Wiley Interdisciplinary Reviews: Developmental Biology最新文献

The macro and micro of chromosome conformation capture. 染色体构象捕获的宏观和微观。

Wiley Interdisciplinary Reviews: Developmental Biology Pub Date : 2021-11-01 Epub Date: 2020-09-28 DOI: 10.1002/wdev.395

Viraat Y Goel, Anders S Hansen

{"title":"The macro and micro of chromosome conformation capture.","authors":"Viraat Y Goel, Anders S Hansen","doi":"10.1002/wdev.395","DOIUrl":"10.1002/wdev.395","url":null,"abstract":"The 3D organization of the genome facilitates gene regulation, replication, and repair, making it a key feature of genomic function and one that remains to be properly understood. Over the past two decades, a variety of chromosome conformation capture (3C) methods have delineated genome folding from megabase-scale compartments and topologically associating domains (TADs) down to kilobase-scale enhancer-promoter interactions. Understanding the functional role of each layer of genome organization is a gateway to understanding cell state, development, and disease. Here, we discuss the evolution of 3C-based technologies for mapping 3D genome organization. We focus on genomics methods and provide a historical account of the development from 3C to Hi-C. We also discuss ChIP-based techniques that focus on 3D genome organization mediated by specific proteins, capture-based methods that focus on particular regions or regulatory elements, 3C-orthogonal methods that do not rely on restriction digestion and proximity ligation, and methods for mapping the DNA-RNA and RNA-RNA interactomes. We consider the biological discoveries that have come from these methods, examine the mechanistic contributions of CTCF, cohesin, and loop extrusion to genomic folding, and detail the 3D genome field's current understanding of nuclear architecture. Finally, we give special consideration to Micro-C as an emerging frontier in chromosome conformation capture and discuss recent Micro-C findings uncovering fine-scale chromatin organization in unprecedented detail. This article is categorized under: Gene Expression and Transcriptional Hierarchies > Regulatory Mechanisms Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics.","PeriodicalId":23630,"journal":{"name":"Wiley Interdisciplinary Reviews: Developmental Biology","volume":"10 6","pages":"e395"},"PeriodicalIF":0.0,"publicationDate":"2021-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wdev.395","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38525670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 22

Human pluripotent stem cell-derived lung organoids: Potential applications in development and disease modeling. 人类多能干细胞衍生的肺类器官:在发育和疾病建模中的潜在应用。

Wiley Interdisciplinary Reviews: Developmental Biology Pub Date : 2021-11-01 Epub Date: 2020-11-03 DOI: 10.1002/wdev.399

Lu Tian, Jinghui Gao, Irving M Garcia, Huanhuan Joyce Chen, Alessandra Castaldi, Ya-Wen Chen

{"title":"Human pluripotent stem cell-derived lung organoids: Potential applications in development and disease modeling.","authors":"Lu Tian, Jinghui Gao, Irving M Garcia, Huanhuan Joyce Chen, Alessandra Castaldi, Ya-Wen Chen","doi":"10.1002/wdev.399","DOIUrl":"https://doi.org/10.1002/wdev.399","url":null,"abstract":"The pulmonary system is comprised of two main compartments, airways and alveolar space. Their tissue and cellular complexity ensure lung function and protection from external agents, for example, virus. Two-dimensional (2D) in vitro systems and animal models have been largely employed to elucidate the molecular mechanisms underlying human lung development, physiology, and pathogenesis. However, neither of these models accurately recapitulate the human lung environment and cellular crosstalk. More recently, human-derived three-dimensional (3D) models have been generated allowing for a deeper understanding of cell-to-cell communication. However, the availability and accessibility of primary human cell sources from which generate the 2D and 3D models may be limited. In the past few years, protocols have been developed to successfully employ human pluripotent stem cells (hPSCs) and differentiate them toward pulmonary fate in vitro. In the present review, we discuss the advantages and pitfalls of hPSC-derived lung 2D and 3D models, including the main characteristics and potentials for these models and their current and future applications for modeling development and diseases. Lung organoids currently represent the closest model to the human pulmonary system. We further focus on the applications of lung organoids for the study of human diseases such as pulmonary fibrosis, infectious diseases, and lung cancer. Finally, we discuss the present limitations and potential future applications of 3D lung organoids. This article is categorized under: Adult Stem Cells, Tissue Renewal, and Regeneration > Stem Cells and Disease Adult Stem Cells, Tissue Renewal, and Regeneration > Stem Cell Differentiation and Reversion.","PeriodicalId":23630,"journal":{"name":"Wiley Interdisciplinary Reviews: Developmental Biology","volume":"10 6","pages":"e399"},"PeriodicalIF":0.0,"publicationDate":"2021-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wdev.399","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38564588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 30

Zebrafish models of acute leukemias: Current models and future directions. 斑马鱼急性白血病模型：当前模型和未来方向。

Wiley Interdisciplinary Reviews: Developmental Biology Pub Date : 2021-11-01 Epub Date: 2020-12-19 DOI: 10.1002/wdev.400

Brandon Molina, Jasmine Chavez, Stephanie Grainger

{"title":"Zebrafish models of acute leukemias: Current models and future directions.","authors":"Brandon Molina, Jasmine Chavez, Stephanie Grainger","doi":"10.1002/wdev.400","DOIUrl":"10.1002/wdev.400","url":null,"abstract":"Acute myeloid leukemias (AML) and acute lymphoid leukemias (ALL) are heterogenous diseases encompassing a wide array of genetic mutations with both loss and gain of function phenotypes. Ultimately, these both result in the clonal overgrowth of blast cells in the bone marrow, peripheral blood, and other tissues. As a consequence of this, normal hematopoietic stem cell function is severely hampered. Technologies allowing for the early detection of genetic alterations and understanding of these varied molecular pathologies have helped to advance our treatment regimens toward personalized targeted therapies. In spite of this, both AML and ALL continue to be a major cause of morbidity and mortality worldwide, in part because molecular therapies for the plethora of genetic abnormalities have not been developed. This underscores the current need for better model systems for therapy development. This article reviews the current zebrafish models of AML and ALL and discusses how novel gene editing tools can be implemented to generate better models of acute leukemias. This article is categorized under: Adult Stem Cells, Tissue Renewal, and Regeneration > Stem Cells and Disease Technologies > Perturbing Genes and Generating Modified Animals.","PeriodicalId":23630,"journal":{"name":"Wiley Interdisciplinary Reviews: Developmental Biology","volume":"10 6","pages":"e400"},"PeriodicalIF":0.0,"publicationDate":"2021-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wdev.400","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38390851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Single-cell RNA sequencing in Drosophila: Technologies and applications. 果蝇的单细胞 RNA 测序：技术与应用。

Wiley Interdisciplinary Reviews: Developmental Biology Pub Date : 2021-09-01 Epub Date: 2020-09-16 DOI: 10.1002/wdev.396

Hongjie Li

{"title":"Single-cell RNA sequencing in Drosophila: Technologies and applications.","authors":"Hongjie Li","doi":"10.1002/wdev.396","DOIUrl":"10.1002/wdev.396","url":null,"abstract":"Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating cell states and functions at the single-cell level. It has greatly revolutionized transcriptomic studies in many life science research fields, such as neurobiology, immunology, and developmental biology. With the fast development of both experimental platforms and bioinformatics approaches over the past decade, scRNA-seq is becoming economically feasible and experimentally practical for many biomedical laboratories. Drosophila has served as an excellent model organism for dissecting cellular and molecular mechanisms that underlie tissue development, adult cell function, disease, and aging. The recent application of scRNA-seq methods to Drosophila tissues has led to a number of exciting discoveries. In this review, I will provide a summary of recent scRNA-seq studies in Drosophila, focusing on technical approaches and biological applications. I will also discuss current challenges and future opportunities of making new discoveries using scRNA-seq in Drosophila. This article is categorized under: Technologies > Analysis of the Transcriptome.","PeriodicalId":23630,"journal":{"name":"Wiley Interdisciplinary Reviews: Developmental Biology","volume":"10 5","pages":"e396"},"PeriodicalIF":0.0,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7960577/pdf/nihms-1656030.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38485845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Schwann cell development: From neural crest to myelin sheath. 雪旺细胞发育:从神经嵴到髓鞘。

Wiley Interdisciplinary Reviews: Developmental Biology Pub Date : 2021-09-01 Epub Date: 2020-11-03 DOI: 10.1002/wdev.398

Anoohya N Muppirala, Lauren E Limbach, Elisabeth F Bradford, Sarah C Petersen

{"title":"Schwann cell development: From neural crest to myelin sheath.","authors":"Anoohya N Muppirala, Lauren E Limbach, Elisabeth F Bradford, Sarah C Petersen","doi":"10.1002/wdev.398","DOIUrl":"https://doi.org/10.1002/wdev.398","url":null,"abstract":"Vertebrate nervous system function requires glial cells, including myelinating glia that insulate axons and provide trophic support that allows for efficient signal propagation by neurons. In vertebrate peripheral nervous systems, neural crest-derived glial cells known as Schwann cells (SCs) generate myelin by encompassing and iteratively wrapping membrane around single axon segments. SC gliogenesis and neurogenesis are intimately linked and governed by a complex molecular environment that shapes their developmental trajectory. Changes in this external milieu drive developing SCs through a series of distinct morphological and transcriptional stages from the neural crest to a variety of glial derivatives, including the myelinating sublineage. Cues originate from the extracellular matrix, adjacent axons, and the developing SC basal lamina to trigger intracellular signaling cascades and gene expression changes that specify stages and transitions in SC development. Here, we integrate the findings from in vitro neuron-glia co-culture experiments with in vivo studies investigating SC development, particularly in zebrafish and mouse, to highlight critical factors that specify SC fate. Ultimately, we connect classic biochemical and mutant studies with modern genetic and visualization tools that have elucidated the dynamics of SC development. This article is categorized under: Signaling Pathways > Cell Fate Signaling Nervous System Development > Vertebrates: Regional Development.","PeriodicalId":23630,"journal":{"name":"Wiley Interdisciplinary Reviews: Developmental Biology","volume":"10 5","pages":"e398"},"PeriodicalIF":0.0,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wdev.398","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38571646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 14

Interorgan communication in development and cancer. 发育和癌症中的器官间通讯。

Wiley Interdisciplinary Reviews: Developmental Biology Pub Date : 2021-07-01 Epub Date: 2020-08-27 DOI: 10.1002/wdev.394

Edel Alvarez-Ochoa, Francesca Froldi, Louise Y Cheng

引用次数: 6

Through veiled mirrors: Fish fins giving insight into size regulation. 透过蒙着面纱的镜子:鱼鳍提供了对大小调节的洞察。

Wiley Interdisciplinary Reviews: Developmental Biology Pub Date : 2021-07-01 Epub Date: 2020-04-23 DOI: 10.1002/wdev.381

Matthew P Harris, Jacob M Daane, Jennifer Lanni

{"title":"Through veiled mirrors: Fish fins giving insight into size regulation.","authors":"Matthew P Harris, Jacob M Daane, Jennifer Lanni","doi":"10.1002/wdev.381","DOIUrl":"https://doi.org/10.1002/wdev.381","url":null,"abstract":"Faithful establishment and maintenance of proportion is seen across biological systems and provides a glimpse at fundamental rules of scaling that underlie development and evolution. Dysregulation of proportion is observed in a range of human diseases and growth disorders, indicating that proper scaling is an essential component of normal anatomy and physiology. However, when viewed through an evolutionary lens, shifts in the regulation of relative proportion are one of the most striking sources of morphological diversity among organisms. To date, the mechanisms via which relative proportion is specified and maintained remain unclear. Through the application of powerful experimental, genetic and molecular approaches, the teleost fin has provided an effective model to investigate the regulation of scaling, size, and relative growth in vertebrate organisms. This article is categorized under: Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing Adult Stem Cells, Tissue Renewal, and Regeneration > Regeneration Comparative Development and Evolution > Regulation of Organ Diversity.","PeriodicalId":23630,"journal":{"name":"Wiley Interdisciplinary Reviews: Developmental Biology","volume":"10 4","pages":"e381"},"PeriodicalIF":0.0,"publicationDate":"2021-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wdev.381","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37863784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11

Regulation of size and scale in vertebrate spinal cord development. 脊椎动物脊髓发育过程中大小和尺度的调节。

Wiley Interdisciplinary Reviews: Developmental Biology Pub Date : 2021-05-01 Epub Date: 2020-05-11 DOI: 10.1002/wdev.383

Katarzyna Kuzmicz-Kowalska, Anna Kicheva

{"title":"Regulation of size and scale in vertebrate spinal cord development.","authors":"Katarzyna Kuzmicz-Kowalska, Anna Kicheva","doi":"10.1002/wdev.383","DOIUrl":"https://doi.org/10.1002/wdev.383","url":null,"abstract":"All vertebrates have a spinal cord with dimensions and shape specific to their species. Yet how species-specific organ size and shape are achieved is a fundamental unresolved question in biology. The formation and sculpting of organs begins during embryonic development. As it develops, the spinal cord extends in anterior-posterior direction in synchrony with the overall growth of the body. The dorsoventral (DV) and apicobasal lengths of the spinal cord neuroepithelium also change, while at the same time a characteristic pattern of neural progenitor subtypes along the DV axis is established and elaborated. At the basis of these changes in tissue size and shape are biophysical determinants, such as the change in cell number, cell size and shape, and anisotropic tissue growth. These processes are controlled by global tissue-scale regulators, such as morphogen signaling gradients as well as mechanical forces. Current challenges in the field are to uncover how these tissue-scale regulatory mechanisms are translated to the cellular and molecular level, and how regulation of distinct cellular processes gives rise to an overall defined size. Addressing these questions will help not only to achieve a better understanding of how size is controlled, but also of how tissue size is coordinated with the specification of pattern. This article is categorized under: Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing Signaling Pathways > Global Signaling Mechanisms Nervous System Development > Vertebrates: General Principles.","PeriodicalId":23630,"journal":{"name":"Wiley Interdisciplinary Reviews: Developmental Biology","volume":"10 3","pages":"e383"},"PeriodicalIF":0.0,"publicationDate":"2021-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wdev.383","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37922758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11

Network-regulated organ allometry: The developmental regulation of morphological scaling. 网络调节的器官异速发育:形态缩放的发育调节。

Wiley Interdisciplinary Reviews: Developmental Biology Pub Date : 2021-05-01 Epub Date: 2020-06-21 DOI: 10.1002/wdev.391

Isabelle M Vea, Alexander W Shingleton

{"title":"Network-regulated organ allometry: The developmental regulation of morphological scaling.","authors":"Isabelle M Vea, Alexander W Shingleton","doi":"10.1002/wdev.391","DOIUrl":"https://doi.org/10.1002/wdev.391","url":null,"abstract":"Morphological scaling relationships, or allometries, describe how traits grow coordinately and covary among individuals in a population. The developmental regulation of scaling is essential to generate correctly proportioned adults across a range of body sizes, while the mis-regulation of scaling may result in congenital birth defects. Research over several decades has identified the developmental mechanisms that regulate the size of individual traits. Nevertheless, we still have poor understanding of how these mechanisms work together to generate correlated size variation among traits in response to environmental and genetic variation. Conceptually, morphological scaling can be generated by size-regulatory factors that act directly on multiple growing traits (trait-autonomous scaling), or indirectly via hormones produced by central endocrine organs (systemically regulated scaling), and there are a number of well-established examples of such mechanisms. There is much less evidence, however, that genetic and environmental variation actually acts on these mechanisms to generate morphological scaling in natural populations. More recent studies indicate that growing organs can themselves regulate the growth of other organs in the body. This suggests that covariation in trait size can be generated by network-regulated scaling mechanisms that respond to changes in the growth of individual traits. Testing this hypothesis, and one of the main challenges of understanding morphological scaling, requires connecting mechanisms elucidated in the laboratory with patterns of scaling observed in the natural world. This article is categorized under: Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing Comparative Development and Evolution > Organ System Comparisons Between Species.","PeriodicalId":23630,"journal":{"name":"Wiley Interdisciplinary Reviews: Developmental Biology","volume":"10 3","pages":"e391"},"PeriodicalIF":0.0,"publicationDate":"2021-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wdev.391","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38074457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 17

Long-distance regressive signaling in neural development and disease. 神经发育和疾病中的长距离回归信号传导

Wiley Interdisciplinary Reviews: Developmental Biology Pub Date : 2021-03-01 Epub Date: 2020-05-11 DOI: 10.1002/wdev.382

Amrita Pathak, Shayla Clark, Francisca C Bronfman, Christopher D Deppmann, Bruce D Carter

{"title":"Long-distance regressive signaling in neural development and disease.","authors":"Amrita Pathak, Shayla Clark, Francisca C Bronfman, Christopher D Deppmann, Bruce D Carter","doi":"10.1002/wdev.382","DOIUrl":"10.1002/wdev.382","url":null,"abstract":"Nervous system development proceeds via well-orchestrated processes involving a balance between progressive and regressive events including stabilization or elimination of axons, synapses, and even entire neurons. These progressive and regressive events are driven by functionally antagonistic signaling pathways with the dominant pathway eventually determining whether a neural element is retained or removed. Many of these developmental sculpting events are triggered by final target innervation necessitating a long-distance mode of communication. While long-distance progressive signaling has been well characterized, particularly for neurotrophic factors, there remains relatively little known about how regressive events are triggered from a distance. Here we discuss the emergent phenomenon of long-distance regressive signaling pathways. In particular, we will cover (a) progressive and regressive cues known to be employed after target innervation, (b) the mechanisms of long-distance signaling from an endosomal platform, (c) recent evidence that long-distance regressive cues emanate from platforms like death receptors or repulsive axon guidance receptors, and (d) evidence that these pathways are exploited in pathological scenarios. This article is categorized under: Nervous System Development > Vertebrates: General Principles Signaling Pathways > Global Signaling Mechanisms Establishment of Spatial and Temporal Patterns > Cytoplasmic Localization.","PeriodicalId":23630,"journal":{"name":"Wiley Interdisciplinary Reviews: Developmental Biology","volume":"10 2","pages":"e382"},"PeriodicalIF":0.0,"publicationDate":"2021-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655682/pdf/nihms-1640413.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37920433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0