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Bacterial intragenic inversions: a new layer of diversity.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-12-19 DOI: 10.1016/j.tig.2024.12.002
Brantley Hall, Xiaofang Jiang
{"title":"Bacterial intragenic inversions: a new layer of diversity.","authors":"Brantley Hall, Xiaofang Jiang","doi":"10.1016/j.tig.2024.12.002","DOIUrl":"https://doi.org/10.1016/j.tig.2024.12.002","url":null,"abstract":"<p><p>DNA inversions in bacteria were known to create diversity through intergenic or partial intergenic changes. Now, Chanin, West, et al. reveal intragenic inversions, enabling single genes to encode multiple protein variants via sequence recoding or truncation - an unexpected mechanism for expanding protein diversity without increasing genome size.</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":"142873498","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.
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":"https://doi.org/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
Mitochondrial-derived microproteins: from discovery to function.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-12-16 DOI: 10.1016/j.tig.2024.11.010
Kelvin Yen, Brendan Miller, Hiroshi Kumagai, Ana Silverstein, Pinchas Cohen
{"title":"Mitochondrial-derived microproteins: from discovery to function.","authors":"Kelvin Yen, Brendan Miller, Hiroshi Kumagai, Ana Silverstein, Pinchas Cohen","doi":"10.1016/j.tig.2024.11.010","DOIUrl":"https://doi.org/10.1016/j.tig.2024.11.010","url":null,"abstract":"<p><p>Given the uniqueness of the mitochondria, and the fact that they have their own genome, mitochondrial-derived microproteins (MDPs) are similar to, but different from, nuclear-encoded microproteins. The discovery of an increasing number of microproteins from this organelle and the importance of mitochondria to cellular and organismal health make it a priority to study this novel class of proteins in search of possible therapeutic targets and cures. In this review, we discuss the history of MDP discovery, describe the function of each MDP, and conclude with future goals and techniques to help discover more MDPs.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142848403","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.
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
Evolution of piRNA-guided defense against transposable elements.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-12-12 DOI: 10.1016/j.tig.2024.11.011
Shashank Pritam, Sarah Signor
{"title":"Evolution of piRNA-guided defense against transposable elements.","authors":"Shashank Pritam, Sarah Signor","doi":"10.1016/j.tig.2024.11.011","DOIUrl":"https://doi.org/10.1016/j.tig.2024.11.011","url":null,"abstract":"<p><p>Transposable elements (TEs) shape every aspect of genome biology, influencing genome stability, size, and organismal fitness. Following the 2007 discovery of the piRNA defense system, researchers have made numerous findings about organisms' defenses against these genomic invaders. TEs are suppressed by a 'genomic immune system', where TE insertions within specialized regions called PIWI-interacting RNA (piRNA) clusters produce small RNAs responsible for their suppression. The evolution of piRNA clusters and the piRNA system is only now being understood, largely because most research has been conducted in developmental biology labs using only one to two genotypes of Drosophila melanogaster. While piRNAs themselves were identified simultaneously in various organisms (flies, mice, rats, and zebrafish) in 2006-2007, detailed work on piRNA clusters has only recently expanded beyond D. melanogaster. By studying piRNA cluster evolution in various organisms from an evolutionary perspective, we are beginning to understand more about TE suppression mechanisms and organism-TE coevolution.</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":"142822812","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
Q-rich activation domains: flexible 'rulers' for transcription start site selection?
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-12-07 DOI: 10.1016/j.tig.2024.11.008
Andrea Bernardini, Roberto Mantovani
{"title":"Q-rich activation domains: flexible 'rulers' for transcription start site selection?","authors":"Andrea Bernardini, Roberto Mantovani","doi":"10.1016/j.tig.2024.11.008","DOIUrl":"https://doi.org/10.1016/j.tig.2024.11.008","url":null,"abstract":"<p><p>Recent findings broadened the function of RNA polymerase II (Pol II) proximal promoter motifs from quantitative regulators of transcription to important determinants of transcription start site (TSS) position. These motifs are recognized by transcription factors (TFs) that we propose to term 'ruler' TFs (rTFs), such as NRF1, NF-Y, YY1, ZNF143, BANP, and members of the SP, ETS, and CRE families, sharing as a common feature a glutamine-rich (Q-rich) effector domain also enriched in valine, isoleucine, and threonine (QVIT-rich). We propose that rTFs guide TSS location by constraining the position of the pre-initiation complex (PIC) during its promoter recognition phase through a specialized, and still enigmatic, class of activation domains.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142796418","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
Leveraging spatial multiomics to unravel tissue architecture in embryo development.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-12-07 DOI: 10.1016/j.tig.2024.11.007
Fuqing Jiang, Haoxian Wang, Zhuxia Li, Guizhong Cui, Guangdun Peng
{"title":"Leveraging spatial multiomics to unravel tissue architecture in embryo development.","authors":"Fuqing Jiang, Haoxian Wang, Zhuxia Li, Guizhong Cui, Guangdun Peng","doi":"10.1016/j.tig.2024.11.007","DOIUrl":"https://doi.org/10.1016/j.tig.2024.11.007","url":null,"abstract":"<p><p>Spatial multiomics technologies have revolutionized biomedical research by enabling the simultaneous measurement of multiple omics modalities within intact tissue sections. This approach facilitates the reconstruction of 3D molecular architectures, providing unprecedented insights into complex cellular interactions and the intricate organization of biological systems, such as those underlying embryonic development.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142796415","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
Advancing evolutionary medicine with complete primate genomes and advanced biotechnologies.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-12-02 DOI: 10.1016/j.tig.2024.11.001
Kaiyue Ma, Xiangyu Yang, Yafei Mao
{"title":"Advancing evolutionary medicine with complete primate genomes and advanced biotechnologies.","authors":"Kaiyue Ma, Xiangyu Yang, Yafei Mao","doi":"10.1016/j.tig.2024.11.001","DOIUrl":"https://doi.org/10.1016/j.tig.2024.11.001","url":null,"abstract":"<p><p>Evolutionary medicine, which integrates evolutionary biology and medicine, significantly enhances our understanding of human traits and disease susceptibility. However, previous studies in this field have often focused on single-nucleotide variants due to technological limitations in characterizing complex genomic regions, hindering the comprehensive analyses of their evolutionary origins and clinical significance. In this review, we summarize recent advancements in complete telomere-to-telomere (T2T), primate genomes and other primate resources, and illustrate how these resources facilitate the research of complex regions. We focus on several biomedically relevant regions to examine the relationship between primate genome evolution and human diseases. We also highlight the potentials of high-throughput functional genomic technologies for assessing candidate loci. Finally, we discuss future directions for primate research within the context of evolutionary medicine.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142774833","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 distinction between epigenetics and epigenomics. 表观遗传学与表观基因组学的区别。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-12-01 Epub Date: 2024-10-24 DOI: 10.1016/j.tig.2024.10.002
Kevin Struhl
{"title":"The distinction between epigenetics and epigenomics.","authors":"Kevin Struhl","doi":"10.1016/j.tig.2024.10.002","DOIUrl":"10.1016/j.tig.2024.10.002","url":null,"abstract":"<p><p>'Epigenetics' is the process by which distinct cell types or cell states are inherited through multiple cell divisions. 'Epigenomics' refers to DNA-associated physical and functional entities including histone modifications and DNA methylation, not concepts of inheritance. Conflating epigenetics and epigenomics is confusing and causes misunderstanding of a fundamental biological process.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"995-997"},"PeriodicalIF":13.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11614679/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513027","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
Emerging links between phase separation and transcription factor haploinsufficiency. 相分离与转录因子单倍体缺陷之间的新联系
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-12-01 Epub Date: 2024-10-26 DOI: 10.1016/j.tig.2024.10.001
Reiner A Veitia
{"title":"Emerging links between phase separation and transcription factor haploinsufficiency.","authors":"Reiner A Veitia","doi":"10.1016/j.tig.2024.10.001","DOIUrl":"10.1016/j.tig.2024.10.001","url":null,"abstract":"<p><p>Recent studies have addressed the relevance of phase separation, by which membrane-less compartments are formed within the nucleus, to understand the impact of genetic variants. They highlight unsuspected links between phase separation and haploinsufficiency of transcription factors.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"998-1000"},"PeriodicalIF":13.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513026","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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