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Current Opinion in Genetics & Development最新文献

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Control of cell fate upon transcription factor–driven cardiac reprogramming 转录因子驱动的心脏重编程对细胞命运的控制
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-11-23 DOI: 10.1016/j.gde.2024.102226
Huitong Shi , Brian M Spurlock , Jiandong Liu , Li Qian
{"title":"Control of cell fate upon transcription factor–driven cardiac reprogramming","authors":"Huitong Shi ,&nbsp;Brian M Spurlock ,&nbsp;Jiandong Liu ,&nbsp;Li Qian","doi":"10.1016/j.gde.2024.102226","DOIUrl":"10.1016/j.gde.2024.102226","url":null,"abstract":"<div><div>Adult mammals are susceptible to substantial cardiomyocyte (CM) loss following various cardiac diseases due to the limited capacity of CM proliferation and regeneration. Recently, direct cardiac reprogramming, converting fibroblasts into induced CMs, has been achieved both <em>in vitro</em> and <em>in vivo</em> through forced expression of transcription factors (TFs). This review encapsulates the advancements made in enhancing reprogramming efficiency and underlying molecular mechanisms. It covers the optimization of TF-based reprogramming cocktails and <em>in vivo</em> delivery platform and recently identified regulators in enhancing reprogramming efficiency. In addition, we discuss recent insights into the molecular mechanisms of direct cardiac reprogramming from single-cell omics analyses. Finally, we briefly touch on remaining challenges and prospective direction of this field.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"89 ","pages":"Article 102226"},"PeriodicalIF":3.7,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142699887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genetic factors mediating long-range enhancer–promoter communication in mammalian development 哺乳动物发育过程中介导长程增强子-启动子通讯的遗传因素
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-11-22 DOI: 10.1016/j.gde.2024.102282
Grace Bower, Evgeny Z Kvon
{"title":"Genetic factors mediating long-range enhancer–promoter communication in mammalian development","authors":"Grace Bower,&nbsp;Evgeny Z Kvon","doi":"10.1016/j.gde.2024.102282","DOIUrl":"10.1016/j.gde.2024.102282","url":null,"abstract":"<div><div>Enhancers are remotely located noncoding DNA sequences that regulate gene expression in response to developmental, homeostatic, and environmental cues. Canonical short-range enhancers located &lt;50 kb from their cognate promoters function by binding transcription factors, coactivators, and chromatin modifiers. In this review, we discuss recent evidence that medium-range (50–400 kb) and long-range (&gt;400 kb) enhancers rely on additional mechanisms, including cohesin, CCCTC-binding factor, and high-affinity protein–protein interactions. These mechanisms are crucial for establishing the physical proximity and interaction between enhancers and their target promoters over extended genomic distances and ensuring robust gene activation during mammalian development. Future studies will be critical to unravel their prevalence and evolutionary significance across various genomic loci, cell types, and species.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"90 ","pages":"Article 102282"},"PeriodicalIF":3.7,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142696046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Editorial overview: Drivers, droplets, and deeds of nuclear genome organization 编辑综述：核基因组组织的驱动力、液滴和契约。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-11-21 DOI: 10.1016/j.gde.2024.102281
Maya Capelson , Eda Yildirim
{"title":"Editorial overview: Drivers, droplets, and deeds of nuclear genome organization","authors":"Maya Capelson ,&nbsp;Eda Yildirim","doi":"10.1016/j.gde.2024.102281","DOIUrl":"10.1016/j.gde.2024.102281","url":null,"abstract":"","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"90 ","pages":"Article 102281"},"PeriodicalIF":3.7,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Archaic hominin admixture and its consequences for modern humans 古人类混居及其对现代人类的影响。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-11-21 DOI: 10.1016/j.gde.2024.102280
Debashree Tagore, Joshua M Akey
{"title":"Archaic hominin admixture and its consequences for modern humans","authors":"Debashree Tagore,&nbsp;Joshua M Akey","doi":"10.1016/j.gde.2024.102280","DOIUrl":"10.1016/j.gde.2024.102280","url":null,"abstract":"<div><div>As anatomically modern humans dispersed out of Africa, they encountered and mated with now extinct hominins, including Neanderthals and Denisovans. It is now well established that all non-African individuals derive approximately 2% of their genome from Neanderthal ancestors and individuals of Melanesian and Australian aboriginal ancestry inherited an additional 2%–5% of their genomes from Denisovan ancestors. Attention has started to shift from documenting amounts of archaic admixture and identifying introgressed segments to understanding their molecular, phenotypic, and evolutionary consequences and refining models of human history. Here, we review recent insights into admixture between modern and archaic humans, emphasizing methodological innovations and the functional and phenotypic effects Neanderthal and Denisovan sequences have in contemporary individuals.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"90 ","pages":"Article 102280"},"PeriodicalIF":3.7,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cell–cell interactions between transplanted retinal organoid cells and recipient tissues 移植视网膜类器官细胞与受体组织之间的细胞间相互作用
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-11-15 DOI: 10.1016/j.gde.2024.102277
Patrick O Nnoromele , McKaily Adams , Annabelle Pan , Ying V Liu , Joyce Wang , Mandeep S Singh
{"title":"Cell–cell interactions between transplanted retinal organoid cells and recipient tissues","authors":"Patrick O Nnoromele ,&nbsp;McKaily Adams ,&nbsp;Annabelle Pan ,&nbsp;Ying V Liu ,&nbsp;Joyce Wang ,&nbsp;Mandeep S Singh","doi":"10.1016/j.gde.2024.102277","DOIUrl":"10.1016/j.gde.2024.102277","url":null,"abstract":"<div><div>The transplantation of human organoid-derived retinal cells is being studied as a potentially viable strategy to treat vision loss due to retinal degeneration. Experiments in animal models have demonstrated the feasibility of organoid-derived photoreceptor transplantation in various recipient contexts. In some cases, vision repair has been shown. However, recipient–donor cell–cell interactions are incompletely understood. This review briefly summarizes these interactions, categorizing them as synaptic structure formation, cellular component transfer, glial activation, immune cell infiltration, and cellular migration. Each of these interactions may affect the survival and functionality of the donor cells and, ultimately, their efficacy as a treatment substrate. Additionally, recipient characteristics, such as the cytoarchitecture of the retina and immune status, may also impact the type and frequency of cell–cell interactions. Despite the procedural challenges associated with culturing human retinal organoids and the technical difficulties in transplanting donor cells into the delicate recipient retina, transplantation of retinal organoid-derived cells is a promising tool for degenerative retinal disease treatment.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"89 ","pages":"Article 102277"},"PeriodicalIF":3.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
How our brains are built: emerging approaches to understand human-specific features 我们的大脑是如何构建的：了解人类特有特征的新方法。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-11-15 DOI: 10.1016/j.gde.2024.102278
Nicole D Moss , Davoneshia Lollis , Debra L Silver
{"title":"How our brains are built: emerging approaches to understand human-specific features","authors":"Nicole D Moss ,&nbsp;Davoneshia Lollis ,&nbsp;Debra L Silver","doi":"10.1016/j.gde.2024.102278","DOIUrl":"10.1016/j.gde.2024.102278","url":null,"abstract":"<div><div>Understanding what makes us uniquely human is a long-standing question permeating fields from genomics, neuroscience, and developmental biology to medicine. The discovery of human-specific genomic sequences has enabled a new understanding of the molecular features of human brain evolution. Advances in sequencing, computational, and <em>in vitro</em> screening approaches collectively reveal new roles of uniquely human sequences in regulating gene expression. Here, we review the landscape of human-specific loci and describe how emerging technologies are being used to understand their molecular functions and impact on brain development. We describe current challenges in the field and the potential of integrating new hypotheses and approaches to propel our understanding of the human brain.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"89 ","pages":"Article 102278"},"PeriodicalIF":3.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Diversity of human skin three-dimensional organotypic cultures 人体皮肤三维有机培养物的多样性。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-11-12 DOI: 10.1016/j.gde.2024.102275
Yunlong Y Jia , Scott X Atwood
{"title":"Diversity of human skin three-dimensional organotypic cultures","authors":"Yunlong Y Jia ,&nbsp;Scott X Atwood","doi":"10.1016/j.gde.2024.102275","DOIUrl":"10.1016/j.gde.2024.102275","url":null,"abstract":"<div><div>Recently, significant strides have been made in the development of high-fidelity skin organoids, encompassing techniques such as 3D bioprinting, skin-on-a-chip systems, and models derived from pluripotent stem cells (PSCs), replicating appendage structures and diverse skin cell types. Despite the emergence of these state-of-the-art skin engineering models, human organotypic cultures (OTCs), initially proposed in the 1970s, continue to reign as the predominant <em>in vitro</em> cultured three-dimensional skin model in the field of tissue engineering. This enduring prevalence is owed to their cost-effectiveness, straight forward setup, time efficiency, and faithful representation of native human skin. In this review, we systematically delineate recent advances in skin OTC models, aiming to inform future efforts to enhance <em>in vitro</em> skin model fidelity and reproducibility.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"89 ","pages":"Article 102275"},"PeriodicalIF":3.7,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Engineering immune organoids to regenerate host immune system 用免疫器官组织工程再生宿主免疫系统
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-11-06 DOI: 10.1016/j.gde.2024.102276
Sefali Patel , Wen Liu , Ravikumar K , Catherine McCormick , Yong Fan
{"title":"Engineering immune organoids to regenerate host immune system","authors":"Sefali Patel ,&nbsp;Wen Liu ,&nbsp;Ravikumar K ,&nbsp;Catherine McCormick ,&nbsp;Yong Fan","doi":"10.1016/j.gde.2024.102276","DOIUrl":"10.1016/j.gde.2024.102276","url":null,"abstract":"<div><div>Recent advances in immunotherapy have underscored the potential of harnessing the immune system to treat disorders associated with immune dysregulation, such as primary and secondary immunodeficiencies, cancer, transplantation rejection, and aging. Owing to the cellular and structural complexity and the dynamic nature of immune responses, engineering immune organoids that replicate the function and key features of their corresponding immune organs continues to be a formidable challenge. In this overview, we will discuss the recent progress in bioengineering organoids of key primary and secondary immune organs and tissues, focusing particularly on their contributions to the host’s immune system in animal models and highlighting their potential roles in regenerative medicine.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"89 ","pages":"Article 102276"},"PeriodicalIF":3.7,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142593216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Better together: how cooperativity influences transcriptional bursting 更好地合作：合作性如何影响转录突变
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-11-05 DOI: 10.1016/j.gde.2024.102274
Charis Fountas, Tineke L Lenstra
{"title":"Better together: how cooperativity influences transcriptional bursting","authors":"Charis Fountas,&nbsp;Tineke L Lenstra","doi":"10.1016/j.gde.2024.102274","DOIUrl":"10.1016/j.gde.2024.102274","url":null,"abstract":"<div><div>Transcriptional bursting refers to the stochastic transition of a promoter between transcriptionally active and inactive states. This dynamic process is highly regulated by the dynamics of transcription factor binding to DNA, their interactions with coactivators, and the 3D interactions between promoters, condensates, and enhancers. In this mini-review, we discuss recent insights into the kinetics of transcription factors and cofactors in both simple and complex regulatory environments to understand their impact on transcriptional bursting. We examine the novel concept of transcription factor exchange and relate it to different cooperativity models. Finally, we discuss recent live-cell imaging studies on the regulation of transcriptional bursting by enhancers and transcriptional condensates.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"89 ","pages":"Article 102274"},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142584729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Strategies for programmable manipulation of alternative splicing 可编程操纵替代剪接的策略。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-10-29 DOI: 10.1016/j.gde.2024.102272
Jonathan C Schmok , Gene W Yeo
{"title":"Strategies for programmable manipulation of alternative splicing","authors":"Jonathan C Schmok ,&nbsp;Gene W Yeo","doi":"10.1016/j.gde.2024.102272","DOIUrl":"10.1016/j.gde.2024.102272","url":null,"abstract":"<div><div>Alternative splicing (AS) plays a pivotal role in protein diversity and mRNA maturation. Programmable control of targeted AS events is of longstanding interest in RNA biology, promising correction of dysregulated splicing in disease and discovery of AS events. This review explores four main strategies for programmable splicing manipulation: (1) inhibiting splicing signals with antisense oligonucleotides (ASOs), exemplified by therapies approved by the U.S. Food and Drug Administration, (2) applying DNA-targeting clustered regularly interspaced short palindromic repeats systems to edit splicing signals, (3) using synthetic splicing factors, including synthetic proteins and ribonucleoproteins, inspired by natural RNA-binding proteins, and (4) guiding endogenous splicing machinery with bifunctional ASOs and engineered small nuclear RNAs. While ASOs remain clinically prominent, emerging technologies aim for broad, scalable, durable, and precise splicing modulation, holding promise for transformative advancements in RNA biology and therapeutic interventions.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"89 ","pages":"Article 102272"},"PeriodicalIF":3.7,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142548683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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