Pub Date : 2026-03-17DOI: 10.1186/s12864-026-12742-7
Shi-Jie Chu, Ning Liu, Anderson Feijó, Zhi-Xin Wen, Ying-Hui Ling, De-Yan Ge
{"title":"Genetic recovery in an alpine climate-sensitive pika species during upward treeline shift.","authors":"Shi-Jie Chu, Ning Liu, Anderson Feijó, Zhi-Xin Wen, Ying-Hui Ling, De-Yan Ge","doi":"10.1186/s12864-026-12742-7","DOIUrl":"https://doi.org/10.1186/s12864-026-12742-7","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147472680","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 : 2026-03-16DOI: 10.1186/s12864-026-12746-3
Miriam Nurm, Tarmo Annilo, Sebastian May-Wilson, Anu Reigo, Reedik Mägi, Urmo Võsa, Neeme Tõnisson, Toomas Haller
{"title":"Unraveling genotype-phenotype relationships in hereditary hemochromatosis through integrated biobank data analysis.","authors":"Miriam Nurm, Tarmo Annilo, Sebastian May-Wilson, Anu Reigo, Reedik Mägi, Urmo Võsa, Neeme Tõnisson, Toomas Haller","doi":"10.1186/s12864-026-12746-3","DOIUrl":"https://doi.org/10.1186/s12864-026-12746-3","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147467068","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 : 2026-03-16DOI: 10.1186/s12864-026-12751-6
Laxman Adhikari, Pablo D Olivera, John Raupp, Hanan Sela, Assaf Distelfeld, Marco Maccaferri, Matteo Bozzoli, Elisabetta Mazzucotelli, Andrea Brandolini, Roberto Tuberosa, Hakan Özkan, Brande B H Wulff, Brian J Steffenson, Jesse Poland
{"title":"Dissecting the population structure, diversity and genetic architecture of rust resistance in wild emmer wheat (Triticum turgidum subsp. dicoccoides).","authors":"Laxman Adhikari, Pablo D Olivera, John Raupp, Hanan Sela, Assaf Distelfeld, Marco Maccaferri, Matteo Bozzoli, Elisabetta Mazzucotelli, Andrea Brandolini, Roberto Tuberosa, Hakan Özkan, Brande B H Wulff, Brian J Steffenson, Jesse Poland","doi":"10.1186/s12864-026-12751-6","DOIUrl":"10.1186/s12864-026-12751-6","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13003665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147467059","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}
Pub Date : 2026-03-16DOI: 10.1186/s12864-026-12666-2
Stephen Lu, Jose M C Ribeiro, Lucas Tirloni
{"title":"Further insights into the sialome switch of Amblyomma americanum adult females.","authors":"Stephen Lu, Jose M C Ribeiro, Lucas Tirloni","doi":"10.1186/s12864-026-12666-2","DOIUrl":"https://doi.org/10.1186/s12864-026-12666-2","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147467033","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 : 2026-03-14DOI: 10.1186/s12864-026-12747-2
Philip Süess, Sabine Ziesemer, Rachel A Steward, Kevin T Roberts, Christian Müller, Christopher W Wheat, Philipp Lehmann
{"title":"The insulin and ecdysone pathways as regulators of diapause termination: transcriptional and protein insights from Pieris napi.","authors":"Philip Süess, Sabine Ziesemer, Rachel A Steward, Kevin T Roberts, Christian Müller, Christopher W Wheat, Philipp Lehmann","doi":"10.1186/s12864-026-12747-2","DOIUrl":"https://doi.org/10.1186/s12864-026-12747-2","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147455688","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 : 2026-03-13DOI: 10.1186/s12864-026-12740-9
Elise M Bull, Viplav Agarwal, Marcus M Dillon
{"title":"Pathological convergence of a bacterial plant pathogen is associated with the horizontal transfer of an effector-containing mobile element.","authors":"Elise M Bull, Viplav Agarwal, Marcus M Dillon","doi":"10.1186/s12864-026-12740-9","DOIUrl":"https://doi.org/10.1186/s12864-026-12740-9","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147455634","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 : 2026-03-13DOI: 10.1186/s12864-026-12667-1
Hong Zhang, Peifen Zhang, Eric Bindels, Eskeatnaf Mulugeta
Pooled CRISPR screening combined with single-cell RNA sequencing (scRNA-seq) has emerged as a powerful strategy for dissecting gene function and reconstructing gene regulatory networks (GRNs) in complex biological systems. This approach enables high-throughput, parallel perturbation of multiple genes while providing transcriptome-wide readouts at single-cell resolution, overcoming many limitations of traditional arrayed screens. However, its broader application remains limited by technical challenges, including variable perturbation efficiency and difficulties in accurately identifying perturbed cells.In this study, we adapted and applied a modified CRISPR droplet sequencing (CROP-seq) protocol using CRISPR interference (CRISPRi) in K562 cells to knockdown six transcription factors (TFs): LMO2, TCF3, LDB1, MYB, GATA2, and RUNX1. Our modified approach, which allows direct capture of sgRNAs from the cDNA library without a separate enrichment step, significantly improved sgRNA assignment per cell. We successfully achieved reproducible knockdown of three TFs (MYB, GATA2, and LMO2), captured the impact of these perturbations on the TF target genes, and enabled us to reconstruct their GRNs and identify key regulons and transcriptional targets. These networks revealed both previously established (such as LMO2 GATA2 interaction) and novel regulatory interactions, which we independently validated, providing new insights into hematopoietic transcriptional control. To assess the efficiency of CRISPRi based pooled perturbation, we additionally analyzed publicly available Perturb-seq CRISPRi datasets and found that only ~40-50% of targeted genes led to effective knockdown, underscoring the variability in perturbation efficiency across experiments.Together, our results demonstrate both the potential and the current technical limitations of pooled CRISPRi-based single-cell screens. While this integrated approach holds great promise for high-resolution functional genomics, further optimization and standardized benchmarking are essential to improve its reliability, scalability, and reproducibility.
{"title":"Insights from pooled CRISPRi single-cell screens in K562 cells reveal gene functions, regulatory networks, and highlight opportunities and limitations.","authors":"Hong Zhang, Peifen Zhang, Eric Bindels, Eskeatnaf Mulugeta","doi":"10.1186/s12864-026-12667-1","DOIUrl":"https://doi.org/10.1186/s12864-026-12667-1","url":null,"abstract":"<p><p>Pooled CRISPR screening combined with single-cell RNA sequencing (scRNA-seq) has emerged as a powerful strategy for dissecting gene function and reconstructing gene regulatory networks (GRNs) in complex biological systems. This approach enables high-throughput, parallel perturbation of multiple genes while providing transcriptome-wide readouts at single-cell resolution, overcoming many limitations of traditional arrayed screens. However, its broader application remains limited by technical challenges, including variable perturbation efficiency and difficulties in accurately identifying perturbed cells.In this study, we adapted and applied a modified CRISPR droplet sequencing (CROP-seq) protocol using CRISPR interference (CRISPRi) in K562 cells to knockdown six transcription factors (TFs): LMO2, TCF3, LDB1, MYB, GATA2, and RUNX1. Our modified approach, which allows direct capture of sgRNAs from the cDNA library without a separate enrichment step, significantly improved sgRNA assignment per cell. We successfully achieved reproducible knockdown of three TFs (MYB, GATA2, and LMO2), captured the impact of these perturbations on the TF target genes, and enabled us to reconstruct their GRNs and identify key regulons and transcriptional targets. These networks revealed both previously established (such as LMO2 GATA2 interaction) and novel regulatory interactions, which we independently validated, providing new insights into hematopoietic transcriptional control. To assess the efficiency of CRISPRi based pooled perturbation, we additionally analyzed publicly available Perturb-seq CRISPRi datasets and found that only ~40-50% of targeted genes led to effective knockdown, underscoring the variability in perturbation efficiency across experiments.Together, our results demonstrate both the potential and the current technical limitations of pooled CRISPRi-based single-cell screens. While this integrated approach holds great promise for high-resolution functional genomics, further optimization and standardized benchmarking are essential to improve its reliability, scalability, and reproducibility.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147455683","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}
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