribution to heritability but have their effects concentrated in the tails of complex traits, where disease typically manifests, then they may have a greater clinical impact than previously inferred. Here, we perform simulations using the forward-in-time simulator SLiM to generate realistic population genetic and complex trait data, in which traits evolve under neutrality or stabilising selection. Recent studies suggest that stabilising selection is the dominant force shaping the genetic architecture of complex traits, consistent with our simulations in that data simulated under stabilising selection here more closely resembles real data. Moreover, we observe a shift of rare, large-effect alleles towards the tails of the complex trait distribution under stabilising selection. In our simulations, individuals in the tails of complex traits are, depending on the strength of selection, 10-20x more likely to harbour singleton or extremely rare alleles of large effect under stabilising selection than neutrality. Such an enrichment of rare, large-effect alleles in the tails of real complex traits subject to stabilising selection could have important implications for the design of studies to detect rare variants, as well as for the prediction and prevention of complex disease.
确定常见变异和罕见变异对复杂性状遗传性的相对贡献是生物医学研究的一个关键目标。最近的统计遗传学推断表明,常见变异解释了大多数复杂性状的遗传率,但人们对遗传结构在性状连续体中的变化知之甚少。如果罕见变异对遗传率的贡献很小,但其影响集中在复杂性状的尾部,而疾病通常就表现在尾部,那么它们对临床的影响可能比以前推断的更大。在这里,我们使用时间前向模拟器 SLiM 进行模拟,生成现实的群体遗传和复杂性状数据,其中性状在中性或稳定选择下进化。最近的研究表明,稳定选择是塑造复杂性状遗传结构的主导力量,这与我们的模拟结果一致,即在稳定选择下模拟的数据更接近真实数据。此外,我们观察到在稳定选择下,稀有的大效应等位基因会向复杂性状分布的尾部移动。在我们的模拟中,根据选择强度的不同,在稳定选择条件下,复杂性状尾部的个体携带单个或极其罕见的大效应等位基因的可能性是中性条件下的 10-20 倍。在实际复杂性状的尾部,稀有、大效应等位基因在稳定选择下的这种富集可能会对检测稀有变异的研究设计以及复杂疾病的预测和预防产生重要影响。
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引用次数: 0
Genetic suppression interactions are highly conserved across genetic backgrounds 不同遗传背景下的遗传抑制相互作用高度一致
Pub Date : 2024-09-12 DOI: 10.1101/2024.08.28.610086
Claire Paltenghi, Jolanda van Leeuwen
Genetic suppression occurs when the phenotypic defects caused by a deleterious mutation are rescued by another mutation. Suppression interactions are of particular interest for genetic diseases, as they identify ways to reduce disease severity, thereby potentially highlighting avenues for therapeutic intervention. To what extent suppression interactions are influenced by the genetic background in which they operate remains largely unknown. However, a high degree of suppression conservation would be crucial for developing therapeutic strategies that target suppressors. To gain an understanding of the effect of the genetic context on suppression, we isolated spontaneous suppressor mutations of temperature sensitive alleles of SEC17, TAO3, and GLN1 in three genetically diverse natural isolates of the budding yeast Saccharomyces cerevisiae. After identifying and validating the genomic variants responsible for suppression, we introduced the suppressors in all three genetic backgrounds, as well as in a laboratory strain, to assess their specificity. Ten out of eleven tested suppression interactions were conserved in the four yeast strains, although the extent to which a suppressor could rescue the temperature sensitive mutant varied across genetic backgrounds. These results suggest that suppression mechanisms are highly conserved across genetic contexts, a finding that is potentially reassuring for the development of therapeutics that mimic genetic suppressors.
当一个有害突变造成的表型缺陷被另一个突变所挽救时,就会发生基因抑制。遗传抑制相互作用对遗传疾病特别重要,因为它们能确定降低疾病严重程度的方法,从而可能为治疗干预提供途径。抑制相互作用在多大程度上受遗传背景的影响,目前仍是一个未知数。然而,高度的抑制保护对于开发针对抑制因子的治疗策略至关重要。为了了解遗传背景对抑制作用的影响,我们在三种不同基因的天然分离芽殖酵母中分离出了对温度敏感的等位基因 SEC17、TAO3 和 GLN1 的自发抑制突变。在确定并验证了导致抑制作用的基因组变异后,我们在所有三种遗传背景以及一个实验室菌株中引入了抑制剂,以评估它们的特异性。在四种酵母菌株中,测试的 11 种抑制相互作用中有 10 种是保守的,尽管抑制因子对温度敏感突变体的拯救程度在不同的遗传背景下有所不同。这些结果表明,抑制机制在不同的遗传背景下是高度保守的,这一发现对开发模拟遗传抑制因子的治疗药物具有潜在的指导意义。
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引用次数: 0
Genetic regulation of microRNAs in the older adult brain and their contribution to neuropsychiatric conditions 老年人大脑中 microRNA 的遗传调控及其对神经精神疾病的影响
Pub Date : 2024-09-12 DOI: 10.1101/2024.09.10.610174
Selina M Vattathil, Ekaterina S Gerasimov, Se Min Canon, Adriana Lori, Sarah Sze Min Tan, Paul J Kim, Yue Liu, Eric C Lai, David A C. Bennett, Thomas S Wingo, Aliza P Wingo
MicroRNAs are essential post-transcriptional regulators of gene expression and involved in many biological processes; however, our understanding of their genetic regulation and role in brain illnesses is limited. Here, we mapped brain microRNA expression quantitative trait loci (miR-QTLs) using genome-wide small RNA sequencing profiles from dorsolateral prefrontal cortex (dlPFC) samples of 604 older adult donors of European ancestry. miR-QTLs were identified for 224 miRNAs (48% of 470 tested miRNAs) at false discovery rate < 1%. We found that miR-QTLs were enriched in brain promoters and enhancers, and that intragenic miRNAs often did not share QTLs with their host gene. Additionally, we integrated the brain miR-QTLs with results from 16 GWAS of psychiatric and neurodegenerative diseases using multiple independent integration approaches and identified four miRNAs that contribute to the pathogenesis of bipolar disorder, major depression, post-traumatic stress disorder, schizophrenia, and Parkinson's disease. This study provides novel insights into the contribution of miRNAs to the complex biological networks that link genetic variation to disease.
微RNA是基因表达的重要转录后调控因子,参与了许多生物过程;然而,我们对它们的遗传调控及其在脑部疾病中的作用了解有限。在这里,我们利用全基因组小 RNA 测序图谱绘制了脑部 microRNA 表达定量性状位点(miR-QTLs),这些图谱来自 604 名欧洲血统的老年供体的背外侧前额叶皮层(dlPFC)样本。我们发现,miR-QTLs 富集在大脑启动子和增强子中,基因内的 miRNA 通常与其宿主基因不共享 QTLs。此外,我们使用多种独立的整合方法,将脑部 miR-QTL 与 16 种精神疾病和神经退行性疾病的 GWAS 结果进行了整合,发现了四种 miRNA,它们有助于双相情感障碍、重度抑郁症、创伤后应激障碍、精神分裂症和帕金森病的发病机制。这项研究为了解 miRNA 对将遗传变异与疾病联系起来的复杂生物网络的贡献提供了新的见解。
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bioRxiv - Genetics
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