Pub Date : 2024-08-01Epub Date: 2024-06-15DOI: 10.1016/j.tig.2024.05.009
Ashwini V Mohan, Paula Escuer, Camille Cornet, Kay Lucek
Genomic information is folded in a three-dimensional (3D) structure, a rarely explored evolutionary driver of speciation. Technological advances now enable the study of 3D genome structures (3DGSs) across the Tree of Life. At the onset of 3D speciation genomics, we discuss the putative roles of 3DGSs in speciation.
{"title":"A three-dimensional genomics view for speciation research.","authors":"Ashwini V Mohan, Paula Escuer, Camille Cornet, Kay Lucek","doi":"10.1016/j.tig.2024.05.009","DOIUrl":"10.1016/j.tig.2024.05.009","url":null,"abstract":"<p><p>Genomic information is folded in a three-dimensional (3D) structure, a rarely explored evolutionary driver of speciation. Technological advances now enable the study of 3D genome structures (3DGSs) across the Tree of Life. At the onset of 3D speciation genomics, we discuss the putative roles of 3DGSs in speciation.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":13.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141332494","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}
Pub Date : 2024-08-01Epub Date: 2024-06-25DOI: 10.1016/j.tig.2024.04.009
Abdella M Habib, James J Cox, Andrei L Okorokov
The dark genome, the nonprotein-coding part of the genome, is replete with long noncoding RNAs (lncRNAs). These functionally versatile transcripts, with specific temporal and spatial expression patterns, are critical gene regulators that play essential roles in health and disease. In recent years, FAAH-OUT was identified as the first lncRNA associated with an inherited human pain insensitivity disorder. Several other lncRNAs have also been studied for their contribution to chronic pain and genome-wide association studies are frequently identifying single nucleotide polymorphisms that map to lncRNAs. For a long time overlooked, lncRNAs are coming out of the dark and into the light as major players in human pain pathways and as potential targets for new RNA-based analgesic medicines.
{"title":"Out of the dark: the emerging roles of lncRNAs in pain.","authors":"Abdella M Habib, James J Cox, Andrei L Okorokov","doi":"10.1016/j.tig.2024.04.009","DOIUrl":"10.1016/j.tig.2024.04.009","url":null,"abstract":"<p><p>The dark genome, the nonprotein-coding part of the genome, is replete with long noncoding RNAs (lncRNAs). These functionally versatile transcripts, with specific temporal and spatial expression patterns, are critical gene regulators that play essential roles in health and disease. In recent years, FAAH-OUT was identified as the first lncRNA associated with an inherited human pain insensitivity disorder. Several other lncRNAs have also been studied for their contribution to chronic pain and genome-wide association studies are frequently identifying single nucleotide polymorphisms that map to lncRNAs. For a long time overlooked, lncRNAs are coming out of the dark and into the light as major players in human pain pathways and as potential targets for new RNA-based analgesic medicines.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":13.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141460706","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}
Pub Date : 2024-07-31DOI: 10.1016/j.tig.2024.07.006
The recent discovery of an association between ribosomal DNA (rDNA) copy number and body mass index (BMI) by Law et al. sheds light on a possible role of 45S rDNA in body-weight regulation. This finding opens new avenues for further investigations into the effect of rDNA on various human phenotypes.
Law 等人最近发现核糖体 DNA(rDNA)拷贝数与体重指数(BMI)之间存在关联,这揭示了 45S rDNA 在体重调节中可能扮演的角色。这一发现为进一步研究 rDNA 对人类各种表型的影响开辟了新途径。
{"title":"The ribosome’s comeback: new role in body weight regulation","authors":"","doi":"10.1016/j.tig.2024.07.006","DOIUrl":"https://doi.org/10.1016/j.tig.2024.07.006","url":null,"abstract":"<p>The recent discovery of an association between ribosomal DNA (rDNA) copy number and body mass index (BMI) by <span><span>Law <em>et al.</em></span><svg aria-label=\"Opens in new window\" focusable=\"false\" height=\"20\" viewbox=\"0 0 8 8\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\"></path></svg></span> sheds light on a possible role of 45S rDNA in body-weight regulation. This finding opens new avenues for further investigations into the effect of rDNA on various human phenotypes.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141863304","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}
Pub Date : 2024-07-29DOI: 10.1016/j.tig.2024.07.005
Xiaojing Li, John K Colbourne
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.
{"title":"A molecular mechanism for environmental sex determination.","authors":"Xiaojing Li, John K Colbourne","doi":"10.1016/j.tig.2024.07.005","DOIUrl":"https://doi.org/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":"2024-07-29","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}
Pub Date : 2024-07-29DOI: 10.1016/j.tig.2024.07.002
Donovan P German
The gastric stomach is a hallmark of vertebrate evolution, yet is missing in nearly 25% of living fish species and some mammals. New work by Kato et al. shows how a cassette of genes relating to acid production, pepsins, cell adhesion, and developmental control are repeatedly lost in animals that have also lost their stomachs.
{"title":"Butterflies in your stomach? Not an issue for nearly 8000 species of fishes.","authors":"Donovan P German","doi":"10.1016/j.tig.2024.07.002","DOIUrl":"https://doi.org/10.1016/j.tig.2024.07.002","url":null,"abstract":"<p><p>The gastric stomach is a hallmark of vertebrate evolution, yet is missing in nearly 25% of living fish species and some mammals. New work by Kato et al. shows how a cassette of genes relating to acid production, pepsins, cell adhesion, and developmental control are repeatedly lost in animals that have also lost their stomachs.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":13.6,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857159","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}
Pub Date : 2024-07-12DOI: 10.1016/j.tig.2024.06.005
Adam P Sharples
The Molecular Transducers of Physical Activity Consortium (MoTrPAC) aims to comprehensively map molecular alterations in response to acute exercise and chronic training. In one of a recent series of papers from MoTrPAC, Nair et al. provide the first multi-epigenomic and transcriptomic integration across eight tissues in both sexes following adaptation to endurance exercise training (EET).
{"title":"A multi-epigenomic map of endurance exercise training.","authors":"Adam P Sharples","doi":"10.1016/j.tig.2024.06.005","DOIUrl":"https://doi.org/10.1016/j.tig.2024.06.005","url":null,"abstract":"<p><p>The Molecular Transducers of Physical Activity Consortium (MoTrPAC) aims to comprehensively map molecular alterations in response to acute exercise and chronic training. In one of a recent series of papers from MoTrPAC, Nair et al. provide the first multi-epigenomic and transcriptomic integration across eight tissues in both sexes following adaptation to endurance exercise training (EET).</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":13.6,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141604508","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}
Pub Date : 2024-07-08DOI: 10.1016/s0168-9525(24)00140-9
No Abstract
无摘要
{"title":"Subscription and Copyright Information","authors":"","doi":"10.1016/s0168-9525(24)00140-9","DOIUrl":"https://doi.org/10.1016/s0168-9525(24)00140-9","url":null,"abstract":"No Abstract","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141569420","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}
Pub Date : 2024-07-08DOI: 10.1016/s0168-9525(24)00137-9
No Abstract
无摘要
{"title":"Advisory Board and Contents","authors":"","doi":"10.1016/s0168-9525(24)00137-9","DOIUrl":"https://doi.org/10.1016/s0168-9525(24)00137-9","url":null,"abstract":"No Abstract","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":11.4,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141569419","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}
Pub Date : 2024-07-05DOI: 10.1016/j.tig.2024.06.003
Leslie S Babonis
Organisms are complex assemblages of cells, cells that produce light, shoot harpoons, and secrete glue. Therefore, identifying the mechanisms that generate novelty at the level of the individual cell is essential for understanding how multicellular life evolves. For decades, the field of evolutionary developmental biology (Evo-Devo) has been developing a framework for connecting genetic variation that arises during embryonic development to the emergence of diverse adult forms. With increasing access to new single cell 'omics technologies and an array of techniques for manipulating gene expression, we can now extend these inquiries inward to the level of the individual cell. In this opinion, I argue that applying an Evo-Devo framework to single cells makes it possible to explore the natural history of cells, where this was once only possible at the organismal level.
{"title":"On the evolutionary developmental biology of the cell.","authors":"Leslie S Babonis","doi":"10.1016/j.tig.2024.06.003","DOIUrl":"https://doi.org/10.1016/j.tig.2024.06.003","url":null,"abstract":"<p><p>Organisms are complex assemblages of cells, cells that produce light, shoot harpoons, and secrete glue. Therefore, identifying the mechanisms that generate novelty at the level of the individual cell is essential for understanding how multicellular life evolves. For decades, the field of evolutionary developmental biology (Evo-Devo) has been developing a framework for connecting genetic variation that arises during embryonic development to the emergence of diverse adult forms. With increasing access to new single cell 'omics technologies and an array of techniques for manipulating gene expression, we can now extend these inquiries inward to the level of the individual cell. In this opinion, I argue that applying an Evo-Devo framework to single cells makes it possible to explore the natural history of cells, where this was once only possible at the organismal level.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":null,"pages":null},"PeriodicalIF":13.6,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141545553","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}
Pub Date : 2024-07-01DOI: 10.1016/j.tig.2024.06.002
Carlo Giaccari, Francesco Cecere, Lucia Argenziano, Angela Pagano, Andrea Riccio
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.
{"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":"https://doi.org/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":"2024-07-01","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}