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RNA Crossing Membranes: Systems and Mechanisms Contextualizing Extracellular RNA and Cell Surface GlycoRNAs. RNA跨膜:细胞外RNA和细胞表面糖蛋白的系统和机制。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2023-08-25 DOI: 10.1146/annurev-genom-101722-101224
Peiyuan Chai, Charlotta G Lebedenko, Ryan A Flynn
{"title":"RNA Crossing Membranes: Systems and Mechanisms Contextualizing Extracellular RNA and Cell Surface GlycoRNAs.","authors":"Peiyuan Chai,&nbsp;Charlotta G Lebedenko,&nbsp;Ryan A Flynn","doi":"10.1146/annurev-genom-101722-101224","DOIUrl":"https://doi.org/10.1146/annurev-genom-101722-101224","url":null,"abstract":"<p><p>The subcellular localization of a biopolymer often informs its function. RNA is traditionally confined to the cytosolic and nuclear spaces, where it plays critical and conserved roles across nearly all biochemical processes. Our recent observation of cell surface glycoRNAs may further explain the extracellular role of RNA. While cellular membranes are efficient gatekeepers of charged polymers such as RNAs, a large body of research has demonstrated the accumulation of specific RNA species outside of the cell, termed extracellular RNAs (exRNAs). Across various species and forms of life, protein pores have evolved to transport RNA across membranes, thus providing a mechanistic path for exRNAs to achieve their extracellular topology. Here, we review types of exRNAs and the pores capable of RNA transport to provide a logical and testable path toward understanding the biogenesis and regulation of cell surface glycoRNAs.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10098662","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: 2
Long-Read DNA Sequencing: Recent Advances and Remaining Challenges. 长读DNA测序:最近的进展和仍然存在的挑战。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2023-08-25 DOI: 10.1146/annurev-genom-101722-103045
Peter E Warburton, Robert P Sebra
{"title":"Long-Read DNA Sequencing: Recent Advances and Remaining Challenges.","authors":"Peter E Warburton,&nbsp;Robert P Sebra","doi":"10.1146/annurev-genom-101722-103045","DOIUrl":"https://doi.org/10.1146/annurev-genom-101722-103045","url":null,"abstract":"<p><p>DNA sequencing has revolutionized medicine over recent decades. However, analysis of large structural variation and repetitive DNA, a hallmark of human genomes, has been limited by short-read technology, with read lengths of 100-300 bp. Long-read sequencing (LRS) permits routine sequencing of human DNA fragments tens to hundreds of kilobase pairs in size, using both real-time sequencing by synthesis and nanopore-based direct electronic sequencing. LRS permits analysis of large structural variation and haplotypic phasing in human genomes and has enabled the discovery and characterization of rare pathogenic structural variants and repeat expansions. It has also recently enabled the assembly of a complete, gapless human genome that includes previously intractable regions, such as highly repetitive centromeres and homologous acrocentric short arms. With the addition of protocols for targeted enrichment, direct epigenetic DNA modification detection, and long-range chromatin profiling, LRS promises to launch a new era of understanding of genetic diversity and pathogenic mutations in human populations.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10099487","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: 4
Padlock Probe-Based Targeted In Situ Sequencing: Overview of Methods and Applications. 基于挂锁探针的靶向原位测序:方法和应用综述。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2023-08-25 DOI: 10.1146/annurev-genom-102722-092013
Anastasia Magoulopoulou, Sergio Marco Salas, Katarína Tiklová, Erik Reinhold Samuelsson, Markus M Hilscher, Mats Nilsson
{"title":"Padlock Probe-Based Targeted In Situ Sequencing: Overview of Methods and Applications.","authors":"Anastasia Magoulopoulou,&nbsp;Sergio Marco Salas,&nbsp;Katarína Tiklová,&nbsp;Erik Reinhold Samuelsson,&nbsp;Markus M Hilscher,&nbsp;Mats Nilsson","doi":"10.1146/annurev-genom-102722-092013","DOIUrl":"https://doi.org/10.1146/annurev-genom-102722-092013","url":null,"abstract":"<p><p>Elucidating spatiotemporal changes in gene expression has been an essential goal in studies of health, development, and disease. In the emerging field of spatially resolved transcriptomics, gene expression profiles are acquired with the tissue architecture maintained, sometimes at cellular resolution. This has allowed for the development of spatial cell atlases, studies of cell-cell interactions, and in situ cell typing. In this review, we focus on padlock probe-based in situ sequencing, which is a targeted spatially resolved transcriptomic method. We summarize recent methodological and computational tool developments and discuss key applications. We also discuss compatibility with other methods and integration with multiomic platforms for future applications.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10099464","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: 1
Avoiding Liability and Other Legal Land Mines in the Evolving Genomics Landscape. 在不断发展的基因组学景观中避免责任和其他法律地雷。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2023-08-25 DOI: 10.1146/annurev-genom-100722-021725
Ellen Wright Clayton, Alex M Tritell, Adrian M Thorogood
{"title":"Avoiding Liability and Other Legal Land Mines in the Evolving Genomics Landscape.","authors":"Ellen Wright Clayton,&nbsp;Alex M Tritell,&nbsp;Adrian M Thorogood","doi":"10.1146/annurev-genom-100722-021725","DOIUrl":"https://doi.org/10.1146/annurev-genom-100722-021725","url":null,"abstract":"<p><p>This article reviews evolving legal implications for clinicians and researchers as genomics is used more widely in both the clinic and in translational research, reflecting rapid changes in scientific knowledge as well as the surrounding cultural and political environment. Professionals will face new and changing duties to make or act upon a genetic diagnosis, address direct-to-consumer genetic testing in patient care, consider the health implications of results for patients' family members, and recontact patients when test results change over time. Professional duties in reproductive genetic testing will need to be recalibrated in response to disruptive changes to reproductive rights in the United States. We also review the debate over who controls the flow of genetic information and who is responsible for its protection, considering the globally influential European Union General Data Protection Regulation and the rapidly evolving data privacy law landscape of the United States.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10088082","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: 1
The Genetic Determinants of Axial Length: From Microphthalmia to High Myopia in Childhood. 眼轴长度的遗传决定因素:从儿童小眼到高度近视。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2023-08-25 DOI: 10.1146/annurev-genom-102722-090617
Daniel Jackson, Mariya Moosajee
{"title":"The Genetic Determinants of Axial Length: From Microphthalmia to High Myopia in Childhood.","authors":"Daniel Jackson,&nbsp;Mariya Moosajee","doi":"10.1146/annurev-genom-102722-090617","DOIUrl":"https://doi.org/10.1146/annurev-genom-102722-090617","url":null,"abstract":"<p><p>The axial length of the eye is critical for normal visual function by enabling light to precisely focus on the retina. The mean axial length of the adult human eye is 23.5 mm, but the molecular mechanisms regulating ocular axial length remain poorly understood. Underdevelopment can lead to microphthalmia (defined as a small eye with an axial length of less than 19 mm at 1 year of age or less than 21 mm in adulthood) within the first trimester of pregnancy. However, continued overgrowth can lead to axial high myopia (an enlarged eye with an axial length of 26.5 mm or more) at any age. Both conditions show high genetic and phenotypic heterogeneity associated with significant visual morbidity worldwide. More than 90 genes can contribute to microphthalmia, and several hundred genes are associated with myopia, yet diagnostic yields are low. Crucially, the genetic pathways underpinning the specification of eye size are only now being discovered, with evidence suggesting that shared molecular pathways regulate under- or overgrowth of the eye. Improving our mechanistic understanding of axial length determination will help better inform us of genotype-phenotype correlations in both microphthalmia and myopia, dissect gene-environment interactions in myopia, and develop postnatal therapies that may influence overall eye growth.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10478535","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: 1
A Journey from Blood Cells to Genes and Back. 从血细胞到基因再回来的旅程。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2023-08-25 DOI: 10.1146/annurev-genom-101022-105018
Lucio Luzzatto
{"title":"A Journey from Blood Cells to Genes and Back.","authors":"Lucio Luzzatto","doi":"10.1146/annurev-genom-101022-105018","DOIUrl":"https://doi.org/10.1146/annurev-genom-101022-105018","url":null,"abstract":"<p><p>I was attracted to hematology because by combining clinical findings with the use of a microscope and simple laboratory tests, one could often make a diagnosis. I was attracted to genetics when I learned about inherited blood disorders, at a time when we had only hints that somatic mutations were also important. It seemed clear that if we understood not only what genetic changes caused what diseases but also the mechanisms through which those genetic changes contribute to cause disease, we could improve management. Thus, I investigated many aspects of the glucose-6-phosphate dehydrogenase system, including cloning of the gene, and in the study of paroxysmal nocturnal hemoglobinuria (PNH), I found that it is a clonal disorder; subsequently, we were able to explain how a nonmalignant clone can expand, and I was involved in the first trial of PNH treatment by complement inhibition. I was fortunate to do clinical and research hematology in five countries; in all of them, I learned from mentors, from colleagues, and from patients.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10101938","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
Genome-Wide Analysis of Human Long Noncoding RNAs: A Provocative Review. 人类长链非编码rna的全基因组分析:一个具有争议性的综述。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-08-31 DOI: 10.1146/annurev-genom-112921-123710
Chris P Ponting, Wilfried Haerty
{"title":"Genome-Wide Analysis of Human Long Noncoding RNAs: A Provocative Review.","authors":"Chris P Ponting,&nbsp;Wilfried Haerty","doi":"10.1146/annurev-genom-112921-123710","DOIUrl":"https://doi.org/10.1146/annurev-genom-112921-123710","url":null,"abstract":"<p><p>Do long noncoding RNAs (lncRNAs) contribute little or substantively to human biology? To address how lncRNA loci and their transcripts, structures, interactions, and functions contribute to human traits and disease, we adopt a genome-wide perspective. We intend to provoke alternative interpretation of questionable evidence and thorough inquiry into unsubstantiated claims. We discuss pitfalls of lncRNA experimental and computational methods as well as opposing interpretations of their results. The majority of evidence, we argue, indicates that most lncRNA transcript models reflect transcriptional noise or provide minor regulatory roles, leaving relatively few human lncRNAs that contribute centrally to human development, physiology, or behavior. These important few tend to be spliced and better conserved but lack a simple syntax relating sequence to structure and mechanism, and so resist simple categorization. This genome-wide view should help investigators prioritize individual lncRNAs based on their likely contribution to human biology.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10748820","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: 35
The Genomics of Auditory Function and Disease. 听觉功能与疾病的基因组学。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-08-31 Epub Date: 2022-06-06 DOI: 10.1146/annurev-genom-121321-094136
Shahar Taiber, Kathleen Gwilliam, Ronna Hertzano, Karen B Avraham
{"title":"The Genomics of Auditory Function and Disease.","authors":"Shahar Taiber, Kathleen Gwilliam, Ronna Hertzano, Karen B Avraham","doi":"10.1146/annurev-genom-121321-094136","DOIUrl":"10.1146/annurev-genom-121321-094136","url":null,"abstract":"<p><p>Current estimates suggest that nearly half a billion people worldwide are affected by hearing loss. Because of the major psychological, social, economic, and health ramifications, considerable efforts have been invested in identifying the genes and molecular pathways involved in hearing loss, whether genetic or environmental, to promote prevention, improve rehabilitation, and develop therapeutics. Genomic sequencing technologies have led to the discovery of genes associated with hearing loss. Studies of the transcriptome and epigenome of the inner ear have characterized key regulators and pathways involved in the development of the inner ear and have paved the way for their use in regenerative medicine. In parallel, the immense preclinical success of using viral vectors for gene delivery in animal models of hearing loss has motivated the industry to work on translating such approaches into the clinic. Here, we review the recent advances in the genomics of auditory function and dysfunction, from patient diagnostics to epigenetics and gene therapy.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10644960/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10853331","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: 10
The Role of Telomeres in Human Disease. 端粒在人类疾病中的作用。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-08-31 DOI: 10.1146/annurev-genom-010422-091101
Mary Armanios
{"title":"The Role of Telomeres in Human Disease.","authors":"Mary Armanios","doi":"10.1146/annurev-genom-010422-091101","DOIUrl":"https://doi.org/10.1146/annurev-genom-010422-091101","url":null,"abstract":"<p><p>Telomere biology was first studied in maize, ciliates, yeast, and mice, and in recent decades, it has informed understanding of common disease mechanisms with broad implications for patient care. Short telomere syndromes are the most prevalent premature aging disorders, with prominent phenotypes affecting the lung and hematopoietic system. Less understood are a newly recognized group of cancer-prone syndromes that are associated with mutations that lengthen telomeres. A large body of new data from Mendelian genetics and epidemiology now provides an opportunity to reconsider paradigms related to the role of telomeres in human aging and cancer, and in some cases, the findings diverge from what was interpreted from model systems. For example, short telomeres have been considered potent drivers of genome instability, but age-associated solid tumors are rare in individuals with short telomere syndromes, and T cell immunodeficiency explains their spectrum. More commonly, short telomeres promote clonal hematopoiesis, including somatic reversion, providing a new leukemogenesis paradigm that is independent of genome instability. Long telomeres, on the other hand, which extend the cellular life span in vitro, are now appreciated to be the most common shared germline risk factor for cancer in population studies. Through this contemporary lens, I revisit here the role of telomeres in human aging, focusing on how short and long telomeres drive cancer evolution but through distinct mechanisms.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10111244/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9312207","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: 29
Population Screening in Health Systems. 卫生系统中的人口筛查。
IF 8.7 2区 生物学
Annual review of genomics and human genetics Pub Date : 2022-08-31 Epub Date: 2022-02-17 DOI: 10.1146/annurev-genom-111221-115239
Marc S Williams
{"title":"Population Screening in Health Systems.","authors":"Marc S Williams","doi":"10.1146/annurev-genom-111221-115239","DOIUrl":"https://doi.org/10.1146/annurev-genom-111221-115239","url":null,"abstract":"<p><p>Applications of genomics to population screening are expanding in the United States and internationally. Many of these programs are being implemented in the context of healthcare systems, mostly in a clinical research setting, but there are some emerging examples of clinical models. This review examines these genomic population screening programs to identify common features and differences in screened conditions, genomic technology employed, approach to results disclosure, health outcomes, financial models, and sustainability. The diversity of approaches provides opportunities to learn and better understand the optimal approach to implementation based on the contextual setting.</p>","PeriodicalId":8231,"journal":{"name":"Annual review of genomics and human genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39628998","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: 7
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