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Cell-autonomous adaptation: an overlooked avenue of adaptation in human evolution. 细胞自主适应：人类进化中被忽视的适应途径。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-01-01 Epub Date: 2024-12-27 DOI: 10.1016/j.tig.2024.10.009
Ruthie Golomb, Orna Dahan, Dvir Dahary, Yitzhak Pilpel
{"title":"Cell-autonomous adaptation: an overlooked avenue of adaptation in human evolution.","authors":"Ruthie Golomb, Orna Dahan, Dvir Dahary, Yitzhak Pilpel","doi":"10.1016/j.tig.2024.10.009","DOIUrl":"10.1016/j.tig.2024.10.009","url":null,"abstract":"<p><p>Adaptation to environmental conditions occurs over diverse evolutionary timescales. In multi-cellular organisms, adaptive traits are often studied in tissues/organs relevant to the environmental challenge. We argue for the importance of an underappreciated layer of evolutionary adaptation manifesting at the cellular level. Cell-autonomous adaptations (CAAs) are inherited traits that boost organismal fitness by enhancing individual cell function. For instance, the cell-autonomous enhancement of mitochondrial oxygen utilization in hypoxic environments differs from an optimized erythropoiesis response, which involves multiple tissues. We explore the breadth of CAAs across challenges and highlight their counterparts in unicellular organisms. Applying these insights, we mine selection signals in Andean highlanders, revealing novel candidate CAAs. The conservation of CAAs across species may reveal valuable insights into multi-cellular evolution.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"12-22"},"PeriodicalIF":13.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900480","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
PIC-king apart PRC1-mediated repression. PIC-king 与 PRC1 介导的抑制相分离。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-01-01 Epub Date: 2024-11-20 DOI: 10.1016/j.tig.2024.10.013
Evan Healy, Adrian P Bracken
{"title":"PIC-king apart PRC1-mediated repression.","authors":"Evan Healy, Adrian P Bracken","doi":"10.1016/j.tig.2024.10.013","DOIUrl":"10.1016/j.tig.2024.10.013","url":null,"abstract":"<p><p>Polycomb repressive complex 1 (PRC1) is an essential repressor of lineage-specific genes central to the establishment and preservation of cellular identity. Recent findings by Szczurek et al. show that the noncanonical form of PRC1 (ncPRC1), which mediates H2AK119ub1, promotes a deep OFF state at promoters by blocking transcription initiation.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"4-5"},"PeriodicalIF":13.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142689668","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
A bioinformatics toolbox to prioritize causal genetic variants in candidate regions. 生物信息学工具箱，用于确定候选区域因果遗传变异的优先次序。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-01-01 Epub Date: 2024-10-16 DOI: 10.1016/j.tig.2024.09.007
Martin Šimon, Maša Čater, Tanja Kunej, Nicholas M Morton, Simon Horvat
{"title":"A bioinformatics toolbox to prioritize causal genetic variants in candidate regions.","authors":"Martin Šimon, Maša Čater, Tanja Kunej, Nicholas M Morton, Simon Horvat","doi":"10.1016/j.tig.2024.09.007","DOIUrl":"10.1016/j.tig.2024.09.007","url":null,"abstract":"<p><p>This review addresses the significant challenge of identifying causal genetic variants within quantitative trait loci (QTLs) for complex traits and diseases. Despite progress in detecting the ever-larger number of such loci, establishing causality remains daunting. We advocate for integrating bioinformatics and multiomics analyses to streamline the prioritization of candidate genes' variants. Our case study on the Pla2g4e gene, identified previously as a positional candidate obesity gene through genetic mapping and expression studies, demonstrates how applying multiomic data filtered through regulatory elements containing SNPs can refine the search for causative variants. This approach can yield results that guide more efficient experimental strategies, accelerating genetic research toward functional validation and therapeutic development.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"33-46"},"PeriodicalIF":13.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481006","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
Amyloids transmit acquired epigenetic feminizing information between generations. 淀粉样蛋白在代之间传递获得的表观遗传雌性化信息。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-01-01 Epub Date: 2024-11-27 DOI: 10.1016/j.tig.2024.11.003
Craig P Hunter
{"title":"Amyloids transmit acquired epigenetic feminizing information between generations.","authors":"Craig P Hunter","doi":"10.1016/j.tig.2024.11.003","DOIUrl":"10.1016/j.tig.2024.11.003","url":null,"abstract":"<p><p>In a recent article in Nature Cell Biology, Eroglu et al. link heritable, environment-induced epigenetic germline feminization to the accumulation, transmission, and replication of amyloid particles in Caenorhabditis elegans.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"1-3"},"PeriodicalIF":13.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142752252","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
Imprinting of the paternal marsupial X chromosome by DNA methylation. DNA甲基化对父系有袋动物X染色体的影响。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-01-01 Epub Date: 2024-11-27 DOI: 10.1016/j.tig.2024.10.011
Jennifer A M Graves
{"title":"Imprinting of the paternal marsupial X chromosome by DNA methylation.","authors":"Jennifer A M Graves","doi":"10.1016/j.tig.2024.10.011","DOIUrl":"10.1016/j.tig.2024.10.011","url":null,"abstract":"<p><p>Why is it that the X chromosome that comes from the male parent is inactivated in female marsupials, female mice, and even female mealy bugs, or the whole paternal chromosome complement in some weird flies? A new paper by Milton et al. now reveals DNA methylation patterns established in the male germline before meiosis in wallabies that may constitute the elusive paternal imprint.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"9-11"},"PeriodicalIF":13.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142752254","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
Disentangling variational bias: the roles of development, mutation, and selection. 分解变异偏差：发育、变异和选择的作用。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-01-01 Epub Date: 2024-10-22 DOI: 10.1016/j.tig.2024.09.008
Haoran Cai, Diogo Melo, David L Des Marais
{"title":"Disentangling variational bias: the roles of development, mutation, and selection.","authors":"Haoran Cai, Diogo Melo, David L Des Marais","doi":"10.1016/j.tig.2024.09.008","DOIUrl":"10.1016/j.tig.2024.09.008","url":null,"abstract":"<p><p>The extraordinary diversity and adaptive fit of organisms to their environment depends fundamentally on the availability of variation. While most population genetic frameworks assume that random mutations produce isotropic phenotypic variation, the distribution of variation available to natural selection is more restricted, as the distribution of phenotypic variation is affected by a range of factors in developmental systems. Here, we revisit the concept of developmental bias - the observation that the generation of phenotypic variation is biased due to the structure, character, composition, or dynamics of the developmental system - and argue that a more rigorous investigation into the role of developmental bias in the genotype-to-phenotype map will produce fundamental insights into evolutionary processes, with potentially important consequences on the relation between micro- and macro-evolution. We discuss the hierarchical relationships between different types of variational biases, including mutation bias and developmental bias, and their roles in shaping the realized phenotypic space. Furthermore, we highlight the challenges in studying variational bias and propose potential approaches to identify developmental bias using modern tools.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"23-32"},"PeriodicalIF":13.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513025","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
Dosage compensation in non-model insects - progress and perspectives. 非模式昆虫的剂量补偿--进展与前景。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-01-01 Epub Date: 2024-09-27 DOI: 10.1016/j.tig.2024.08.010
Agata Izabela Kalita, Claudia Isabelle Keller Valsecchi
{"title":"Dosage compensation in non-model insects - progress and perspectives.","authors":"Agata Izabela Kalita, Claudia Isabelle Keller Valsecchi","doi":"10.1016/j.tig.2024.08.010","DOIUrl":"10.1016/j.tig.2024.08.010","url":null,"abstract":"<p><p>In many multicellular eukaryotes, heteromorphic sex chromosomes are responsible for determining the sexual characteristics and reproductive functions of individuals. Sex chromosomes can cause a dosage imbalance between sexes, which in some species is re-equilibrated by dosage compensation (DC). Recent genomic advances have extended our understanding of DC mechanisms in insects beyond model organisms such as Drosophila melanogaster. We review current knowledge of insect DC, focusing on its conservation and divergence across orders, the evolutionary dynamics of neo-sex chromosomes, and the diversity of molecular mechanisms. We propose a framework to uncover DC regulators in non-model insects that relies on integrating evolutionary, genomic, and functional approaches. This comprehensive approach will facilitate a deeper understanding of the evolution and essentiality of gene regulatory mechanisms.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"76-98"},"PeriodicalIF":13.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332463","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
Crossover recombination between homologous chromosomes in meiosis: recent progress and remaining mysteries. 减数分裂过程中同源染色体间的交叉重组：最新进展与未解之谜。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-01-01 Epub Date: 2024-10-25 DOI: 10.1016/j.tig.2024.09.009
Lisette Payero, Eric Alani
{"title":"Crossover recombination between homologous chromosomes in meiosis: recent progress and remaining mysteries.","authors":"Lisette Payero, Eric Alani","doi":"10.1016/j.tig.2024.09.009","DOIUrl":"10.1016/j.tig.2024.09.009","url":null,"abstract":"<p><p>Crossing over between homologous chromosomes in meiosis is essential in most eukaryotes to produce gametes with the correct ploidy. Meiotic crossovers are typically evenly spaced, with each homolog pair receiving at least one crossover. The association of crossovers with distal sister chromatid cohesion is critical for the proper segregation of homologs in the first meiotic division. Studies in baker's yeast (Saccharomyces cerevisiae) have shown that meiotic crossovers result primarily from the biased resolution of double Holliday junction (dHJ) recombination intermediates through the actions of factors that belong to the DNA mismatch repair family. These findings and studies involving fine-scale mapping of meiotic crossover events have led to a new generation of mechanistic models for crossing over that are currently being tested.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"47-59"},"PeriodicalIF":13.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142569948","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 long and short of hyperdivergent regions. 超发散区域的长和短
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-12-19 DOI: 10.1016/j.tig.2024.11.005
Nicolas D Moya, Stephanie M Yan, Rajiv C McCoy, Erik C Andersen
{"title":"The long and short of hyperdivergent regions.","authors":"Nicolas D Moya, Stephanie M Yan, Rajiv C McCoy, Erik C Andersen","doi":"10.1016/j.tig.2024.11.005","DOIUrl":"10.1016/j.tig.2024.11.005","url":null,"abstract":"<p><p>The increasing prevalence of genome sequencing and assembly has uncovered evidence of hyperdivergent genomic regions - loci with excess genetic diversity - in species across the tree of life. Hyperdivergent regions are often enriched for genes that mediate environmental responses, such as immunity, parasitism, and sensory perception. Especially in self-fertilizing species where the majority of the genome is homozygous, the existence of hyperdivergent regions might imply the historical action of evolutionary forces such as introgression and/or balancing selection. We anticipate that the application of new sequencing technologies, broader taxonomic sampling, and evolutionary modeling of hyperdivergent regions will provide insights into the mechanisms that generate and maintain genetic diversity within and between species.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873501","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
Keeping it safe: control of meiotic chromosome breakage. 保证安全：控制减数分裂染色体断裂。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-12-12 DOI: 10.1016/j.tig.2024.11.006
Adhithi R Raghavan, Andreas Hochwagen
{"title":"Keeping it safe: control of meiotic chromosome breakage.","authors":"Adhithi R Raghavan, Andreas Hochwagen","doi":"10.1016/j.tig.2024.11.006","DOIUrl":"https://doi.org/10.1016/j.tig.2024.11.006","url":null,"abstract":"<p><p>Meiotic cells introduce numerous programmed DNA double-strand breaks (DSBs) into their genome to stimulate crossover recombination. DSB numbers must be high enough to ensure each homologous chromosome pair receives the obligate crossover required for accurate meiotic chromosome segregation. However, every DSB also increases the risk of aberrant or incomplete DNA repair, and thus genome instability. To mitigate these risks, meiotic cells have evolved an intricate network of controls that modulates the timing, levels, and genomic location of meiotic DSBs. This Review summarizes our current understanding of these controls with a particular focus on the mechanisms that prevent meiotic DSB formation at the wrong time or place, thereby guarding the genome from potentially catastrophic meiotic errors.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142822852","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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