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Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing. 从时间分辨单细胞 RNA 测序的动态相关性中揭示全球转录调控。
Pub Date : 2024-08-21 Epub Date: 2024-08-08 DOI: 10.1016/j.cels.2024.07.002
Dimitris Volteras, Vahid Shahrezaei, Philipp Thomas

Single-cell transcriptomics reveals significant variations in transcriptional activity across cells. Yet, it remains challenging to identify mechanisms of transcription dynamics from static snapshots. It is thus still unknown what drives global transcription dynamics in single cells. We present a stochastic model of gene expression with cell size- and cell cycle-dependent rates in growing and dividing cells that harnesses temporal dimensions of single-cell RNA sequencing through metabolic labeling protocols and cel lcycle reporters. We develop a parallel and highly scalable approximate Bayesian computation method that corrects for technical variation and accurately quantifies absolute burst frequency, burst size, and degradation rate along the cell cycle at a transcriptome-wide scale. Using Bayesian model selection, we reveal scaling between transcription rates and cell size and unveil waves of gene regulation across the cell cycle-dependent transcriptome. Our study shows that stochastic modeling of dynamical correlations identifies global mechanisms of transcription regulation. A record of this paper's transparent peer review process is included in the supplemental information.

单细胞转录组学揭示了细胞间转录活性的显著变化。然而,从静态快照中确定转录动态机制仍具有挑战性。因此,我们仍然不知道是什么驱动了单细胞中的全局转录动态。我们提出了一个基因表达的随机模型,该模型通过代谢标记协议和细胞周期报告器,利用单细胞 RNA 测序的时间维度,计算生长和分裂细胞中与细胞大小和细胞周期相关的速率。我们开发了一种并行且高度可扩展的近似贝叶斯计算方法,该方法可纠正技术差异,并在整个转录组范围内准确量化细胞周期中的绝对突变频率、突变大小和降解率。利用贝叶斯模型选择,我们揭示了转录率与细胞大小之间的比例关系,并揭示了依赖于细胞周期的转录组中的基因调控波。我们的研究表明,动态相关性的随机建模可以识别转录调控的全球机制。补充信息中包含了本文透明的同行评审过程记录。
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引用次数: 0
Evaluation of Kernfeld et al.: Toward best practices for tackling false positives in regulatory network inference. 对 Kernfeld 等人的评估:解决调控网络推断中假阳性问题的最佳实践。
Pub Date : 2024-08-21 DOI: 10.1016/j.cels.2024.07.009
Anthony Gitter

One snapshot of the peer review process for "Transcriptome data are insufficient to control false discoveries in regulatory network inference" (Kernfeld et al., 2024).1.

转录组数据不足以控制调控网络推断中的错误发现"(Kernfeld et al.
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引用次数: 0
Transcriptome data are insufficient to control false discoveries in regulatory network inference. 转录组数据不足以控制调控网络推断中的错误发现。
Pub Date : 2024-08-21 DOI: 10.1016/j.cels.2024.07.006
Eric Kernfeld, Rebecca Keener, Patrick Cahan, Alexis Battle

Inference of causal transcriptional regulatory networks (TRNs) from transcriptomic data suffers notoriously from false positives. Approaches to control the false discovery rate (FDR), for example, via permutation, bootstrapping, or multivariate Gaussian distributions, suffer from several complications: difficulty in distinguishing direct from indirect regulation, nonlinear effects, and causal structure inference requiring "causal sufficiency," meaning experiments that are free of any unmeasured, confounding variables. Here, we use a recently developed statistical framework, model-X knockoffs, to control the FDR while accounting for indirect effects, nonlinear dose-response, and user-provided covariates. We adjust the procedure to estimate the FDR correctly even when measured against incomplete gold standards. However, benchmarking against chromatin immunoprecipitation (ChIP) and other gold standards reveals higher observed than reported FDR. This indicates that unmeasured confounding is a major driver of FDR in TRN inference. A record of this paper's transparent peer review process is included in the supplemental information.

从转录组数据推断转录调控网络(TRN)的因果关系时,往往会出现假阳性。控制假阳性发现率(FDR)的方法(例如,通过置换、引导或多元高斯分布)有几个并发症:难以区分直接调控和间接调控、非线性效应,以及因果结构推断需要 "因果充分性",即实验中没有任何未测量的混杂变量。在此,我们使用最近开发的统计框架--X模型山寨版--来控制FDR,同时考虑间接效应、非线性剂量反应和用户提供的协变量。我们对程序进行了调整,即使根据不完整的黄金标准进行测量,也能正确估计 FDR。然而,以染色质免疫沉淀(ChIP)和其他黄金标准为基准,发现观察到的 FDR 比报告的要高。这表明,未测量的混杂因素是 TRN 推断中 FDR 的主要驱动因素。补充信息中包含了本文透明的同行评审过程记录。
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引用次数: 0
Enhanced cellular longevity arising from environmental fluctuations. 环境波动导致细胞寿命延长。
Pub Date : 2024-08-21 DOI: 10.1016/j.cels.2024.07.007
Yuting Liu, Zhen Zhou, Hetian Su, Songlin Wu, Gavin Ni, Alex Zhang, Lev S Tsimring, Jeff Hasty, Nan Hao

Cellular longevity is regulated by both genetic and environmental factors. However, the interactions of these factors in the context of aging remain largely unclear. Here, we formulate a mathematical model for dynamic glucose modulation of a core gene circuit in yeast aging, which not only guided the design of pro-longevity interventions but also revealed the theoretical principles underlying these interventions. We introduce the dynamical systems theory to capture two general means for promoting longevity-the creation of a stable fixed point in the "healthy" state of the cell and the "dynamic stabilization" of the system around this healthy state through environmental oscillations. Guided by the model, we investigate how both of these can be experimentally realized by dynamically modulating environmental glucose levels. The results establish a paradigm for theoretically analyzing the trajectories and perturbations of aging that can be generalized to aging processes in diverse cell types and organisms.

细胞寿命受遗传和环境因素的调节。然而,这些因素在衰老过程中的相互作用在很大程度上仍不清楚。在这里,我们建立了一个数学模型,用于对酵母衰老过程中的核心基因回路进行动态葡萄糖调节,该模型不仅指导了促长寿干预措施的设计,还揭示了这些干预措施的理论基础。我们引入了动力系统理论来捕捉促进长寿的两种一般手段--在细胞的 "健康 "状态下创建一个稳定的固定点,以及通过环境振荡使系统围绕这一健康状态实现 "动态稳定"。在该模型的指导下,我们研究了如何通过动态调节环境中的葡萄糖水平在实验中实现这两种方法。研究结果为从理论上分析衰老的轨迹和扰动建立了一个范例,该范例可推广到不同细胞类型和生物体的衰老过程中。
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引用次数: 0
Brain dynamics supported by a hierarchy of complex correlation patterns defining a robust functional architecture. 复杂相关模式的层次结构支持大脑动态,定义了一个强大的功能架构。
Pub Date : 2024-08-21 Epub Date: 2024-08-13 DOI: 10.1016/j.cels.2024.07.003
Levente Varga, Vasile V Moca, Botond Molnár, Laura Perez-Cervera, Mohamed Kotb Selim, Antonio Díaz-Parra, David Moratal, Balázs Péntek, Wolfgang H Sommer, Raul C Mureșan, Santiago Canals, Maria Ercsey-Ravasz

Functional magnetic resonance imaging (fMRI) provides insights into cognitive processes with significant clinical potential. However, delays in brain region communication and dynamic variations are often overlooked in functional network studies. We demonstrate that networks extracted from fMRI cross-correlation matrices, considering time lags between signals, show remarkable reliability when focusing on statistical distributions of network properties. This reveals a robust brain functional connectivity pattern, featuring a sparse backbone of strong 0-lag correlations and weaker links capturing coordination at various time delays. This dynamic yet stable network architecture is consistent across rats, marmosets, and humans, as well as in electroencephalogram (EEG) data, indicating potential universality in brain dynamics. Second-order properties of the dynamic functional network reveal a remarkably stable hierarchy of functional correlations in both group-level comparisons and test-retest analyses. Validation using alcohol use disorder fMRI data uncovers broader shifts in network properties than previously reported, demonstrating the potential of this method for identifying disease biomarkers.

功能磁共振成像(fMRI)为认知过程提供了重要的临床潜力。然而,在功能网络研究中,脑区通信的延迟和动态变化往往被忽视。我们证明,考虑到信号之间的时滞,从 fMRI 交叉相关矩阵中提取的网络在关注网络属性的统计分布时显示出显著的可靠性。这揭示了一种稳健的大脑功能连接模式,其特点是由强 0 滞后相关和捕捉不同时间延迟下协调的较弱链接组成的稀疏主干。这种动态而稳定的网络结构在大鼠、狨猴、人类以及脑电图(EEG)数据中都是一致的,表明了大脑动态的潜在普遍性。动态功能网络的二阶特性显示,在组级比较和测试-重复分析中,功能相关性的层次结构非常稳定。通过使用酒精使用障碍的 fMRI 数据进行验证,发现了比以前报道的更广泛的网络属性变化,证明了这种方法在确定疾病生物标记物方面的潜力。
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引用次数: 0
Systematic identification of transcriptional activation domains from non-transcription factor proteins in plants and yeast. 系统鉴定植物和酵母中非转录因子蛋白的转录激活结构域。
Pub Date : 2024-07-17 Epub Date: 2024-06-11 DOI: 10.1016/j.cels.2024.05.007
Niklas F C Hummel, Kasey Markel, Jordan Stefani, Max V Staller, Patrick M Shih

Transcription factors can promote gene expression through activation domains. Whole-genome screens have systematically mapped activation domains in transcription factors but not in non-transcription factor proteins (e.g., chromatin regulators and coactivators). To fill this knowledge gap, we employed the activation domain predictor PADDLE to analyze the proteomes of Arabidopsis thaliana and Saccharomyces cerevisiae. We screened 18,000 predicted activation domains from >800 non-transcription factor genes in both species, confirming that 89% of candidate proteins contain active fragments. Our work enables the annotation of hundreds of nuclear proteins as putative coactivators, many of which have never been ascribed any function in plants. Analysis of peptide sequence compositions reveals how the distribution of key amino acids dictates activity. Finally, we validated short, "universal" activation domains with comparable performance to state-of-the-art activation domains used for genome engineering. Our approach enables the genome-wide discovery and annotation of activation domains that can function across diverse eukaryotes.

转录因子可通过激活结构域促进基因表达。全基因组筛选系统地绘制了转录因子的激活结构域,但没有绘制非转录因子蛋白(如染色质调节因子和辅助激活因子)的激活结构域。为了填补这一知识空白,我们利用激活结构域预测工具 PADDLE 分析了拟南芥和酿酒酵母的蛋白质组。我们筛选了这两个物种中超过 800 个非转录因子基因的 18,000 个预测激活结构域,证实 89% 的候选蛋白质含有活性片段。我们的工作使我们能够将数百种核蛋白注释为推定的辅助激活因子,其中许多在植物中从未被赋予任何功能。对肽序列组成的分析揭示了关键氨基酸的分布是如何决定活性的。最后,我们验证了简短的 "通用 "激活结构域,其性能与用于基因组工程的最先进激活结构域相当。我们的方法能够在全基因组范围内发现和注释能够在不同真核生物中发挥作用的激活结构域。
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引用次数: 0
SEMPER: Stoichiometric expression of mRNA polycistrons by eukaryotic ribosomes for compact, ratio-tunable multi-gene expression. SEMPER:真核核糖体对 mRNA 多单元的定量表达,实现紧凑、比例可调的多基因表达。
Pub Date : 2024-07-17 Epub Date: 2024-07-05 DOI: 10.1016/j.cels.2024.06.001
Mengtong Duan, Ishaan Dev, Andrew Lu, Goar Ayrapetyan, Mei Yi You, Mikhail G Shapiro

Here, we present a method for expressing multiple open reading frames (ORFs) from single transcripts using the leaky scanning model of translation initiation. In this approach termed "stoichiometric expression of mRNA polycistrons by eukaryotic ribosomes" (SEMPER), adjacent ORFs are translated from a single mRNA at tunable ratios determined by their order in the sequence and the strength of their translation initiation sites. We validate this approach by expressing up to three fluorescent proteins from one plasmid in two different cell lines. We then use it to encode a stoichiometrically tuned polycistronic construct encoding gas vesicle acoustic reporter genes that enables efficient formation of the multi-protein complex while minimizing cellular toxicity. We also demonstrate that SEMPER enables polycistronic expression of recombinant monoclonal antibodies from plasmid DNA and of two fluorescent proteins from single mRNAs made through in vitro transcription. Finally, we provide a probabilistic model to elucidate the mechanisms underlying SEMPER. A record of this paper's transparent peer review process is included in the supplemental information.

在这里,我们介绍了一种利用翻译起始的漏扫描模式从单个转录本表达多个开放阅读框(ORF)的方法。在这种被称为 "真核核糖体对 mRNA 多单链体的定量表达"(SEMPER)的方法中,相邻的 ORF 以可调节的比例从单个 mRNA 翻译出来,这种比例由它们在序列中的顺序和翻译起始位点的强度决定。我们通过在两种不同的细胞系中用一个质粒表达多达三种荧光蛋白来验证这种方法。然后,我们用它来编码一个按比例调整的多聚组蛋白构建体,该构建体编码气泡声学报告基因,能有效地形成多蛋白复合物,同时将细胞毒性降到最低。我们还证明,SEMPER 可使质粒 DNA 中的重组单克隆抗体和体外转录的单个 mRNA 中的两种荧光蛋白实现多聚体表达。最后,我们提供了一个概率模型来阐明 SEMPER 的内在机制。本文的同行评审过程透明,其记录见补充信息。
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引用次数: 0
Highly parallel production of designer organoids by mosaic patterning of progenitors. 通过对祖细胞进行镶嵌图案化,高度并行地生产出设计器官。
Pub Date : 2024-07-17 Epub Date: 2024-07-08 DOI: 10.1016/j.cels.2024.06.004
Catherine M Porter, Grace C Qian, Samuel H Grindel, Alex J Hughes

Organoids derived from human stem cells are a promising approach for disease modeling, regenerative medicine, and fundamental research. However, organoid variability and limited control over morphological outcomes remain as challenges. One open question is the extent to which engineering control over culture conditions can guide organoids to specific compositions. Here, we extend a DNA "velcro" cell patterning approach, precisely controlling the number and ratio of human induced pluripotent stem cell-derived progenitors contributing to nephron progenitor (NP) organoids and mosaic NP/ureteric bud (UB) tip cell organoids within arrays of microwells. We demonstrate long-term control over organoid size and morphology, decoupled from geometric constraints. We then show emergent trends in organoid tissue proportions that depend on initial progenitor cell composition. These include higher nephron and stromal cell representation in mosaic NP/UB organoids vs. NP-only organoids and a "goldilocks" initial cell ratio in mosaic organoids that optimizes the formation of proximal tubule structures.

从人类干细胞中提取的类器官是一种用于疾病建模、再生医学和基础研究的前景广阔的方法。然而,类器官的可变性和对形态结果的有限控制仍是一项挑战。一个悬而未决的问题是,对培养条件的工程控制能在多大程度上引导类器官形成特定的成分。在这里,我们扩展了一种DNA "魔术贴 "细胞模式化方法,在微孔阵列中精确控制人类诱导多能干细胞衍生祖细胞的数量和比例,从而形成肾小球祖细胞(NP)类器官和镶嵌NP/输尿管芽(UB)顶端细胞类器官。我们展示了与几何限制脱钩的对器官大小和形态的长期控制。然后,我们展示了取决于初始祖细胞组成的器官组织比例的新趋势。这些趋势包括在镶嵌式 NP/UB 有机体与纯 NP 有机体中肾小球和基质细胞的比例较高,以及镶嵌式有机体中的 "金锁 "初始细胞比例能优化近端小管结构的形成。
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引用次数: 0
Signal integration and adaptive sensory diversity tuning in Escherichia coli chemotaxis. 大肠杆菌趋化过程中的信号整合与适应性感觉多样性调整
Pub Date : 2024-07-17 Epub Date: 2024-07-08 DOI: 10.1016/j.cels.2024.06.003
Jeremy Philippe Moore, Keita Kamino, Rafaela Kottou, Thomas S Shimizu, Thierry Emonet

In uncertain environments, phenotypic diversity can be advantageous for survival. However, as the environmental uncertainty decreases, the relative advantage of having diverse phenotypes decreases. Here, we show how populations of E. coli integrate multiple chemical signals to adjust sensory diversity in response to changes in the prevalence of each ligand in the environment. Measuring kinase activity in single cells, we quantified the sensitivity distribution to various chemoattractants in different mixtures of background stimuli. We found that when ligands bind uncompetitively, the population tunes sensory diversity to each signal independently, decreasing diversity when the signal's ambient concentration increases. However, among competitive ligands, the population can only decrease sensory diversity one ligand at a time. Mathematical modeling suggests that sensory diversity tuning benefits E. coli populations by modulating how many cells are committed to tracking each signal proportionally as their prevalence changes.

在不确定的环境中,表型多样性对生存有利。然而,随着环境不确定性的降低,表型多样性的相对优势也会降低。在这里,我们展示了大肠杆菌种群如何整合多种化学信号来调整感官多样性,以应对环境中每种配体流行率的变化。通过测量单细胞中激酶的活性,我们量化了不同背景刺激混合物中各种趋化物质的敏感性分布。我们发现,当配体非竞争性地结合时,种群会独立地调整对每种信号的感觉多样性,当信号的环境浓度增加时,多样性就会降低。然而,在竞争性配体中,种群每次只能降低一种配体的感觉多样性。数学建模表明,感官多样性调整可以调节有多少细胞致力于跟踪每种信号,使之与这些信号的流行程度成比例,从而使大肠杆菌种群受益。
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引用次数: 0
The unreasonable effectiveness of equilibrium gene regulation through the cell cycle. 细胞周期中平衡基因调控的不合理有效性。
Pub Date : 2024-07-17 Epub Date: 2024-07-08 DOI: 10.1016/j.cels.2024.06.002
Jose M G Vilar, Leonor Saiz

Systems like the prototypical lac operon can reliably hold repression of transcription upon DNA replication across cell cycles with just 10 repressor molecules per cell and behave as if they were at equilibrium. The origin of this phenomenology is still an unresolved question. Here, we develop a general theory to analyze strong perturbations in quasi-equilibrium systems and use it to quantify the effects of DNA replication in gene regulation. We find a scaling law linking actual with predicted equilibrium transcription via a single kinetic parameter. We show that even the lac operon functions beyond the physical limits of naive regulation through compensatory mechanisms that suppress non-equilibrium effects. Synthetic systems without adjuvant activators, such as the cAMP receptor protein (CRP), lack this reliability. Our results provide a rationale for the function of CRP, beyond just being a tunable activator, as a mitigator of cell cycle perturbations.

像典型的lac操作子这样的系统,在DNA复制时,每个细胞只需10个抑制剂分子,就能在整个细胞周期中可靠地保持转录抑制,其表现就像处于平衡状态一样。这种现象的起源仍是一个悬而未决的问题。在这里,我们提出了一种通用理论来分析准平衡系统中的强扰动,并用它来量化 DNA 复制对基因调控的影响。我们发现了一个通过单一动力学参数将实际平衡转录与预测平衡转录联系起来的缩放定律。我们发现,即使是 lac 操作子也能通过补偿机制抑制非均衡效应,从而超越天真调控的物理极限。没有辅助激活剂的合成系统,如 cAMP 受体蛋白(CRP),缺乏这种可靠性。我们的研究结果为 CRP 的功能提供了理论依据,它不仅是一种可调节的激活剂,还是细胞周期扰动的缓解剂。
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引用次数: 0
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Cell systems
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