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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 : 2024-10-24 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":"https://doi.org/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":null,"pages":null},"PeriodicalIF":13.6,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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 : 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":"https://doi.org/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":null,"pages":null},"PeriodicalIF":13.6,"publicationDate":"2024-10-22","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
Unraveling aging from transcriptomics. 从转录组学揭示衰老。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-17 DOI: 10.1016/j.tig.2024.09.006
Yuanfang Huang, Shouxuan Zhu, Shuai Yao, Haotian Zhai, Chenyang Liu, Jing-Dong J Han
{"title":"Unraveling aging from transcriptomics.","authors":"Yuanfang Huang, Shouxuan Zhu, Shuai Yao, Haotian Zhai, Chenyang Liu, Jing-Dong J Han","doi":"10.1016/j.tig.2024.09.006","DOIUrl":"https://doi.org/10.1016/j.tig.2024.09.006","url":null,"abstract":"<p><p>Research into aging constitutes a pivotal endeavor aimed at elucidating the underlying biological mechanisms governing aging and age-associated diseases, as well as promoting healthy longevity. Recent advances in transcriptomic technologies, such as bulk RNA sequencing (RNA-seq), single-cell transcriptomics, and spatial transcriptomics, have revolutionized our ability to study aging at unprecedented resolution and scale. These technologies present novel opportunities for the discovery of biomarkers, elucidation of molecular pathways, and development of targeted therapeutic strategies for age-related disorders. This review surveys recent breakthroughs in different types of transcripts on aging, such as mRNA, long noncoding (lnc)RNA, tRNA, and miRNA, highlighting key findings and discussing their potential implications for future studies in this field.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":13.6,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142480921","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 : 2024-10-15 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":"https://doi.org/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":null,"pages":null},"PeriodicalIF":13.6,"publicationDate":"2024-10-15","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
Exploring the world of small proteins in plant biology and bioengineering. 探索植物生物学和生物工程中的小蛋白质世界。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-14 DOI: 10.1016/j.tig.2024.09.004
Louise Petri, Anne Van Humbeeck, Huanying Niu, Casper Ter Waarbeek, Ashleigh Edwards, Maurizio Junior Chiurazzi, Ylenia Vittozzi, Stephan Wenkel
{"title":"Exploring the world of small proteins in plant biology and bioengineering.","authors":"Louise Petri, Anne Van Humbeeck, Huanying Niu, Casper Ter Waarbeek, Ashleigh Edwards, Maurizio Junior Chiurazzi, Ylenia Vittozzi, Stephan Wenkel","doi":"10.1016/j.tig.2024.09.004","DOIUrl":"https://doi.org/10.1016/j.tig.2024.09.004","url":null,"abstract":"<p><p>Small proteins are ubiquitous in all kingdoms of life. MicroProteins, initially characterized as small proteins with protein interaction domains that enable them to interact with larger multidomain proteins, frequently modulate the function of these proteins. The study of these small proteins has contributed to a greater comprehension of protein regulation. In addition to sequence homology, sequence-divergent small proteins have the potential to function as microProtein mimics, binding to structurally related proteins. Moreover, a multitude of other small proteins encoded by short open reading frames (sORFs) and peptides, derived from diverse sources such as long noncoding RNAs (lncRNAs) and miRNAs, contribute to a variety of biological processes. The potential of small proteins is evident, offering promising avenues for bioengineering that could revolutionize crop performance and reduce reliance on agrochemicals in future agriculture.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":13.6,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481007","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 cryptic immunopeptidome in health and disease. 健康和疾病中的隐性免疫肽组。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-09 DOI: 10.1016/j.tig.2024.09.003
Eralda Kina, Jean-David Larouche, Pierre Thibault, Claude Perreault
{"title":"The cryptic immunopeptidome in health and disease.","authors":"Eralda Kina, Jean-David Larouche, Pierre Thibault, Claude Perreault","doi":"10.1016/j.tig.2024.09.003","DOIUrl":"https://doi.org/10.1016/j.tig.2024.09.003","url":null,"abstract":"<p><p>Peptides presented by MHC proteins regulate all aspects of T cell biology. These MHC-associated peptides (MAPs) form what is known as the immunopeptidome and their comprehensive analysis has catalyzed the burgeoning field of immunopeptidomics. Advances in mass spectrometry (MS) and next-generation sequencing have facilitated significant breakthroughs in this area, some of which are highlighted in this article on the cryptic immunopeptidome. Here, 'cryptic' refers to peptides and proteins encoded by noncanonical open reading frames (ORFs). Cryptic MAPs derive mainly from short unstable proteins found in normal, infected, and neoplastic cells. Cryptic MAPs show minimal overlap with cryptic proteins found in whole-cell extracts. In many cancer types, most cancer-specific MAPs are cryptic.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":13.6,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142401991","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
Microproteins in cancer: identification, biological functions, and clinical implications. 癌症中的微蛋白：识别、生物功能和临床意义。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-07 DOI: 10.1016/j.tig.2024.09.002
Damon A Hofman, John R Prensner, Sebastiaan van Heesch
{"title":"Microproteins in cancer: identification, biological functions, and clinical implications.","authors":"Damon A Hofman, John R Prensner, Sebastiaan van Heesch","doi":"10.1016/j.tig.2024.09.002","DOIUrl":"https://doi.org/10.1016/j.tig.2024.09.002","url":null,"abstract":"<p><p>Cancer continues to be a major global health challenge, accounting for 10 million deaths annually worldwide. Since the inception of genome-wide cancer sequencing studies 20 years ago, a core set of ~700 oncogenes and tumor suppressor genes has become the basis for cancer research. However, this research has been based largely on an understanding that the human genome encodes ~19 500 protein-coding genes. Complementing this genomic landscape, recent advances have described numerous microproteins which are now poised to redefine our understanding of oncogenic processes and open new avenues for therapeutic intervention. This review explores the emerging evidence for microprotein involvement in cancer mechanisms and discusses potential therapeutic applications, with an emphasis on highlighting recent advances in the field.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":13.6,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395250","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 molecular mechanism for environmental sex determination. 环境性别决定的分子机制
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-01 Epub Date: 2024-07-29 DOI: 10.1016/j.tig.2024.07.005
Xiaojing Li, John K Colbourne
{"title":"A molecular mechanism for environmental sex determination.","authors":"Xiaojing Li, John K Colbourne","doi":"10.1016/j.tig.2024.07.005","DOIUrl":"10.1016/j.tig.2024.07.005","url":null,"abstract":"<p><p>Daphnia produce genetically identical males and females; their sex is determined by environmental conditions. Recently, Kato et al. identified isoform switching events in Daphnia as a gene regulatory mechanism for sex-specific development. This finding uncovers the impact of alternative usage of gene isoforms on this extreme phenotypic plasticity trait.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":13.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857158","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
New insights into oocyte cytoplasmic lattice-associated proteins. 对卵母细胞胞质晶格相关蛋白的新认识。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-01 Epub Date: 2024-07-01 DOI: 10.1016/j.tig.2024.06.002
Carlo Giaccari, Francesco Cecere, Lucia Argenziano, Angela Pagano, Andrea Riccio
{"title":"New insights into oocyte cytoplasmic lattice-associated proteins.","authors":"Carlo Giaccari, Francesco Cecere, Lucia Argenziano, Angela Pagano, Andrea Riccio","doi":"10.1016/j.tig.2024.06.002","DOIUrl":"10.1016/j.tig.2024.06.002","url":null,"abstract":"<p><p>Oocyte maturation and preimplantation embryo development are critical to successful pregnancy outcomes and the correct establishment and maintenance of genomic imprinting. Thanks to novel technologies and omics studies in human patients and mouse models, the importance of the proteins associated with the cytoplasmic lattices (CPLs), highly abundant structures found in the cytoplasm of mammalian oocytes and preimplantation embryos, in the maternal to zygotic transition is becoming increasingly evident. This review highlights the recent discoveries on the role of these proteins in protein storage and other oocyte cytoplasmic processes, epigenetic reprogramming, and zygotic genome activation (ZGA). A better comprehension of these events may significantly improve clinical diagnosis and pave the way for targeted interventions aiming to correct or mitigate female fertility issues and genomic imprinting disorders.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":13.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141494289","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
Artificial intelligence in plant breeding. 人工智能在植物育种中的应用。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-01 Epub Date: 2024-08-07 DOI: 10.1016/j.tig.2024.07.001
Muhammad Amjad Farooq, Shang Gao, Muhammad Adeel Hassan, Zhangping Huang, Awais Rasheed, Sarah Hearne, Boddupalli Prasanna, Xinhai Li, Huihui Li
{"title":"Artificial intelligence in plant breeding.","authors":"Muhammad Amjad Farooq, Shang Gao, Muhammad Adeel Hassan, Zhangping Huang, Awais Rasheed, Sarah Hearne, Boddupalli Prasanna, Xinhai Li, Huihui Li","doi":"10.1016/j.tig.2024.07.001","DOIUrl":"10.1016/j.tig.2024.07.001","url":null,"abstract":"<p><p>Harnessing cutting-edge technologies to enhance crop productivity is a pivotal goal in modern plant breeding. Artificial intelligence (AI) is renowned for its prowess in big data analysis and pattern recognition, and is revolutionizing numerous scientific domains including plant breeding. We explore the wider potential of AI tools in various facets of breeding, including data collection, unlocking genetic diversity within genebanks, and bridging the genotype-phenotype gap to facilitate crop breeding. This will enable the development of crop cultivars tailored to the projected future environments. Moreover, AI tools also hold promise for refining crop traits by improving the precision of gene-editing systems and predicting the potential effects of gene variants on plant phenotypes. Leveraging AI-enabled precision breeding can augment the efficiency of breeding programs and holds promise for optimizing cropping systems at the grassroots level. This entails identifying optimal inter-cropping and crop-rotation models to enhance agricultural sustainability and productivity in the field.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":13.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141908320","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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