Open Biology最新文献_第5页

Cell fate acquisition and reprogramming by the proneural transcription factor ASCL1. 前体细胞转录因子ASCL1的细胞命运获取和重编程。

IF 4.5 3区生物学

Open Biology Pub Date : 2025-06-01 Epub Date: 2025-06-18 DOI: 10.1098/rsob.250018

Jethro Lundie-Brown, Francesca Puletti, Anna Philpott, Roberta Azzarelli

{"title":"Cell fate acquisition and reprogramming by the proneural transcription factor ASCL1.","authors":"Jethro Lundie-Brown, Francesca Puletti, Anna Philpott, Roberta Azzarelli","doi":"10.1098/rsob.250018","DOIUrl":"10.1098/rsob.250018","url":null,"abstract":"ASCL1 is a key member of the proneural basic helix-loop-helix (bHLH) transcription factor (TF) family and it plays diverse roles in nervous system development and maintenance. ASCL1 is also one of the most studied bHLH TFs in the field of somatic cell reprogramming, as it can reconfigure the chromatin of the cell of origin to impose a neuronal identity. However, the ability of ASCL1 to drive neuronal fate does not come without exceptions, as there are cell types that are refractory to ASCL1-mediated reprogramming, and there are developmental contexts where ASCL1 does not drive neurogenesis but supports the generation of other lineages. ASCL1 has also emerged as an important player in cancers like neuroblastoma and glioblastoma, underscoring the clinical need for a robust understanding of how ASCL1 controls cell identity. In this review, we revisit the foundational studies that established ASCL1 as a critical regulator of neuronal differentiation and incorporate recent advances in our understanding of ASCL1 post-translational regulation and transcriptional control. By integrating these perspectives, this review provides a comprehensive overview of the diverse roles of ASCL1 in development, reprogramming and cancer, offering insights into its molecular functions and therapeutic potential.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 6","pages":"250018"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12173495/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144317564","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The role of endothelial-derived factors in neural tube development: implications for organoid models. 内皮衍生因子在神经管发育中的作用：对类器官模型的影响。

IF 4.5 3区生物学

Open Biology Pub Date : 2025-06-01 Epub Date: 2025-06-11 DOI: 10.1098/rsob.240341

Amy van der Hoven, Mubeen Goolam

引用次数: 0

Kaiso mediates transcription and RNA splicing in colorectal carcinoma: role of BRCA1 in the Kaiso enhanceosome. Kaiso介导结直肠癌的转录和RNA剪接：BRCA1在Kaiso增强体中的作用

IF 4.5 3区生物学

Open Biology Pub Date : 2025-06-01 Epub Date: 2025-06-04 DOI: 10.1098/rsob.240329

Weifeng Luo, Manish K Tripathi, Qi Liu, Lei Chen, Robert W Cowan, Juliet M Daniel, Chi Yan, Ann Richmond, Albert B Reynolds

{"title":"Kaiso mediates transcription and RNA splicing in colorectal carcinoma: role of BRCA1 in the Kaiso enhanceosome.","authors":"Weifeng Luo, Manish K Tripathi, Qi Liu, Lei Chen, Robert W Cowan, Juliet M Daniel, Chi Yan, Ann Richmond, Albert B Reynolds","doi":"10.1098/rsob.240329","DOIUrl":"10.1098/rsob.240329","url":null,"abstract":"Kaiso (ZBTB33) is a transcription factor involved in mitotic clonal expansion and tumorigenesis in association with Adenomatous Polyposis Coli (APC) loss of heterozygosity. ENCODE data show strong overlap of the Kaiso promoter-binding site-encode-derived Kaiso-binding site (eKBS) and many other transcription factors, including BRCA1. Here we sought to determine whether BRCA1 is a component of the Kaiso enhanceosome that regulates gene transcription. Using proximal ligation assays, immunoprecipitation followed by mass spectrometry, luciferase assays and ChIP-seq experiments, we evaluated the association between BRCA1 and Kaiso. Kaiso nuclear extract immunoprecipitation experiments revealed that Kaiso associates strongly with genes involved in RNA splicing and processing. When Kaiso was not crosslinked to DNA, BRCA1 was not detected among Kaiso-binding proteins. However, overexpression of BRCA1 increased Kaiso-mediated gene transcription in luciferase assays in a Kaiso-dependent manner. Comparison of BRCA1 ChIP-seq and Kaiso ChIP-seq data from HCT116 cells revealed both BRCA1 and Kaiso commonly bind to the promoters of 379 genes. The most enriched term associated with these genes where BRCA1 and Kaiso bind their promoters is metabolism of RNA. Disease processes associated with these BRCA1/Kaiso gene promoters indicate that BRCA1 is functionally linked to a Kaiso-directed programme of RNAP2-mediated gene transcription and likely associated with colorectal cancer development and maintenance.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 6","pages":"240329"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12133338/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enterohaemorrhagic Escherichia coli AdhE spirosome length correlates with enzymatic directionality and is perturbed by salicylidene acylhydrazides. 肠出血性大肠杆菌AdhE螺旋体长度与酶的方向性相关，并受到水杨基酰肼的干扰。

IF 4.5 3区生物学

Open Biology Pub Date : 2025-06-01 Epub Date: 2025-06-18 DOI: 10.1098/rsob.250041

Ester Serrano, Tianxiao Zhao, David R Mark, Mostafa Soroor, Iris Floria, Nicholas J Terrill, Nikil Kapur, Arwen I I Tyler, Mathew H Horrocks, Andrew J Roe, Olwyn Byron

{"title":"Enterohaemorrhagic Escherichia coli AdhE spirosome length correlates with enzymatic directionality and is perturbed by salicylidene acylhydrazides.","authors":"Ester Serrano, Tianxiao Zhao, David R Mark, Mostafa Soroor, Iris Floria, Nicholas J Terrill, Nikil Kapur, Arwen I I Tyler, Mathew H Horrocks, Andrew J Roe, Olwyn Byron","doi":"10.1098/rsob.250041","DOIUrl":"10.1098/rsob.250041","url":null,"abstract":"Enterohaemorrhagic Escherichia coli causes sporadic, and sometimes large-scale, food poisoning outbreaks, for which antibiotic treatment in humans is contraindicated. As an alternative form of therapy, previous studies developed the family of salicylidene acylhydrazide (SA) anti-virulence compounds. One target of the SA compounds is AdhE, an enzyme that converts acetyl-CoA to ethanol and vice versa. AdhE oligomerizes, forming helicoidal filaments, heterogeneous in length, called spirosomes. We show it is possible to only partially fractionate AdhE spirosomes because in vitro they oligomerize in the absence of stimuli, and that spirosome formation is necessary to regulate the direction of AdhE enzymatic reactions. We also show that the SA compound ME0054 binds and perturbs AdhE spirosomes, enhancing the conversion of ethanol to acetyl-CoA. This mechanistic understanding of how ME0054 impacts AdhE function will help in the development of SA compounds as novel anti-virulence inhibitors.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 6","pages":"250041"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12173503/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144317565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Sex-specific loss of mitochondrial membrane integrity in the auditory brainstem of a mouse model of Fragile X Syndrome. 脆性X综合征小鼠听觉脑干中线粒体膜完整性的性别特异性丧失。

IF 4.5 3区生物学

Open Biology Pub Date : 2025-05-01 Epub Date: 2025-05-14 DOI: 10.1098/rsob.240384

Claire Caron, Elizabeth Anne McCullagh, Giulia Bertolin

{"title":"Sex-specific loss of mitochondrial membrane integrity in the auditory brainstem of a mouse model of Fragile X Syndrome.","authors":"Claire Caron, Elizabeth Anne McCullagh, Giulia Bertolin","doi":"10.1098/rsob.240384","DOIUrl":"10.1098/rsob.240384","url":null,"abstract":"Sound sensitivity is a common sensory complaint for people with autism spectrum disorder (ASD). How and why sounds are perceived as overwhelming by affected people is unknown. To process sound information properly, the brain requires high activity and fast processing, as seen in areas like the medial nucleus of the trapezoid body (MNTB) of the auditory brainstem. Recent work has shown dysfunction in mitochondria in a genetic model of ASD, Fragile X Syndrome (FXS). Whether mitochondrial functions are also altered in sound-processing neurons has not been characterized yet. To address this question, we imaged MNTB in a mouse model of FXS. We stained MNTB brain slices from wild-type and FXS mice with two mitochondrial markers, TOMM20 and PMPCB, located on the outer mitochondrial membrane and in the matrix, respectively. Our imaging reveals significant sex-specific differences between genotypes. Colocalization analyses between TOMM20 and PMPCB show that the integrity of mitochondrial subcompartments is most disrupted in female FXS mice compared with female wild-type mice. We highlight a quantitative fluorescence microscopy pipeline to monitor mitochondrial functions in the MNTB from control or FXS mice and provide four complementary readouts, paving the way to understanding how cellular mechanisms important to sound encoding are altered in ASD.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 5","pages":"240384"},"PeriodicalIF":4.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12082877/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143974224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploration of gene presence/absence variations in Oncorhynchus mykiss and their differentiation between wild and selection populations. 野生种群与选择种群间褐蝽基因存在/缺失差异的探讨。

IF 4.5 3区生物学

Open Biology Pub Date : 2025-05-01 Epub Date: 2025-05-21 DOI: 10.1098/rsob.240382

Hancheng Bao, Na Xue, Boyuan Wang, Han Yu, Ming Huang, Jinghong He, Shuanglin Dong, Yangen Zhou, Qinfeng Gao, Yuan Tian

{"title":"Exploration of gene presence/absence variations in Oncorhynchus mykiss and their differentiation between wild and selection populations.","authors":"Hancheng Bao, Na Xue, Boyuan Wang, Han Yu, Ming Huang, Jinghong He, Shuanglin Dong, Yangen Zhou, Qinfeng Gao, Yuan Tian","doi":"10.1098/rsob.240382","DOIUrl":"10.1098/rsob.240382","url":null,"abstract":"Gene presence/absence variations (PAVs) have been considered as the important determinants of genome evolution and phenotypic diversity. However, studies on gene PAVs have been poorly documented, especially in fishes. In the present study, the pan-genome of rainbow trout was constructed based on 268 whole-genome re-sequencing accessions (4.38 Tb data). It recovered an additional 62 Mb sequences and 1288 protein-coding genes. Then, 9831 (22.77%) gene PAVs were genotyped across the 268 individuals. PAV-based PCA analysis, together with phylogenetic topology and STRUCTURE, revealed the clear separation among the different wild and selection populations. Additionally, a PAV-based genome-wide association study (GWAS) identified three candidate PAVs significantly associated with artificial selection. Meanwhile, fixation index analysis revealed 35 PAVs with significant frequency differences between wild and selection populations in Canada, while 15 candidate PAVs were detected between the populations in America. Their biological functions have been reported to participate in the regulation of growth performance and stress response. The present study deepens our understanding of widespread gene PAVs and facilitates the identification of key candidates that contribute to important traits.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 5","pages":"240382"},"PeriodicalIF":4.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12092107/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144111658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Reviewers in 2024. 2024年的评论家。

IF 4.5 3区生物学

Open Biology Pub Date : 2025-05-01 Epub Date: 2025-05-07 DOI: 10.1098/rsob.250082

Jon Pines

引用次数: 0

Beyond pathogenicity: the immunomodulatory role of the type III secretion system in beneficial plant-microbe interactions. 超越致病性：III型分泌系统在有益植物-微生物相互作用中的免疫调节作用。

IF 4.5 3区生物学

Open Biology Pub Date : 2025-05-01 Epub Date: 2025-05-28 DOI: 10.1098/rsob.240318

Iva Atanasković, Marija Nedeljković, Jelena Lozo

引用次数: 0

Genomic, transcriptomic and epigenomic signatures of ageing and cold adaptation in the Antarctic clam Laternula elliptica. 南极椭圆蛤衰老和寒冷适应的基因组、转录组学和表观基因组特征。

IF 4.5 3区生物学

Open Biology Pub Date : 2025-05-01 Epub Date: 2025-05-21 DOI: 10.1098/rsob.250009

Victoria A Sleight, Melody S Clark, Meghan K Yap-Chiongco, Frances Turner, Kevin M Kocot

{"title":"Genomic, transcriptomic and epigenomic signatures of ageing and cold adaptation in the Antarctic clam Laternula elliptica.","authors":"Victoria A Sleight, Melody S Clark, Meghan K Yap-Chiongco, Frances Turner, Kevin M Kocot","doi":"10.1098/rsob.250009","DOIUrl":"10.1098/rsob.250009","url":null,"abstract":"Genomic data are lacking for most Antarctic marine invertebrates, predicating our ability to understand physiological adaptation and specific life-history traits, such as longevity. The environmental stress response of the Antarctic infaunal clam Laternula elliptica is much diminished in older adult animals compared with younger juvenile individuals. However, the mechanism underlying this reduced capacity is unknown. In this study, we describe and analyse the genome of L. elliptica and use it as a tool to understand transcriptomic responses to shell damage across different age cohorts. Gene expression data were combined with reduced representation enzymic methyl sequencing to identify if methylation was acting as an epigenetic mechanism driving age-dependent transcriptional profiles. Our transcriptomic results demonstrated a clear bipartite molecular response in L. elliptica, associated with a rapid growth phase in juveniles and a stabilization phase in reproductively mature adults. Genes active in the response to damage repair in juvenile animals are silent in adults but can be reactivated after several months following damage stimulus; however, these genes were not methylated. Hence, the trigger for this critical and imprinted change in physiological state is, as yet, unknown. While epigenetics is likely involved in this process, the mechanism is unlikely to be methylation.","PeriodicalId":19629,"journal":{"name":"Open Biology","volume":"15 5","pages":"250009"},"PeriodicalIF":4.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12092138/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144111659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cancer cells' chamber of secrets: the link between micronuclei, chromothripsis and malignancy. 癌细胞的密室：微核、染色体分裂和恶性肿瘤之间的联系。

IF 4.5 3区生物学

Open Biology Pub Date : 2025-05-01 Epub Date: 2025-05-14 DOI: 10.1098/rsob.240388

Truman Raleigh Mcneil, Sweta Sikder, Yamini Dalal

引用次数: 0