Gene regulatory networks controlling vertebrate retinal regeneration.
Gene regulatory networks controlling vertebrate retinal regeneration.
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DOI：
10.1126/science.abb8598
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发表时间：
2020-11-20
期刊：
影响因子：
--
通讯作者：
Blackshaw S
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文献类型：
--
作者：
Hoang T;Wang J;Boyd P;Wang F;Santiago C;Jiang L;Yoo S;Lahne M;Todd LJ;Jia M;Saez C;Keuthan C;Palazzo I;Squires N;Campbell WA;Rajaii F;Parayil T;Trinh V;Kim DW;Wang G;Campbell LJ;Ash J;Fischer AJ;Hyde DR;Qian J;Blackshaw S
损伤诱导某些冷血脊椎动物的视网膜<s:1>神经胶质细胞再生神经元，而哺乳动物却没有。为了确定将m<s:1> ller胶质细胞重编程为祖细胞的基因调控网络，我们分析了斑马鱼、小鸡和小鼠m<s:1> ller胶质细胞在不同刺激下的基因表达和染色质可及性变化。我们确定了进化上保守的和物种特异性的基因网络控制神经胶质静止，反应性和神经发生。在斑马鱼和小鸡中，从静止到反应性的转变对视网膜再生至关重要，而在小鼠中，一个专门的网络抑制神经源性能力并恢复静止。核因子I转录因子的破坏，维持和恢复静止，诱导成年小鼠损伤后神经胶质细胞增殖和产生神经元。这些发现可能有助于设计治疗方法，以恢复因退行性疾病而失去的视网膜神经元。损伤后视网膜神经元的再生能力在脊椎动物物种中差别很大。硬骨鱼如斑马鱼可以再生所有主要的视网膜细胞类型损伤后，通过重新编程神经胶质到一个类似祖细胞的状态。在孵化后的小鸡中，m<s:1> ller神经胶质细胞在受伤后可以产生少量神经元，但在以后的生活中失去再生能力。相反，哺乳动物的神经胶质不能自发地再生失去的视网膜神经元。虽然已经发现了一些促进视网膜再生的基因，但控制<s:1> ller神经胶质细胞重编程的核心基因调控网络在很大程度上仍然未知，但可以通过跨物种转录组学和表观基因组学分析来确定。为了确定损伤诱导的突触神经胶质的变化，我们进行了大量RNA测序（RNA-seq）和高通量测序（ATAC-seq），分别分析了小鼠和斑马鱼的基因表达和染色质可及性。这些实验包括n -甲基-d-天冬氨酸（NMDA）和光处理后的多个时间点，分别损伤视网膜内神经元和光感受器。我们还对小鼠、斑马鱼和鸡视网膜进行了单细胞RNA-seq （scRNA-seq）检测，以确定NMDA处理、光损伤以及外源因素诱导的非损伤重编程后基因表达的变化。然后，我们开发了一个计算工具，我们称之为综合调控网络分析（IReNA），整合基因表达和染色质可及性，以重建<s:1>勒神经胶质细胞在不同刺激下的调控网络。最后，使用功能损失方法，我们验证了控制<s:1>勒神经胶质细胞重编程的候选因子的功能。我们从斑马鱼和小鼠中提取了100个RNA-seq样本和40个ATAC-seq样本，分别从斑马鱼、小鸡和小鼠中获得105,666个、85,051个和77,924个视网膜细胞。在这三个物种中，神经胶质细胞在治疗后获得反应状态。在小鸡和斑马鱼中，<s:1>勒神经胶质细胞在增殖和神经源性之前经历了这种反应状态。然而，在小鼠中，<s:1> ller神经胶质细胞在损伤后恢复到静息状态。通过整合这些数据集，我们确定了每次治疗后基因表达和染色质可及性的变化。跨物种分析确定了进化上保守的和物种特异性的基因调控网络，这些基因调控网络控制刺激后静止、反应和增殖的突触神经胶质的转变。在小鼠中，一个专门的网络将<s:1>勒神经胶质细胞恢复到静止状态。相反，在斑马鱼和小鸡中，基因选择性地表达在反应性<s:1>神经胶质细胞中，促进了向增殖和神经源性祖细胞状态的过渡。在反应性马勒神经胶质中选择性表达的基因hmga1和yap1的功能丧失抑制了斑马鱼马勒神经胶质的重编程。在鸡中，对脂肪酸结合蛋白5、7和8 （FABP5/7/8）活性的药物破坏可抑制损伤诱导的从静止到神经原性能力的转变。最后，核因子I因子a、b和x （Nfia/b/x）的缺失，维持和恢复神经胶质的静止状态，导致成年小鼠损伤后<s:1> ller神经胶质重编程为视网膜双极和无分泌中间神经元。我们发现，在斑马鱼和小鸡等具有再生能力的物种中，从静止状态到反应状态的转变对于<s:1>勒神经胶质细胞重编程至关重要。此外，增殖能力和神经原性能力都受到小鼠<s:1>勒神经胶质细胞中一个专门的基因调控网络的抑制。跨物种RNA-seq和ATAC-seq数据为研究细胞对损伤和神经胶质重编程的反应提供了全面的资源。我们的研究结果表明，针对抑制神经原性能力的基因调控网络的治疗可能有助于促进哺乳动物<s:1>勒神经胶质细胞向神经元的重编程。视网膜<s:1>勒神经胶质细胞重编程的控制。对斑马鱼、小鸡和小鼠不同处理后的神经胶质细胞进行RNA-seq和ATAC-seq检测。综合转录组学和表观基因组学分析揭示了控制视网膜再生的核心调控网络。斑马鱼反应性海马神经胶质中表达的基因功能丧失阻断了重编程，而在小鼠海马神经胶质中，维持和恢复静止的Nfia/b/x的破坏导致神经原性能力的获得。
Injury induces retinal Müller glia of certain cold-blooded vertebrates, but not those of mammals, to regenerate neurons. To identify gene regulatory networks that reprogram Müller glia into progenitor cells, we profiled changes in gene expression and chromatin accessibility in Müller glia from zebrafish, chick, and mice in response to different stimuli. We identified evolutionarily conserved and species-specific gene networks controlling glial quiescence, reactivity, and neurogenesis. In zebrafish and chick, the transition from quiescence to reactivity is essential for retinal regeneration, whereas in mice, a dedicated network suppresses neurogenic competence and restores quiescence. Disruption of nuclear factor I transcription factors, which maintain and restore quiescence, induces Müller glia to proliferate and generate neurons in adult mice after injury. These findings may aid in designing therapies to restore retinal neurons lost to degenerative diseases. The ability to regenerate retinal neurons after injury varies drastically among vertebrate species. Teleost fish such as zebrafish can regenerate all major retinal cell types after injury by reprogramming Müller glia to a progenitor-like state. In the post-hatch chick, Müller glia can generate small numbers of neurons after injury but lose regenerative ability later in life. In contrast, mammalian Müller glia do not spontaneously regenerate lost retinal neurons. Although some genes that promote retinal regeneration have been identified, the core gene regulatory networks controlling Müller glia reprogramming remain largely unknown but can be identified through cross-species transcriptomic and epigenomic analysis. To identify injury-induced changes in Müller glia, we performed bulk RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to separately profile gene expression and chromatin accessibility in both mouse and zebrafish. These assays included multiple time points following N-methyl-d-aspartate (NMDA) and light treatments, which damage inner retinal neurons and photoreceptors, respectively. We also conducted single-cell RNA-seq (scRNA-seq) to identify changes in gene expression after NMDA treatment and light damage, as well as after treatment with exogenous factors that induced injury-independent reprogramming, in mouse, zebrafish, and chick retinas. We then developed a computational tool, which we call integrated regulatory network analysis (IReNA), to integrate gene expression and chromatin accessibility in order to reconstruct regulatory networks of Müller glia in response to diverse stimuli. Finally, using loss-of-function approaches, we validated functions of candidate factors controlling Müller glia reprogramming. We generated 100 RNA-seq and 40 ATAC-seq samples from zebrafish and mice, and obtained 105,666, 85,051, and 77,924 single retinal cells from zebrafish, chick, and mice, respectively. In all three species, Müller glia acquired a reactive state after treatments. In chick and zebrafish, Müller glia passed through this reactive state before becoming proliferative and neurogenic. In mice, however, Müller glia reverted to a resting state after injury. By integrating these datasets, we identified changes in gene expression and chromatin accessibility after each treatment. Cross-species analysis identified evolutionarily conserved and species-specific gene regulatory networks that control the transition of the quiescent, reactive, and proliferative Müller glia after stimulation. In mice, a dedicated network restored Müller glia to a quiescent state. In contrast, in zebrafish and chick, genes selectively expressed in reactive Müller glia promoted the transition to a proliferative and neurogenic progenitor state. Loss of function of genes selectively expressed in reactive Müller glia, such as hmga1 and yap1, inhibited Müller glia reprogramming in zebrafish. In chick, pharmacological disruption of fatty acid–binding protein 5, 7, and 8 (FABP5/7/8) activity inhibited injury-induced transition from quiescence to neurogenic competence. Finally, deletion of nuclear factor I factors a, b, and x (Nfia/b/x), which maintain and restore a glial quiescent state, resulted in Müller glia reprogramming into retinal bipolar and amacrine interneurons in adult mice after injury. We found that transition from quiescence through the reactive state is essential for Müller glia reprogramming in regeneration-competent species such as zebrafish and chick. Furthermore, proliferative and neurogenic competence are both suppressed by a dedicated gene regulatory network in mouse Müller glia. Cross-species RNA-seq and ATAC-seq data provide a comprehensive resource to study cellular responses to injury and Müller glia reprogramming. Our findings indicate that treatments targeting gene regulatory networks that repress neurogenic competence may help to facilitate reprogramming of mammalian Müller glia to neurons. Control of retinal Müller glia reprogramming. RNA-seq and ATAC-seq were performed on Müller glia from zebrafish, chick, and mouse after different treatments. Integrative transcriptomic and epigenomic analysis revealed core regulatory networks controlling retinal regeneration. Loss of function of zebrafish genes expressed in reactive Müller glia blocked reprogramming, while in mouse Müller glia, disruption of Nfia/b/x, which maintain and restore quiescence, resulted in acquisition of neurogenic competence.
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DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
影响因子：
46.9
作者：
Becht, Etienne;McInnes, Leland;Newell, Evan W.
通讯作者：
Newell, Evan W.
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
3.2
作者：
Abdi, Herve;Williams, Lynne J.
通讯作者：
Williams, Lynne J.