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Evolution of piRNA-guided defense against transposable elements. pirna引导的转座因子防御的进化。
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? 富q激活域：转录起始位点选择的灵活“尺子”？
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. 利用空间多组学揭示胚胎发育中的组织结构。
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
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
The complex universe of inactive PARP1. 非活性 PARP1 的复杂世界。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-12-01 Epub Date: 2024-09-20 DOI: 10.1016/j.tig.2024.08.009
Doudou Huang, Ziyi Su, Yanxia Mei, Zhengping Shao
{"title":"The complex universe of inactive PARP1.","authors":"Doudou Huang, Ziyi Su, Yanxia Mei, Zhengping Shao","doi":"10.1016/j.tig.2024.08.009","DOIUrl":"10.1016/j.tig.2024.08.009","url":null,"abstract":"<p><p>Poly(ADP-ribose) polymerase 1 (PARP1) is a crucial member of the PARP family, which modifies targets through ADP-ribosylation and plays key roles in a variety of biological processes. PARP inhibitors (PARPis) hinder ADP-ribosylation and lead to the retention of PARP1 at the DNA lesion (also known as trapping), which underlies their toxicity. However, inhibitors and mutations that make PARP1 inactive do not necessarily correlate with trapping potency, challenging the current understanding of inactivation-caused trapping. Recent studies on mouse models indicate that both trapping and non-trapping inactivating mutations of PARP1 lead to embryonic lethality, suggesting the unexpected toxicity of the current inhibition strategy. The allosteric model, complicated automodification, and various biological functions of PARP1 all contribute to the complexity of PARP1 inactivation.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"1074-1085"},"PeriodicalIF":13.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301092","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
Yes, polygenic sex determination is a thing! 是的，多基因性别决定是个东西！
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-12-01 Epub Date: 2024-11-05 DOI: 10.1016/j.tig.2024.10.003
Thomas D Kocher, Richard P Meisel, Tony Gamble, Kristen A Behrens, William J Gammerdinger
{"title":"Yes, polygenic sex determination is a thing!","authors":"Thomas D Kocher, Richard P Meisel, Tony Gamble, Kristen A Behrens, William J Gammerdinger","doi":"10.1016/j.tig.2024.10.003","DOIUrl":"10.1016/j.tig.2024.10.003","url":null,"abstract":"<p><p>The process of sexual development in animals is modulated by a variety of mechanisms. Some species respond to environmental cues, while, in others, sex determination is thought to be controlled by a single 'master regulator' gene. However, many animals respond to a combination of environmental cues (e.g., temperature) and genetic factors (e.g., sex chromosomes). Even among species in which genetic factors predominate, there is a continuum between monofactorial and polygenic systems. The perception that polygenic systems are rare may result from experiments that lack the statistical power to detect multiple loci. Intellectual biases against the existence of polygenic sex determination (PSD) may further arise from misconceptions about the regulation of developmental processes and a misreading of theoretical results on the stability of polygenic systems of sex determination.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"1001-1017"},"PeriodicalIF":13.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142592117","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 origins, regulators, and biomarkers of cellular senescence. 细胞衰老的遗传起源、调节因子和生物标志物。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-12-01 Epub Date: 2024-09-27 DOI: 10.1016/j.tig.2024.08.007
Grasiela Torres, Ivan A Salladay-Perez, Anika Dhingra, Anthony J Covarrubias
{"title":"Genetic origins, regulators, and biomarkers of cellular senescence.","authors":"Grasiela Torres, Ivan A Salladay-Perez, Anika Dhingra, Anthony J Covarrubias","doi":"10.1016/j.tig.2024.08.007","DOIUrl":"10.1016/j.tig.2024.08.007","url":null,"abstract":"<p><p>This review comprehensively examines the molecular biology and genetic origins of cellular senescence. We focus on various cellular stressors and pathways leading to senescence, including recent advances in the understanding of the genetic influences driving senescence, such as telomere attrition, chemotherapy-induced DNA damage, pathogens, oncogene activation, and cellular and metabolic stress. This review also highlights the complex interplay of various signaling and metabolic pathways involved in cellular senescence and provides insights into potential therapeutic targets for aging-related diseases. Furthermore, this review outlines future research directions to deepen our understanding of senescence biology and develop effective interventions targeting senescent cells (SnCs).</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"1018-1031"},"PeriodicalIF":13.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11717094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332464","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
Can developmental signals shatter or mend our genomes? 发育信号能粉碎或修补我们的基因组吗？
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-12-01 Epub Date: 2024-11-07 DOI: 10.1016/j.tig.2024.10.006
Yimiao Qu, Kyle M Loh
{"title":"Can developmental signals shatter or mend our genomes?","authors":"Yimiao Qu, Kyle M Loh","doi":"10.1016/j.tig.2024.10.006","DOIUrl":"10.1016/j.tig.2024.10.006","url":null,"abstract":"<p><p>Consensus holds that most cells in the embryo are genetically identical and have healthy genomes. However, embryonic cells with abnormal chromosomes are surprisingly frequent. In a recent publication, de Jaime-Soguero et al. report that extracellular developmental signaling pathways, including BMP, FGF, and WNT, can promote or prevent chromosome instability in certain cell types.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"993-994"},"PeriodicalIF":13.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142607437","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 more elaborate genetic clock for clonal species. 克隆物种的遗传时钟更加精细。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-11-26 DOI: 10.1016/j.tig.2024.11.002
Jinhee Ryu, Yeonjin Kim, Young Seok Ju
{"title":"A more elaborate genetic clock for clonal species.","authors":"Jinhee Ryu, Yeonjin Kim, Young Seok Ju","doi":"10.1016/j.tig.2024.11.002","DOIUrl":"https://doi.org/10.1016/j.tig.2024.11.002","url":null,"abstract":"<p><p>The genetic clock is a well-established tool used in evolutionary biology for estimating divergence times between species, individuals, or cells based on DNA sequence changes. Yu et al. have revisited the clock to make it applicable to clonal multicellular organisms that expand through asexual reproduction mechanisms, enabling more comprehensive evolutionary tracking.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142740780","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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