We systematically examine the application of different phasing strategies to decrypt strawberry genome organization and produce a fully phased and accurate reference genome for Fragaria x ananassa cv. “EA78” (2n = 8x = 56). We identify 147 bp canonical centromeric repeats across 50 strawberry chromosomes and uncover the formation of six neocentromeres through centromere turnover. Our findings indicate strawberry genomes have diverged centromeric satellite arrays among chromosomes, particularly across homoeologs, while maintaining high sequence similarity between homologs. We trace the evolutionary dynamics of centromeric repeats and find substantial centromere size expansion in wild and cultivated octoploids compared to the diploid ancestor, F. vesca.
{"title":"A fully phased octoploid strawberry genome reveals the evolutionary dynamism of centromeric satellites","authors":"Xin Jin, Haiyuan Du, Maoxian Chen, Xu Zheng, Yiying He, Andan Zhu","doi":"10.1186/s13059-025-03482-0","DOIUrl":"https://doi.org/10.1186/s13059-025-03482-0","url":null,"abstract":"We systematically examine the application of different phasing strategies to decrypt strawberry genome organization and produce a fully phased and accurate reference genome for Fragaria x ananassa cv. “EA78” (2n = 8x = 56). We identify 147 bp canonical centromeric repeats across 50 strawberry chromosomes and uncover the formation of six neocentromeres through centromere turnover. Our findings indicate strawberry genomes have diverged centromeric satellite arrays among chromosomes, particularly across homoeologs, while maintaining high sequence similarity between homologs. We trace the evolutionary dynamics of centromeric repeats and find substantial centromere size expansion in wild and cultivated octoploids compared to the diploid ancestor, F. vesca.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"122 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant residue microbial decomposition, subject to significant environmental regulation, represents a crucial ecological process shaping and cycling the largest terrestrial soil organic carbon pool. However, the fundamental understanding of the functional dynamics and interactions between the principal participants, fungi and bacteria, in natural habitats remains limited. In this study, the evolution of fungal and bacterial communities and their functional interactions were elucidated during the degradation of complexity-gradient plant residues. The results reveal that with increasing residue complexity, fungi exhibit heightened adaptability, while bacterial richness declines sharply. The differential functional evolution of fungi and bacteria is driven by residue complexity but follows distinct trajectories. Fundamentally, fungi evolve towards promoting plant residue degradation and so consistently act as the dominant decomposers. Conversely, bacteria predominantly increase expression of genes of glycosidases to exploit fungal degradation products, thereby consistently acting as exploiters. The presence of fungi enables and endures bacterial exploitation. This study introduces a novel framework of fungal decomposers and bacterial exploiters during plant residue microbial decomposition, advancing our comprehensive understanding of microbial processes governing the organic carbon cycling.
{"title":"A novel decomposer-exploiter interaction framework of plant residue microbial decomposition","authors":"Youzhi Miao, Wei Wang, Huanhuan Xu, Yanwei Xia, Qingxin Gong, Zhihui Xu, Nan Zhang, Weibing Xun, Qirong Shen, Ruifu Zhang","doi":"10.1186/s13059-025-03486-w","DOIUrl":"https://doi.org/10.1186/s13059-025-03486-w","url":null,"abstract":"Plant residue microbial decomposition, subject to significant environmental regulation, represents a crucial ecological process shaping and cycling the largest terrestrial soil organic carbon pool. However, the fundamental understanding of the functional dynamics and interactions between the principal participants, fungi and bacteria, in natural habitats remains limited. In this study, the evolution of fungal and bacterial communities and their functional interactions were elucidated during the degradation of complexity-gradient plant residues. The results reveal that with increasing residue complexity, fungi exhibit heightened adaptability, while bacterial richness declines sharply. The differential functional evolution of fungi and bacteria is driven by residue complexity but follows distinct trajectories. Fundamentally, fungi evolve towards promoting plant residue degradation and so consistently act as the dominant decomposers. Conversely, bacteria predominantly increase expression of genes of glycosidases to exploit fungal degradation products, thereby consistently acting as exploiters. The presence of fungi enables and endures bacterial exploitation. This study introduces a novel framework of fungal decomposers and bacterial exploiters during plant residue microbial decomposition, advancing our comprehensive understanding of microbial processes governing the organic carbon cycling.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"6 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-03DOI: 10.1186/s13059-025-03480-2
Jeffrey Okamoto, Xianyong Yin, Brady Ryan, Joshua Chiou, Francesca Luca, Roger Pique-Regi, Hae Kyung Im, Jean Morrison, Charles Burant, Eric B. Fauman, Markku Laakso, Michael Boehnke, Xiaoquan Wen
We present multi-integration of transcriptome-wide association studies and colocalization (Multi-INTACT), an algorithm that models multiple “gene products” (e.g., encoded RNA transcript and protein levels) to implicate causal genes and relevant gene products. In simulations, Multi-INTACT achieves higher power than existing methods, maintains calibrated false discovery rates, and detects the true causal gene product(s). We apply Multi-INTACT to GWAS on 1408 metabolites, integrating the GTEx expression and UK Biobank protein QTL datasets. Multi-INTACT infers 52 to 109% more metabolite causal genes than protein-alone or expression-alone analyses and indicates both gene products are relevant for most gene nominations.
{"title":"Multi-INTACT: integrative analysis of the genome, transcriptome, and proteome identifies causal mechanisms of complex traits","authors":"Jeffrey Okamoto, Xianyong Yin, Brady Ryan, Joshua Chiou, Francesca Luca, Roger Pique-Regi, Hae Kyung Im, Jean Morrison, Charles Burant, Eric B. Fauman, Markku Laakso, Michael Boehnke, Xiaoquan Wen","doi":"10.1186/s13059-025-03480-2","DOIUrl":"https://doi.org/10.1186/s13059-025-03480-2","url":null,"abstract":"We present multi-integration of transcriptome-wide association studies and colocalization (Multi-INTACT), an algorithm that models multiple “gene products” (e.g., encoded RNA transcript and protein levels) to implicate causal genes and relevant gene products. In simulations, Multi-INTACT achieves higher power than existing methods, maintains calibrated false discovery rates, and detects the true causal gene product(s). We apply Multi-INTACT to GWAS on 1408 metabolites, integrating the GTEx expression and UK Biobank protein QTL datasets. Multi-INTACT infers 52 to 109% more metabolite causal genes than protein-alone or expression-alone analyses and indicates both gene products are relevant for most gene nominations.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"77 2 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-27DOI: 10.1186/s13059-025-03481-1
Jeffry M. Gaston, Eric J. Alm, An-Ni Zhang
<p><b>Correction</b><b>: </b><b>Genome Biol 26, 15 (2025)</b></p><p><b>https://doi.org/10.1186/s13059-024-03473-7</b></p><br/><p>Following publication of the original article [1], the authors identified that one of the headings in the results section is incorrect.</p><p>The incorrect heading is: Alignment accuracy of X‑Mapper in samples with various ties</p><p>The correct heading is: Alignment accuracy of X‑Mapper in samples with various complexities</p><p>The original article [1] has been updated.</p><ol data-track-component="outbound reference" data-track-context="references section"><li data-counter="1."><p>Gaston JM, Alm EJ, Zhang AN. X-Mapper: fast and accurate sequence alignment via gapped x-mers. Genome Biol. 2025;26:15. https://doi.org/10.1186/s13059-024-03473-7.</p><p>Article CAS PubMed PubMed Central Google Scholar </p></li></ol><p>Download references<svg aria-hidden="true" focusable="false" height="16" role="img" width="16"><use xlink:href="#icon-eds-i-download-medium" xmlns:xlink="http://www.w3.org/1999/xlink"></use></svg></p><span>Author notes</span><ol><li><p>Jeffry M. Gaston and An-Ni Zhang contributed equally to this work.</p></li></ol><h3>Authors and Affiliations</h3><ol><li><p>Google, Cambridge, MA, USA</p><p>Jeffry M. Gaston</p></li><li><p>Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA</p><p>Eric J. Alm & An-Ni Zhang</p></li><li><p>School of Biological Sciences, Nanyang Technological University, Singapore, Singapore</p><p>Jeffry M. Gaston & An-Ni Zhang</p></li></ol><span>Authors</span><ol><li><span>Jeffry M. Gaston</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Eric J. Alm</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>An-Ni Zhang</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li></ol><h3>Corresponding authors</h3><p>Correspondence to Eric J. Alm or An-Ni Zhang.</p><p><b>Open Access</b> This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.</p> <p>
{"title":"Author Correction: X-Mapper: fast and accurate sequence alignment via gapped x-mers","authors":"Jeffry M. Gaston, Eric J. Alm, An-Ni Zhang","doi":"10.1186/s13059-025-03481-1","DOIUrl":"https://doi.org/10.1186/s13059-025-03481-1","url":null,"abstract":"<p><b>Correction</b><b>: </b><b>Genome Biol 26, 15 (2025)</b></p><p><b>https://doi.org/10.1186/s13059-024-03473-7</b></p><br/><p>Following publication of the original article [1], the authors identified that one of the headings in the results section is incorrect.</p><p>The incorrect heading is: Alignment accuracy of X‑Mapper in samples with various ties</p><p>The correct heading is: Alignment accuracy of X‑Mapper in samples with various complexities</p><p>The original article [1] has been updated.</p><ol data-track-component=\"outbound reference\" data-track-context=\"references section\"><li data-counter=\"1.\"><p>Gaston JM, Alm EJ, Zhang AN. X-Mapper: fast and accurate sequence alignment via gapped x-mers. Genome Biol. 2025;26:15. https://doi.org/10.1186/s13059-024-03473-7.</p><p>Article CAS PubMed PubMed Central Google Scholar </p></li></ol><p>Download references<svg aria-hidden=\"true\" focusable=\"false\" height=\"16\" role=\"img\" width=\"16\"><use xlink:href=\"#icon-eds-i-download-medium\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"></use></svg></p><span>Author notes</span><ol><li><p>Jeffry M. Gaston and An-Ni Zhang contributed equally to this work.</p></li></ol><h3>Authors and Affiliations</h3><ol><li><p>Google, Cambridge, MA, USA</p><p>Jeffry M. Gaston</p></li><li><p>Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA</p><p>Eric J. Alm & An-Ni Zhang</p></li><li><p>School of Biological Sciences, Nanyang Technological University, Singapore, Singapore</p><p>Jeffry M. Gaston & An-Ni Zhang</p></li></ol><span>Authors</span><ol><li><span>Jeffry M. Gaston</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Eric J. Alm</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>An-Ni Zhang</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li></ol><h3>Corresponding authors</h3><p>Correspondence to Eric J. Alm or An-Ni Zhang.</p><p><b>Open Access</b> This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.</p>\u0000<p>","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"58 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143044067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-22DOI: 10.1186/s13059-025-03475-z
Miguel Vasconcelos Almeida, Moritz Blumer, Chengwei Ulrika Yuan, Pío Sierra, Jonathan L. Price, Fu Xiang Quah, Aleksandr Friman, Alexandra Dallaire, Grégoire Vernaz, Audrey L. K. Putman, Alan M. Smith, Domino A. Joyce, Falk Butter, Astrid D. Haase, Richard Durbin, M. Emília Santos, Eric A. Miska
East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. We set out to bridge this gap and to understand the interactions between TEs and their cichlid hosts. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed strong conservation of TE silencing factors in cichlids, and an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that targets TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci. Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity.
{"title":"Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes","authors":"Miguel Vasconcelos Almeida, Moritz Blumer, Chengwei Ulrika Yuan, Pío Sierra, Jonathan L. Price, Fu Xiang Quah, Aleksandr Friman, Alexandra Dallaire, Grégoire Vernaz, Audrey L. K. Putman, Alan M. Smith, Domino A. Joyce, Falk Butter, Astrid D. Haase, Richard Durbin, M. Emília Santos, Eric A. Miska","doi":"10.1186/s13059-025-03475-z","DOIUrl":"https://doi.org/10.1186/s13059-025-03475-z","url":null,"abstract":"East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. We set out to bridge this gap and to understand the interactions between TEs and their cichlid hosts. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed strong conservation of TE silencing factors in cichlids, and an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that targets TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci. Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"74 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142992762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-22DOI: 10.1186/s13059-024-03473-7
Jeffry M. Gaston, Eric J. Alm, An-Ni Zhang
Sequence alignment is foundational to many bioinformatic analyses. Many aligners start by splitting sequences into contiguous, fixed-length seeds, called k-mers. Alignment is faster with longer, unique seeds, but more accurate with shorter seeds avoiding mutations. Here, we introduce X-Mapper, aiming to offer high speed and accuracy via dynamic-length seeds containing gaps, called gapped x-mers. We observe 11–24-fold fewer suboptimal alignments analyzing a human reference and 3–579-fold lower inconsistency across bacterial references than other aligners, improving on 53% and 30% of reads aligned to non-target strains and species, respectively. Other seed-based analysis algorithms might benefit from gapped x-mers too.
{"title":"X-Mapper: fast and accurate sequence alignment via gapped x-mers","authors":"Jeffry M. Gaston, Eric J. Alm, An-Ni Zhang","doi":"10.1186/s13059-024-03473-7","DOIUrl":"https://doi.org/10.1186/s13059-024-03473-7","url":null,"abstract":"Sequence alignment is foundational to many bioinformatic analyses. Many aligners start by splitting sequences into contiguous, fixed-length seeds, called k-mers. Alignment is faster with longer, unique seeds, but more accurate with shorter seeds avoiding mutations. Here, we introduce X-Mapper, aiming to offer high speed and accuracy via dynamic-length seeds containing gaps, called gapped x-mers. We observe 11–24-fold fewer suboptimal alignments analyzing a human reference and 3–579-fold lower inconsistency across bacterial references than other aligners, improving on 53% and 30% of reads aligned to non-target strains and species, respectively. Other seed-based analysis algorithms might benefit from gapped x-mers too.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"3 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142992821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-21DOI: 10.1186/s13059-025-03476-y
Alan F. Rubin, Jeremy Stone, Aisha Haley Bianchi, Benjamin J. Capodanno, Estelle Y. Da, Mafalda Dias, Daniel Esposito, Jonathan Frazer, Yunfan Fu, Sally B. Grindstaff, Matthew R. Harrington, Iris Li, Abbye E. McEwen, Joseph K. Min, Nick Moore, Olivia G. Moscatelli, Jesslyn Ong, Polina V. Polunina, Joshua E. Rollins, Nathan J. Rollins, Ashley E. Snyder, Amy Tam, Matthew J. Wakefield, Shenyi Sunny Ye, Lea M. Starita, Vanessa L. Bryant, Debora S. Marks, Douglas M. Fowler
Multiplexed assays of variant effect (MAVEs) are a critical tool for researchers and clinicians to understand genetic variants. Here we describe the 2024 update to MaveDB ( https://www.mavedb.org/ ) with four key improvements to the MAVE community’s database of record: more available data including over 7 million variant effect measurements, an improved data model supporting assays such as saturation genome editing, new built-in exploration and visualization tools, and powerful APIs for data federation and streamlined submission and access. Together these changes support MaveDB’s role as a hub for the analysis and dissemination of MAVEs now and into the future.
{"title":"MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays","authors":"Alan F. Rubin, Jeremy Stone, Aisha Haley Bianchi, Benjamin J. Capodanno, Estelle Y. Da, Mafalda Dias, Daniel Esposito, Jonathan Frazer, Yunfan Fu, Sally B. Grindstaff, Matthew R. Harrington, Iris Li, Abbye E. McEwen, Joseph K. Min, Nick Moore, Olivia G. Moscatelli, Jesslyn Ong, Polina V. Polunina, Joshua E. Rollins, Nathan J. Rollins, Ashley E. Snyder, Amy Tam, Matthew J. Wakefield, Shenyi Sunny Ye, Lea M. Starita, Vanessa L. Bryant, Debora S. Marks, Douglas M. Fowler","doi":"10.1186/s13059-025-03476-y","DOIUrl":"https://doi.org/10.1186/s13059-025-03476-y","url":null,"abstract":"Multiplexed assays of variant effect (MAVEs) are a critical tool for researchers and clinicians to understand genetic variants. Here we describe the 2024 update to MaveDB ( https://www.mavedb.org/ ) with four key improvements to the MAVE community’s database of record: more available data including over 7 million variant effect measurements, an improved data model supporting assays such as saturation genome editing, new built-in exploration and visualization tools, and powerful APIs for data federation and streamlined submission and access. Together these changes support MaveDB’s role as a hub for the analysis and dissemination of MAVEs now and into the future.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"162 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142990650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-20DOI: 10.1186/s13059-025-03477-x
Marleen Balvert, Johnathan Cooper-Knock, Julian Stamp, Ross P. Byrne, Soufane Mourragui, Juami van Gils, Stefania Benonisdottir, Johannes Schlüter, Kevin Kenna, Sanne Abeln, Alfredo Iacoangeli, Joséphine T. Daub, Brian L. Browning, Gizem Taş, Jiajing Hu, Yan Wang, Elham Alhathli, Calum Harvey, Luna Pianesi, Sara C. Schulte, Jorge González-Domínguez, Erik Garrisson, Michael P. Snyder, Alexander Schönhuth, Letitia M. F. Sng, Natalie A. Twine
<p><b>Correction: Genome Biol 25, 296 (2024)</b></p><p><b>https://doi.org/10.1186/s13059-024-03427-z</b></p><br/><p>Following publication of the original article [1], the authors identified that two author affiliations were incorrect.</p><p>Joséphine Daub is affiliated with Utrecht University (21) and not affiliation 9.</p><p>Sanne Abeln is affiliated with Utrecht University only (21) and not affiliation 1.</p><p>The original article [1] has been corrected.</p><ol data-track-component="outbound reference" data-track-context="references section"><li data-counter="1"><p>Balvert M, Cooper-Knock J, Stamp J, et al. Considerations in the search for epistasis. Genome Biol. 2024;25:296. https://doi.org/10.1186/s13059-024-03427-z.</p><p>Article PubMed PubMed Central Google Scholar </p></li></ol><p>Download references<svg aria-hidden="true" focusable="false" height="16" role="img" width="16"><use xlink:href="#icon-eds-i-download-medium" xmlns:xlink="http://www.w3.org/1999/xlink"></use></svg></p><span>Author notes</span><ol><li><p>Marleen Balvert and Johnathan Cooper-Knock contributed equally to this work.</p></li><li><p>Alexander Schönhuth, Letitia M. F. Sng, and Natalie A. Twine contributed equally to this work.</p></li></ol><h3>Authors and Affiliations</h3><ol><li><p>Tilburg University, Tilburg, The Netherlands</p><p>Marleen Balvert & Gizem Taş</p></li><li><p>SITraN, University of Sheffield, Sheffield, UK</p><p>Johnathan Cooper-Knock, Elham Alhathli & Calum Harvey</p></li><li><p>Brown University, Providence, USA</p><p>Julian Stamp</p></li><li><p>Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland</p><p>Ross P. Byrne</p></li><li><p>Hubrecht Institute, Utrecht, The Netherlands</p><p>Soufane Mourragui</p></li><li><p>Vrije Universiteit Amsterdam, Amsterdam, The Netherlands</p><p>Juami van Gils</p></li><li><p>University of Oxford, Oxford, UK</p><p>Stefania Benonisdottir</p></li><li><p>Bielefeld University, Bielefeld, Germany</p><p>Johannes Schlüter, Luna Pianesi & Alexander Schönhuth</p></li><li><p>UMC Utrecht, Utrecht, The Netherlands</p><p>Kevin Kenna, Gizem Taş & Yan Wang</p></li><li><p>Department of Biostatistics and Health Informatics, King’s College London, London, UK</p><p>Alfredo Iacoangeli & Jiajing Hu</p></li><li><p>Department of Basic and Clinical Neuroscience, King’s College London, London, UK</p><p>Alfredo Iacoangeli</p></li><li><p>NIHR BRC SLAM NHS Foundation Trust, London, UK</p><p>Alfredo Iacoangeli</p></li><li><p>University of Washington, Seattle, USA</p><p>Brian L. Browning</p></li><li><p>Algorithmic Bioinformatics and Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany</p><p>Sara C. Schulte</p></li><li><p>CITIC, University of A Coruña, A Coruña, Spain</p><p>Jorge González-Domínguez</p></li><li><p>University of Tennessee, Knoxville, USA</p><p>Erik Garrisson</p></li><li><p>Department of Genetics, Stanford University, Stanford, USA</p><p>Michael P. Snyder</p></li><li><p>Commonwealt
更正：Genome Biol 25, 296 (2024)https://doi.org/10.1186/s13059-024-03427-zFollowing 原文[1]发表后，作者发现有两位作者所属单位有误。Joséphine Daub隶属于乌特勒支大学（21），而非所属单位9。Sanne Abeln仅隶属于乌特勒支大学（21），而非所属单位1。原文[1]已更正。Balvert M, Cooper-Knock J, Stamp J, et al. Considerations in the search for epistasis.Genome Biol. 2024;25:296. https://doi.org/10.1186/s13059-024-03427-z.Article PubMed PubMed Central Google Scholar Download references作者注释Marleen Balvert 和 Johnathan Cooper-Knock 对本研究做出了同样的贡献。Alexander Schönhuth, Letitia M. F. Sng, and Natalie A. Twine 对本研究做出了同样的贡献。作者和工作单位荷兰蒂尔堡蒂尔堡大学Marleen Balvert & Gizem TaşSITraN, University of Sheffield, Sheffield, UKJohnathan Cooper-Knock, Elham Alhathli & Calum Harvey美国普罗维登斯布朗大学Julian Stamp爱尔兰都柏林都柏林三一学院斯莫非特遗传学研究所Ross P.ByrneHubrecht Institute, Utrecht, The NetherlandsSoufane MourraguiVrije Universiteit Amsterdam, Amsterdam, The NetherlandsJuami van GilsUniversity of Oxford, Oxford, UKStefania BenonisdottirBielefeld University, Bielefeld, GermanyJohannes Schlüter, Luna Pianesi & Alexander SchönhuthUMC Utrecht, Utrecht, The NetherlandsKevin Kenna, Gizem Taş &；Yan WangDepartment of Biostatistics and Health Informatics，King's College London，London，UKAlfredo Iacoangeli &；Jiajing HuDepartment of Basic and Clinical Neuroscience，King's College London，London，UKAlfredo IacoangeliNIHR BRC SLAM NHS Foundation Trust，London，UKAlfredo IacoangeliUniversity of Washington，Seattle，USABrian L．Browning Algorithmic Bioinformatics and Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany萨拉．SchulteCITIC, University of A Coruña, A Coruña, SpainJorge González-DomínguezUniversity of Tennessee, Knoxville, USAErik GarrissonDepartment of Genetics, Stanford University, Stanford, USMichael P. SnyderCommonwealth Scientific and Industrial Research Organisation, Westmead, AustraliaLetitia M. F. Sng & Natalie A. Twine冰岛大学，冰岛科鲁尼亚TwineUniversity of Iceland, Reykjavik, IcelandStefania BenonisdottirUtrecht University, Utrecht, The NetherlandsSanne Abeln & Joséphine T. Daub作者Marleen Balvert查看作者发表的文章您也可以在PubMed Google ScholarJohnathan Cooper-Knock中搜索该作者查看作者发表的文章您也可以在PubMed Google ScholarJulian Stamp中搜索该作者查看作者发表的文章您也可以在PubMed Google ScholarRoss P.ByrneView 作者发表作品您也可以在 PubMed Google ScholarSoufane MourraguiView 作者发表作品您也可以在 PubMed Google ScholarJuami van GilsView 作者发表作品您也可以在 PubMed Google ScholarStefania BenonisdottirView 作者发表作品您也可以在 PubMed Google ScholarJohannesSchlüterView 作者发表作品您也可以在 PubMed Google Scholar中搜索该作者Kevin KennaView 作者发表作品您也可以在 PubMed Google Scholar中搜索该作者Sanne AbelnView 作者发表作品您也可以在 PubMed Google Scholar中搜索该作者Alfredo IacoangeliView 作者发表作品您也可以在 PubMed Google Scholar中搜索该作者Joséphine T．Daub查看作者发表的作品您也可以在PubMed Google Scholar中搜索该作者Brian L.BrowningView 作者发表的作品您也可以在 PubMed Google ScholarGizem TaşView 作者发表的作品您也可以在 PubMed Google ScholarJiajing HuView 作者发表的作品您也可以在 PubMed Google ScholarYan WangView 作者发表的作品您也可以在 PubMed Google ScholarGoogle ScholarElham Alhathli查看作者发表的论文您也可以在 PubMed Google ScholarCalum Harvey查看作者发
{"title":"Author Correction: Considerations in the search for epistasis","authors":"Marleen Balvert, Johnathan Cooper-Knock, Julian Stamp, Ross P. Byrne, Soufane Mourragui, Juami van Gils, Stefania Benonisdottir, Johannes Schlüter, Kevin Kenna, Sanne Abeln, Alfredo Iacoangeli, Joséphine T. Daub, Brian L. Browning, Gizem Taş, Jiajing Hu, Yan Wang, Elham Alhathli, Calum Harvey, Luna Pianesi, Sara C. Schulte, Jorge González-Domínguez, Erik Garrisson, Michael P. Snyder, Alexander Schönhuth, Letitia M. F. Sng, Natalie A. Twine","doi":"10.1186/s13059-025-03477-x","DOIUrl":"https://doi.org/10.1186/s13059-025-03477-x","url":null,"abstract":"<p><b>Correction: Genome Biol 25, 296 (2024)</b></p><p><b>https://doi.org/10.1186/s13059-024-03427-z</b></p><br/><p>Following publication of the original article [1], the authors identified that two author affiliations were incorrect.</p><p>Joséphine Daub is affiliated with Utrecht University (21) and not affiliation 9.</p><p>Sanne Abeln is affiliated with Utrecht University only (21) and not affiliation 1.</p><p>The original article [1] has been corrected.</p><ol data-track-component=\"outbound reference\" data-track-context=\"references section\"><li data-counter=\"1\"><p>Balvert M, Cooper-Knock J, Stamp J, et al. Considerations in the search for epistasis. Genome Biol. 2024;25:296. https://doi.org/10.1186/s13059-024-03427-z.</p><p>Article PubMed PubMed Central Google Scholar </p></li></ol><p>Download references<svg aria-hidden=\"true\" focusable=\"false\" height=\"16\" role=\"img\" width=\"16\"><use xlink:href=\"#icon-eds-i-download-medium\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"></use></svg></p><span>Author notes</span><ol><li><p>Marleen Balvert and Johnathan Cooper-Knock contributed equally to this work.</p></li><li><p>Alexander Schönhuth, Letitia M. F. Sng, and Natalie A. Twine contributed equally to this work.</p></li></ol><h3>Authors and Affiliations</h3><ol><li><p>Tilburg University, Tilburg, The Netherlands</p><p>Marleen Balvert & Gizem Taş</p></li><li><p>SITraN, University of Sheffield, Sheffield, UK</p><p>Johnathan Cooper-Knock, Elham Alhathli & Calum Harvey</p></li><li><p>Brown University, Providence, USA</p><p>Julian Stamp</p></li><li><p>Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland</p><p>Ross P. Byrne</p></li><li><p>Hubrecht Institute, Utrecht, The Netherlands</p><p>Soufane Mourragui</p></li><li><p>Vrije Universiteit Amsterdam, Amsterdam, The Netherlands</p><p>Juami van Gils</p></li><li><p>University of Oxford, Oxford, UK</p><p>Stefania Benonisdottir</p></li><li><p>Bielefeld University, Bielefeld, Germany</p><p>Johannes Schlüter, Luna Pianesi & Alexander Schönhuth</p></li><li><p>UMC Utrecht, Utrecht, The Netherlands</p><p>Kevin Kenna, Gizem Taş & Yan Wang</p></li><li><p>Department of Biostatistics and Health Informatics, King’s College London, London, UK</p><p>Alfredo Iacoangeli & Jiajing Hu</p></li><li><p>Department of Basic and Clinical Neuroscience, King’s College London, London, UK</p><p>Alfredo Iacoangeli</p></li><li><p>NIHR BRC SLAM NHS Foundation Trust, London, UK</p><p>Alfredo Iacoangeli</p></li><li><p>University of Washington, Seattle, USA</p><p>Brian L. Browning</p></li><li><p>Algorithmic Bioinformatics and Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany</p><p>Sara C. Schulte</p></li><li><p>CITIC, University of A Coruña, A Coruña, Spain</p><p>Jorge González-Domínguez</p></li><li><p>University of Tennessee, Knoxville, USA</p><p>Erik Garrisson</p></li><li><p>Department of Genetics, Stanford University, Stanford, USA</p><p>Michael P. Snyder</p></li><li><p>Commonwealt","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"31 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142990080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-20DOI: 10.1186/s13059-024-03466-6
Valentin Hure, Florence Piron-Prunier, Tamara Yehouessi, Clémentine Vitte, Aleksandra E. Kornienko, Gabrielle Adam, Magnus Nordborg, Angélique Déléris
The DNA/H3K9 methylation and Polycomb-group proteins (PcG)-H3K27me3 silencing pathways have long been considered mutually exclusive and specific to transposable elements (TEs) and genes, respectively in mammals, plants, and fungi. However, H3K27me3 can be recruited to many TEs in the absence of DNA/H3K9 methylation machinery and sometimes also co-occur with DNA methylation. In this study, we show that TEs can also be solely targeted and silenced by H3K27me3 in wild-type Arabidopsis plants. These H3K27me3-marked TEs not only comprise degenerate relics but also seemingly intact copies that display the epigenetic features of responsive PcG target genes as well as an active H3K27me3 regulation. We also show that H3K27me3 can be deposited on newly inserted transgenic TE sequences in a TE-specific manner indicating that silencing is determined in cis. Finally, a comparison of Arabidopsis natural accessions reveals the existence of a category of TEs—which we refer to as “bifrons”—that are marked by DNA methylation or H3K27me3 depending on the accession. This variation can be linked to intrinsic TE features and to trans-acting factors and reveals a change in epigenetic status across the TE lifespan. Our study sheds light on an alternative mode of TE silencing associated with H3K27me3 instead of DNA methylation in flowering plants. It also suggests dynamic switching between the two epigenetic marks at the species level, a new paradigm that might extend to other multicellular eukaryotes.
长期以来，在哺乳动物、植物和真菌中，DNA/H3K9甲基化和多聚核糖体群蛋白（PcG）-H3K27me3沉默途径一直被认为是相互排斥的，并分别对转座元件（TE）和基因具有特异性。然而，在没有DNA/H3K9甲基化机制的情况下，H3K27me3可以被招募到许多TEs上，有时也会与DNA甲基化同时发生。在本研究中，我们发现在野生型拟南芥植株中，TEs 也可以被 H3K27me3 单独定向和沉默。这些被 H3K27me3 标记的 TEs 不仅包括退化的遗迹，还包括看似完整的拷贝，这些拷贝显示了响应性 PcG 靶基因的表观遗传特征以及活跃的 H3K27me3 调控。我们还发现，H3K27me3 可以以 TE 特异性的方式沉积在新插入的转基因 TE 序列上，这表明沉默是顺式决定的。最后，通过比较拟南芥的天然种属，我们发现存在一类 TE（我们称之为 "bifrons"），根据种属的不同，它们具有 DNA 甲基化或 H3K27me3 标记。这种变化可以与 TE 的内在特征和反式作用因子联系起来，并揭示了整个 TE 生命周期中表观遗传状态的变化。我们的研究揭示了开花植物中与 H3K27me3 而不是 DNA 甲基化相关的 TE 沉默的另一种模式。它还表明这两种表观遗传标记在物种水平上的动态切换，这种新范式可能会扩展到其他多细胞真核生物。
{"title":"Alternative silencing states of transposable elements in Arabidopsis associated with H3K27me3","authors":"Valentin Hure, Florence Piron-Prunier, Tamara Yehouessi, Clémentine Vitte, Aleksandra E. Kornienko, Gabrielle Adam, Magnus Nordborg, Angélique Déléris","doi":"10.1186/s13059-024-03466-6","DOIUrl":"https://doi.org/10.1186/s13059-024-03466-6","url":null,"abstract":"The DNA/H3K9 methylation and Polycomb-group proteins (PcG)-H3K27me3 silencing pathways have long been considered mutually exclusive and specific to transposable elements (TEs) and genes, respectively in mammals, plants, and fungi. However, H3K27me3 can be recruited to many TEs in the absence of DNA/H3K9 methylation machinery and sometimes also co-occur with DNA methylation. In this study, we show that TEs can also be solely targeted and silenced by H3K27me3 in wild-type Arabidopsis plants. These H3K27me3-marked TEs not only comprise degenerate relics but also seemingly intact copies that display the epigenetic features of responsive PcG target genes as well as an active H3K27me3 regulation. We also show that H3K27me3 can be deposited on newly inserted transgenic TE sequences in a TE-specific manner indicating that silencing is determined in cis. Finally, a comparison of Arabidopsis natural accessions reveals the existence of a category of TEs—which we refer to as “bifrons”—that are marked by DNA methylation or H3K27me3 depending on the accession. This variation can be linked to intrinsic TE features and to trans-acting factors and reveals a change in epigenetic status across the TE lifespan. Our study sheds light on an alternative mode of TE silencing associated with H3K27me3 instead of DNA methylation in flowering plants. It also suggests dynamic switching between the two epigenetic marks at the species level, a new paradigm that might extend to other multicellular eukaryotes.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"56 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142990078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-17DOI: 10.1186/s13059-025-03474-0
Yihan Wang, Daniel A. Armendariz, Lei Wang, Huan Zhao, Shiqi Xie, Gary C. Hon
Genetic studies have associated thousands of enhancers with breast cancer (BC). However, the vast majority have not been functionally characterized. Thus, it remains unclear how BC-associated enhancers contribute to cancer. Here, we perform single-cell CRISPRi screens of 3513 regulatory elements associated with breast cancer to measure the impact of these regions on transcriptional phenotypes. Analysis of > 500,000 single-cell transcriptomes in two breast cancer cell lines shows that perturbation of BC-associated enhancers disrupts breast cancer gene programs. We observe BC-associated enhancers that directly or indirectly regulate the expression of cancer genes. We also find one-to-multiple and multiple-to-one network motifs where enhancers indirectly regulate cancer genes. Notably, multiple BC-associated enhancers indirectly regulate TP53. Comparative studies illustrate subtype specific functions between enhancers in ER + and ER − cells. Finally, we develop the pySpade package to facilitate analysis of single-cell enhancer screens. Overall, we demonstrate that enhancers form regulatory networks that link cancer genes in the genome, providing a more comprehensive understanding of the contribution of enhancers to breast cancer development.
{"title":"Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes","authors":"Yihan Wang, Daniel A. Armendariz, Lei Wang, Huan Zhao, Shiqi Xie, Gary C. Hon","doi":"10.1186/s13059-025-03474-0","DOIUrl":"https://doi.org/10.1186/s13059-025-03474-0","url":null,"abstract":"Genetic studies have associated thousands of enhancers with breast cancer (BC). However, the vast majority have not been functionally characterized. Thus, it remains unclear how BC-associated enhancers contribute to cancer. Here, we perform single-cell CRISPRi screens of 3513 regulatory elements associated with breast cancer to measure the impact of these regions on transcriptional phenotypes. Analysis of > 500,000 single-cell transcriptomes in two breast cancer cell lines shows that perturbation of BC-associated enhancers disrupts breast cancer gene programs. We observe BC-associated enhancers that directly or indirectly regulate the expression of cancer genes. We also find one-to-multiple and multiple-to-one network motifs where enhancers indirectly regulate cancer genes. Notably, multiple BC-associated enhancers indirectly regulate TP53. Comparative studies illustrate subtype specific functions between enhancers in ER + and ER − cells. Finally, we develop the pySpade package to facilitate analysis of single-cell enhancer screens. Overall, we demonstrate that enhancers form regulatory networks that link cancer genes in the genome, providing a more comprehensive understanding of the contribution of enhancers to breast cancer development.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"30 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142987508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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