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Massively parallel approaches for characterizing noncoding functional variation in human evolution 用大规模并行方法描述人类进化中的非编码功能变异
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-08-31 DOI: 10.1016/j.gde.2024.102256
Stephen Rong , Elise Root , Steven K Reilly
{"title":"Massively parallel approaches for characterizing noncoding functional variation in human evolution","authors":"Stephen Rong ,&nbsp;Elise Root ,&nbsp;Steven K Reilly","doi":"10.1016/j.gde.2024.102256","DOIUrl":"10.1016/j.gde.2024.102256","url":null,"abstract":"<div><p>The genetic differences underlying unique phenotypes in humans compared to our closest primate relatives have long remained a mystery. Similarly, the genetic basis of adaptations between human groups during our expansion across the globe is poorly characterized. Uncovering the downstream phenotypic consequences of these genetic variants has been difficult, as a substantial portion lies in noncoding regions, such as <em>cis</em>-regulatory elements (CREs). Here, we review recent high-throughput approaches to measure the functions of CREs and the impact of variation within them. CRISPR screens can directly perturb CREs in the genome to understand downstream impacts on gene expression and phenotypes, while massively parallel reporter assays can decipher the regulatory impact of sequence variants. Machine learning has begun to be able to predict regulatory function from sequence alone, further scaling our ability to characterize genome function. Applying these tools across diverse phenotypes, model systems, and ancestries is beginning to revolutionize our understanding of noncoding variation underlying human evolution.</p></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"88 ","pages":"Article 102256"},"PeriodicalIF":3.7,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142097379","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
Advances in skeletal genomics research across tissues and cells 跨组织和细胞的骨骼基因组研究取得进展
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-08-23 DOI: 10.1016/j.gde.2024.102245
Genevieve Housman
{"title":"Advances in skeletal genomics research across tissues and cells","authors":"Genevieve Housman","doi":"10.1016/j.gde.2024.102245","DOIUrl":"10.1016/j.gde.2024.102245","url":null,"abstract":"<div><p>Phenotypic variation within the skeleton has biological, behavioral, and biomedical functional implications for individuals and species. Thus, it is critical to understand how genomic, environmental, and mediating regulatory factors combine and interact to drive skeletal trait development and evolution. Recent research efforts to clarify these mechanisms have been made possible by expanded collections of genomic and phenotypic data from <em>in vivo</em> skeletal tissues, as well as the development of relevant <em>in vitro</em> skeletal cell culture systems. This review outlines this current work and recommends that continued exploration of this complexity should include an increased focus on how interactions between genomic and physiologically relevant contexts contribute to skeletal trait variation at population and evolutionary scales.</p></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"88 ","pages":"Article 102245"},"PeriodicalIF":3.7,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959437X24000947/pdfft?md5=dc8f4465356de6f5ec2b769754b11bbf&pid=1-s2.0-S0959437X24000947-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142049351","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
Evolutionary innovations in the primate dopaminergic system 灵长类多巴胺能系统的进化创新
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-08-16 DOI: 10.1016/j.gde.2024.102236
Hannah M Doll , Ryan D Risgaard , Hailey Thurston , Rachel J Chen , André MM Sousa
{"title":"Evolutionary innovations in the primate dopaminergic system","authors":"Hannah M Doll ,&nbsp;Ryan D Risgaard ,&nbsp;Hailey Thurston ,&nbsp;Rachel J Chen ,&nbsp;André MM Sousa","doi":"10.1016/j.gde.2024.102236","DOIUrl":"10.1016/j.gde.2024.102236","url":null,"abstract":"<div><p>The human brain has evolved unique capabilities compared to other vertebrates. The mechanistic basis of these derived traits remains a fundamental question in biology due to its relevance to the origin of our cognitive abilities and behavioral repertoire, as well as to human-specific aspects of neuropsychiatric and neurodegenerative diseases. Comparisons of the human brain to those of nonhuman primates and other mammals have revealed that differences in the neuromodulatory systems, especially in the dopaminergic system, may govern some of these behavioral and cognitive alterations, including increased vulnerability to certain brain disorders. In this review, we highlight and discuss recent findings of human- and primate-specific alterations of the dopaminergic system, focusing on differences in anatomy, circuitry, and molecular properties.</p></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"88 ","pages":"Article 102236"},"PeriodicalIF":3.7,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959437X24000856/pdfft?md5=c90354b2ea654feaf66231c0258bda15&pid=1-s2.0-S0959437X24000856-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141992972","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
Factors that determine cell type–specific CTCF binding in health and disease 决定健康和疾病中细胞类型特异性 CTCF 结合的因素
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-08-13 DOI: 10.1016/j.gde.2024.102244
Catherine Do , Jane A Skok
{"title":"Factors that determine cell type–specific CTCF binding in health and disease","authors":"Catherine Do ,&nbsp;Jane A Skok","doi":"10.1016/j.gde.2024.102244","DOIUrl":"10.1016/j.gde.2024.102244","url":null,"abstract":"<div><p>A number of factors contribute to cell type–specific CTCF chromatin binding, but how they act in concert to determine binding stability and functionality has not been fully elucidated. In this review, we tie together different layers of regulation to provide a holistic view of what is known. What emerges from these studies is a multifaceted system in which DNA sequence, DNA and chromatin accessibility, and cell type–specific transcription factors together contribute to CTCF binding profile and function. We discuss these findings in the light of disease settings in which changes in the chromatin landscape and transcriptional programming can disrupt CTCF’s binding profile and involvement in looping.</p></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"88 ","pages":"Article 102244"},"PeriodicalIF":3.7,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141985087","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
Xenotransplantation — a shortcut to construct tissue complexity in organoids 异种移植--在器官组织中构建复杂组织的捷径
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-08-13 DOI: 10.1016/j.gde.2024.102243
Yuan Yuan , Yixuan Wang , Yun Xia
{"title":"Xenotransplantation — a shortcut to construct tissue complexity in organoids","authors":"Yuan Yuan ,&nbsp;Yixuan Wang ,&nbsp;Yun Xia","doi":"10.1016/j.gde.2024.102243","DOIUrl":"10.1016/j.gde.2024.102243","url":null,"abstract":"<div><p>Our knowledge of human biology is mainly originated from studies using animal models. However, interspecies differences between human and model organisms may lead to imprecise extrapolation of results obtained from model organisms. Organoids are three-dimensional cell clusters derived from pluripotent or adult stem cells that self-organize into organ-like structures reminiscent of the cognate organ. The establishment of human organoids makes it possible to study organ or tissue pathophysiology that is specific to human beings. However, most organoids do not have organ-specific vasculature, neurons, and immune cells, hence limiting their utility in emulating complex pathophysiological phenotypes. Among the various approaches to address these limitations, xenotransplantation represents a promising ‘shortcut’. We will discuss recent advance in constructing tissue complexity in organoids, with a special focus on xenotransplantation.</p></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"88 ","pages":"Article 102243"},"PeriodicalIF":3.7,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141978596","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
Deciphering the role of structural variation in human evolution: a functional perspective 解读结构变异在人类进化中的作用：功能视角。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-08-08 DOI: 10.1016/j.gde.2024.102240
Charikleia Karageorgiou , Omer Gokcumen , Megan Y Dennis
{"title":"Deciphering the role of structural variation in human evolution: a functional perspective","authors":"Charikleia Karageorgiou ,&nbsp;Omer Gokcumen ,&nbsp;Megan Y Dennis","doi":"10.1016/j.gde.2024.102240","DOIUrl":"10.1016/j.gde.2024.102240","url":null,"abstract":"<div><p>Advances in sequencing technologies have enabled the comparison of high-quality genomes of diverse primate species, revealing vast amounts of divergence due to structural variation. Given their large size, structural variants (SVs) can simultaneously alter the function and regulation of multiple genes. Studies estimate that collectively more than 3.5% of the genome is divergent in humans versus other great apes, impacting thousands of genes. Functional genomics and gene-editing tools in various model systems recently emerged as an exciting frontier — investigating the wide-ranging impacts of SVs on molecular, cellular, and systems-level phenotypes. This review examines existing research and identifies future directions to broaden our understanding of the functional roles of SVs on phenotypic innovations and diversity impacting uniquely human features, ranging from cognition to metabolic adaptations.</p></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"88 ","pages":"Article 102240"},"PeriodicalIF":3.7,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959437X24000893/pdfft?md5=fa24fdab79f82513633e9a56eff9dd35&pid=1-s2.0-S0959437X24000893-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914449","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
Human-specific genetic modifiers of cortical architecture and function 大脑皮层结构和功能的人类特异性遗传修饰因子
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-08-06 DOI: 10.1016/j.gde.2024.102241
Hanzhi T Zhao, Ewoud RE Schmidt
{"title":"Human-specific genetic modifiers of cortical architecture and function","authors":"Hanzhi T Zhao,&nbsp;Ewoud RE Schmidt","doi":"10.1016/j.gde.2024.102241","DOIUrl":"10.1016/j.gde.2024.102241","url":null,"abstract":"<div><p>Evolution of the cerebral cortex is thought to have been critical for the emergence of our cognitive abilities. Major features of cortical evolution include increased neuron number and connectivity and altered morpho-electric properties of cortical neurons. Significant progress has been made in identifying human-specific genetic modifiers (HSGMs), some of which are involved in shaping these features of cortical architecture. But how did these evolutionary changes support the emergence of our cognitive abilities? Here, we highlight recent studies aimed at examining the impact of HSGMs on cortical circuit function and behavior. We also discuss the need for greater insight into the link between evolution of cortical architecture and the functional and computational properties of neuronal circuits, as we seek to provide a neurobiological foundation for human cognition.</p></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"88 ","pages":"Article 102241"},"PeriodicalIF":3.7,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141903471","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
Refining the role of N6-methyladenosine in cancer 完善 N6-甲基腺苷在癌症中的作用。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-08-06 DOI: 10.1016/j.gde.2024.102242
Jonas Koch, Frank Lyko
{"title":"Refining the role of N6-methyladenosine in cancer","authors":"Jonas Koch,&nbsp;Frank Lyko","doi":"10.1016/j.gde.2024.102242","DOIUrl":"10.1016/j.gde.2024.102242","url":null,"abstract":"<div><p>N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) is the most abundant internal modification of eukaryotic mRNAs. m<sup>6</sup>A affects the fate of its targets in all aspects of the mRNA life cycle and has important roles in various physiological and pathophysiological processes. Aberrant m<sup>6</sup>A patterns have been observed in numerous cancers and appear closely linked to oncogenic phenotypes. However, most studies relied on antibody-dependent modification detection, which is known to suffer from important limitations. Novel, antibody-independent, quantitative approaches will be critical to investigate changes in the m<sup>6</sup>A landscape of cancers. Furthermore, pharmaceutical targeting of the m<sup>6</sup>A writer Methyltransferase-like 3 (METTL3) has demonstrated the potential to modulate cancer cell phenotypes. However, the enzyme also appears to be essential for the viability of healthy cells. Further refinement of therapeutic strategies is therefore needed to fully realize the potential of m<sup>6</sup>A-related cancer therapies.</p></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"88 ","pages":"Article 102242"},"PeriodicalIF":3.7,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959437X24000911/pdfft?md5=4732d3b06b3d83e6fff7e80d2ffd7fe9&pid=1-s2.0-S0959437X24000911-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141903481","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
Vascular and immune interactions in islets transplantation and 3D islet models 胰岛移植和三维胰岛模型中的血管与免疫相互作用。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-08-06 DOI: 10.1016/j.gde.2024.102237
Adriana Migliorini , M Cristina Nostro
{"title":"Vascular and immune interactions in islets transplantation and 3D islet models","authors":"Adriana Migliorini ,&nbsp;M Cristina Nostro","doi":"10.1016/j.gde.2024.102237","DOIUrl":"10.1016/j.gde.2024.102237","url":null,"abstract":"<div><p>The aim of regenerative medicine is to restore specific functions to damaged cells or tissues. A crucial aspect of success lies in effectively reintegrating these cells or tissues within the recipient organism. This is particularly pertinent for diabetes, where islet function relies on the close connection of beta cells to the bloodstream for glucose sensing and insulin release. Central to this approach is the need to establish a fast connection with the host’s vascular system. In this review, we explore the intricate relationships between endocrine, vascular, and immune cell interactions in transplantation outcomes. We also delve into recent strategies aimed at enhancing engraftment, along with the utilization of <em>in vitro</em> platforms to model cellular interactions.</p></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"88 ","pages":"Article 102237"},"PeriodicalIF":3.7,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959437X24000868/pdfft?md5=ef5b9437dc85a56389b37911de2cdf35&pid=1-s2.0-S0959437X24000868-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141903482","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
Structural variation in humans and our primate kin in the era of telomere-to-telomere genomes and pangenomics 端粒到端粒基因组和泛基因组学时代人类和灵长类亲属的结构变异。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-08-01 DOI: 10.1016/j.gde.2024.102233
Joana L Rocha , Runyang N Lou , Peter H Sudmant
{"title":"Structural variation in humans and our primate kin in the era of telomere-to-telomere genomes and pangenomics","authors":"Joana L Rocha ,&nbsp;Runyang N Lou ,&nbsp;Peter H Sudmant","doi":"10.1016/j.gde.2024.102233","DOIUrl":"10.1016/j.gde.2024.102233","url":null,"abstract":"<div><p>Structural variants (SVs) account for the majority of base pair differences both within and between primate species. However, our understanding of inter- and intra-species SV has been historically hampered by the quality of draft primate genomes and the absence of genome resources for key taxa. Recently, advances in long-read sequencing and genome assembly have begun to radically reshape our understanding of SVs. Two landmark achievements include the publication of a human telomere-to-telomere (T2T) genome as well as the development of the first human pangenome reference. In this review, we first look back to the major works laying the foundation for these projects. We then examine the ways in which T2T genome assemblies and pangenomes are transforming our understanding of and approach to primate SV. Finally, we discuss what the future of primate SV research may look like in the era of T2T genomes and pangenomics.</p></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"87 ","pages":"Article 102233"},"PeriodicalIF":3.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959437X24000820/pdfft?md5=9162f226bec2a0f7ba9c1132f8bac91d&pid=1-s2.0-S0959437X24000820-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141753241","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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