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Why do sex chromosomes progressively lose recombination? 为什么性染色体会逐渐失去重组能力？
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-27 DOI: 10.1016/j.tig.2024.03.005
Paul Jay, Daniel Jeffries, Fanny E. Hartmann, Amandine Véber, Tatiana Giraud
{"title":"Why do sex chromosomes progressively lose recombination?","authors":"Paul Jay, Daniel Jeffries, Fanny E. Hartmann, Amandine Véber, Tatiana Giraud","doi":"10.1016/j.tig.2024.03.005","DOIUrl":"https://doi.org/10.1016/j.tig.2024.03.005","url":null,"abstract":"<p>Progressive recombination loss is a common feature of sex chromosomes. Yet, the evolutionary drivers of this phenomenon remain a mystery. For decades, differences in trait optima between sexes (sexual antagonism) have been the favoured hypothesis, but convincing evidence is lacking. Recent years have seen a surge of alternative hypotheses to explain progressive extensions and maintenance of recombination suppression: neutral accumulation of sequence divergence, selection of nonrecombining fragments with fewer deleterious mutations than average, sheltering of recessive deleterious mutations by linkage to heterozygous alleles, early evolution of dosage compensation, and constraints on recombination restoration. Here, we explain these recent hypotheses and dissect their assumptions, mechanisms, and predictions. We also review empirical studies that have brought support to the various hypotheses.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140799585","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
Assessing autosomal aneuploidy in ancient genomes 评估古代基因组中的常染色体非整倍体
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-24 DOI: 10.1016/j.tig.2024.04.006
Julia Gresky
{"title":"Assessing autosomal aneuploidy in ancient genomes","authors":"Julia Gresky","doi":"10.1016/j.tig.2024.04.006","DOIUrl":"https://doi.org/10.1016/j.tig.2024.04.006","url":null,"abstract":"<p>Using genetic methods, aneuploidies can be detected in ancient human remains, which is so far the only way to reliably prove their existence in the past. As highlighted in recent studies by <span>Rohrlach <em>et al.</em></span><svg aria-label=\"Opens in new window\" focusable=\"false\" height=\"8px\" viewbox=\"0 0 8 8\" width=\"8px\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\"></path></svg> and by <span>Anastasiadou <em>et al.</em></span><svg aria-label=\"Opens in new window\" focusable=\"false\" height=\"8px\" viewbox=\"0 0 8 8\" width=\"8px\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\"></path></svg>, this initial step enables a deeper exploration of the history of rare diseases, encompassing the social and historical contexts of the afflicted individuals.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140799647","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
Ancestral desiccation tolerance tools repurposed throughout plant evolution 在整个植物进化过程中重新利用祖先的干燥耐受工具
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-24 DOI: 10.1016/j.tig.2024.04.007
Alyssa Kearly
{"title":"Ancestral desiccation tolerance tools repurposed throughout plant evolution","authors":"Alyssa Kearly","doi":"10.1016/j.tig.2024.04.007","DOIUrl":"https://doi.org/10.1016/j.tig.2024.04.007","url":null,"abstract":"<p>The ability to tolerate and recover from desiccation is an adaptation that permitted primitive plants to colonize land, and it persists in select species today. <span>Zhang <em>et al</em></span><svg aria-label=\"Opens in new window\" focusable=\"false\" height=\"8px\" viewbox=\"0 0 8 8\" width=\"8px\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\"></path></svg><em>.</em> dissected desiccation tolerance in moss species, and traced a key regulator through evolution to identify a conserved mechanism of water sensing in angiosperms.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140799589","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
Discovering mechanisms of human genetic variation and controlling cell states at scale 发现人类基因变异机制，大规模控制细胞状态
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-24 DOI: 10.1016/j.tig.2024.03.010
Max Frenkel, Srivatsan Raman
{"title":"Discovering mechanisms of human genetic variation and controlling cell states at scale","authors":"Max Frenkel, Srivatsan Raman","doi":"10.1016/j.tig.2024.03.010","DOIUrl":"https://doi.org/10.1016/j.tig.2024.03.010","url":null,"abstract":"<p>Population-scale sequencing efforts have catalogued substantial genetic variation in humans such that variant discovery dramatically outpaces interpretation. We discuss how single-cell sequencing is poised to reveal genetic mechanisms at a rate that may soon approach that of variant discovery. The functional genomics toolkit is sufficiently modular to systematically profile almost any type of variation within increasingly diverse contexts and with molecularly comprehensive and unbiased readouts. As a result, we can construct deep phenotypic atlases of variant effects that span the entire regulatory cascade. The same conceptual approach to interpreting genetic variation should be applied to engineering therapeutic cell states. In this way, variant mechanism discovery and cell state engineering will become reciprocating and iterative processes towards genomic medicine.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140806586","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
Gene-environmental regulation of the postnatal post-mitotic neuronal maturation 基因-环境对出生后有丝分裂期神经元成熟的调控
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-23 DOI: 10.1016/j.tig.2024.03.006
Gabrielle S. Prince, Molly Reynolds, Verdion Martina, HaoSheng Sun
{"title":"Gene-environmental regulation of the postnatal post-mitotic neuronal maturation","authors":"Gabrielle S. Prince, Molly Reynolds, Verdion Martina, HaoSheng Sun","doi":"10.1016/j.tig.2024.03.006","DOIUrl":"https://doi.org/10.1016/j.tig.2024.03.006","url":null,"abstract":"<p>Embryonic neurodevelopment, particularly neural progenitor differentiation into post-mitotic neurons, has been extensively studied. While the number and composition of post-mitotic neurons remain relatively constant from birth to adulthood, the brain undergoes significant postnatal maturation marked by major property changes frequently disrupted in neural diseases. This review first summarizes recent characterizations of the functional and molecular maturation of the postnatal nervous system. We then review regulatory mechanisms controlling the precise gene expression changes crucial for the intricate sequence of maturation events, highlighting experience-dependent versus cell-intrinsic genetic timer mechanisms. Despite significant advances in understanding of the gene-environmental regulation of postnatal neuronal maturation, many aspects remain unknown. The review concludes with our perspective on exciting future research directions in the next decade.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140799584","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 mechanisms of animal camouflage: an interdisciplinary perspective 动物伪装的遗传机制：跨学科视角
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-20 DOI: 10.1016/j.tig.2024.03.009
Guangping Huang, Yubo Zhang, Wei Zhang, Fuwen Wei
{"title":"Genetic mechanisms of animal camouflage: an interdisciplinary perspective","authors":"Guangping Huang, Yubo Zhang, Wei Zhang, Fuwen Wei","doi":"10.1016/j.tig.2024.03.009","DOIUrl":"https://doi.org/10.1016/j.tig.2024.03.009","url":null,"abstract":"<p>Camouflage is a classic example of a trait wherein animals respond to natural selection to avoid predation or attract prey. This unique phenomenon has attracted significant recent attention and the rapid development of integrative research methods is facilitating advances in our understanding of the in-depth genetic mechanisms of camouflage. In this review article, we revisit camouflage definitions and strategies and then we examine the underlying mechanisms of the two most common forms of camouflage, crypsis and masquerade, that have recently been elucidated using multiple approaches. We also discuss unresolved questions related to camouflage. Ultimately, we highlight the implications of camouflage for informing various key issues in ecology and evolution.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140629298","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
Towards fair and clinically relevant polygenic predictions 实现公平且与临床相关的多基因预测
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-19 DOI: 10.1016/j.tig.2024.04.002
Bjarni Jóhann Vilhjálmsson
{"title":"Towards fair and clinically relevant polygenic predictions","authors":"Bjarni Jóhann Vilhjálmsson","doi":"10.1016/j.tig.2024.04.002","DOIUrl":"https://doi.org/10.1016/j.tig.2024.04.002","url":null,"abstract":"<p><span>Lennon <em>et al.</em></span><svg aria-label=\"Opens in new window\" focusable=\"false\" height=\"8px\" viewbox=\"0 0 8 8\" width=\"8px\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\"></path></svg> recently proposed a clinical polygenic score (PGS) pipeline as part of the Electronic Medical Records and Genomics (eMERGE) network initiative. In this spotlight article we discuss the broader context for the use of PGS in preventive medicine and highlight key limitations and challenges facing their inclusion in prediction models.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140624516","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
Non-canonical functions of enhancers: regulation of RNA polymerase III transcription, DNA replication, and V(D)J recombination 增强子的非规范功能：调节 RNA 聚合酶 III 转录、DNA 复制和 V(D)J 重组
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-19 DOI: 10.1016/j.tig.2024.04.001
Kevin Struhl
{"title":"Non-canonical functions of enhancers: regulation of RNA polymerase III transcription, DNA replication, and V(D)J recombination","authors":"Kevin Struhl","doi":"10.1016/j.tig.2024.04.001","DOIUrl":"https://doi.org/10.1016/j.tig.2024.04.001","url":null,"abstract":"<p>Enhancers are the key regulators of other DNA-based processes by virtue of their unique ability to generate nucleosome-depleted regions in a highly regulated manner. Enhancers regulate cell-type-specific transcription of tRNA genes by RNA polymerase III (Pol III). They are also responsible for the binding of the origin replication complex (ORC) to DNA replication origins, thereby regulating origin utilization, replication timing, and replication-dependent chromosome breaks. Additionally, enhancers regulate V(D)J recombination by increasing access of the recombination-activating gene (RAG) recombinase to target sites and by generating non-coding enhancer RNAs and localized regions of trimethylated histone H3-K4 recognized by the RAG2 PHD domain. Thus, enhancers represent the first step in decoding the genome, and hence they regulate biological processes that, unlike RNA polymerase II (Pol II) transcription, do not have dedicated regulatory proteins.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140629308","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
The making and breaking of tRNAs by ribonucleases 核糖核酸酶制造和分解 tRNA
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-18 DOI: 10.1016/j.tig.2024.03.007
Jessica J.H. Elder, Ry Papadopoulos, Cassandra K. Hayne, Robin E. Stanley
{"title":"The making and breaking of tRNAs by ribonucleases","authors":"Jessica J.H. Elder, Ry Papadopoulos, Cassandra K. Hayne, Robin E. Stanley","doi":"10.1016/j.tig.2024.03.007","DOIUrl":"https://doi.org/10.1016/j.tig.2024.03.007","url":null,"abstract":"<p>Ribonucleases (RNases) play important roles in supporting canonical and non-canonical roles of tRNAs by catalyzing the cleavage of the tRNA phosphodiester backbone. Here, we highlight how recent advances in cryo-electron microscopy (cryo-EM), protein structure prediction, reconstitution experiments, tRNA sequencing, and other studies have revealed new insight into the nucleases that process tRNA. This represents a very diverse group of nucleases that utilize distinct mechanisms to recognize and cleave tRNA during different stages of a tRNA’s life cycle including biogenesis, fragmentation, surveillance, and decay. In this review, we provide a synthesis of the structure, mechanism, regulation, and modes of tRNA recognition by tRNA nucleases, along with open questions for future investigation.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140624679","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
Patient privacy in AI-driven omics methods 人工智能驱动的全息方法中的患者隐私
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-17 DOI: 10.1016/j.tig.2024.03.004
Juexiao Zhou, Chao Huang, Xin Gao
{"title":"Patient privacy in AI-driven omics methods","authors":"Juexiao Zhou, Chao Huang, Xin Gao","doi":"10.1016/j.tig.2024.03.004","DOIUrl":"https://doi.org/10.1016/j.tig.2024.03.004","url":null,"abstract":"<p>Artificial intelligence (AI) in omics analysis raises privacy threats to patients. Here, we briefly discuss risk factors to patient privacy in data sharing, model training, and release, as well as methods to safeguard and evaluate patient privacy in AI-driven omics methods.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140630621","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
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