Biochimica et Biophysica Acta-Gene Regulatory Mechanisms最新文献_第2页

The Catsper3 promoter activity is regulated by the cAMP-Response Element Modulator tau (CREMτ) and the cAMP-Response Element Binding protein 1A (CREBA) transcription factors Catsper3启动子活性受cAMP-Response Element Modulator tau （CREMτ）和cAMP-Response Element Binding protein 1A （CREBA）转录因子调控

IF 3.1 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2025-12-01 Epub Date: 2025-08-25 DOI: 10.1016/j.bbagrm.2025.195114

Diego Eduardo Sánchez-Jasso , Sergio Federico López-Guzmán , Javier Hernández-Sánchez , Rosa María Bermúdez-Cruz , Norma Oviedo

{"title":"The Catsper3 promoter activity is regulated by the cAMP-Response Element Modulator tau (CREMτ) and the cAMP-Response Element Binding protein 1A (CREBA) transcription factors","authors":"Diego Eduardo Sánchez-Jasso , Sergio Federico López-Guzmán , Javier Hernández-Sánchez , Rosa María Bermúdez-Cruz , Norma Oviedo","doi":"10.1016/j.bbagrm.2025.195114","DOIUrl":"10.1016/j.bbagrm.2025.195114","url":null,"abstract":"<div><div>Catsper3 has been shown to be essential for the proper functioning of CatSper calcium channel, sperm hyperactivation and egg fertilization. Although its function and physiological relevance to male fertility have been characterized, nothing is known about its regulation at the transcriptional level. Here, we identified the murine <em>Catsper3</em> promoter and evaluated the role of CREBA and CREMτ transcription factors (TF) on its regulation. Cloning of a predicted <em>Catsper3</em> promoter region and further deletion analysis indicates that <em>Catsper3</em> core promoter is located at −157 to +152 relative to the transcription start site (TSS). Mutation of a TATA box and a Downstream Promoter Element (DPE) did not alter the promoter activity, indicating that this promoter is TATA and DPE independent. Exogenous expression of CREBA and CREMτ increase the <em>Catsper3</em> promoter activity in the presence of the +268 to +439 region, where two CRE sites were predicted, and mutation of both CRE sites prevents the transactivation by both TFs, suggesting that CREMτ and CREBA may use these sites to promote <em>Catsper3</em> transcription. Finally, binding of CREBA and CREMτ to both CRE sites was confirmed <em>in vitro</em> by EMSA and ChIP-qPCR assays demonstrated an enrichment of CREBA and CREMτ at the <em>Catsper3</em> promoter <em>in vivo</em> in the testis but not in liver, indicating its tissue-specific binding. Altogether, these results strongly suggest that <em>Catsper3</em> gene has a TATA-less, DPE independent promoter encompassed by −157 to +152 region around TSS and that <em>Catsper3</em> gene expression is directly regulated through two CRE sites by CREBA and CREMτ.</div></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1868 4","pages":"Article 195114"},"PeriodicalIF":3.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144919682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Transcriptional activation of the PKLR gene by novel erythroid-specific regulatory elements 新的红细胞特异性调控元件对plklr基因转录激活的影响。

IF 3.1 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2025-12-01 Epub Date: 2025-09-16 DOI: 10.1016/j.bbagrm.2025.195116

Yea Woon Kim , Jin Kang , AeRi Kim

{"title":"Transcriptional activation of the PKLR gene by novel erythroid-specific regulatory elements","authors":"Yea Woon Kim , Jin Kang , AeRi Kim","doi":"10.1016/j.bbagrm.2025.195116","DOIUrl":"10.1016/j.bbagrm.2025.195116","url":null,"abstract":"<div><div>The pyruvate kinase L/R (PKLR) gene encodes the L- and R-type isoforms of pyruvate kinase, which catalyze the final step of glycolysis in mammals. The L-type isozyme is mainly found in liver cells, whereas the R-type isozyme is produced specifically in erythroid cells. To investigate the transcriptional activation of the PKLR gene for the R-type isozyme, we analyzed chromatin features—including DNase I sensitivity, histone modifications, and enhancer–promoter interactions—in erythroid K562 and non-erythroid HUVEC cells. Putative regulatory elements, including a promoter and two enhancers, were identified near the PKLR locus in K562 cells. Depletion of H3K4me1 and H3K27ac, histone marks associated with active enhancers, through mutation of histone methyltransferases led to a marked reduction in PKLR transcription, while transcription of a nearby gene remained stable. These regulatory elements were highly occupied by the erythroid-specific transcription factors GATA1 and TAL1. Loss of either factors disrupted local H3K27ac and reduced the recruitment of chromatin-looping factors, resulting in decreased PKLR transcription. Furthermore, CRISPR/Cas9-mediated deletion of the putative regulatory elements significantly diminished PKLR transcription, demonstrating their functional importance. Collectively, these findings highlight the essential role of these regulatory elements in activating PKLR transcription in erythroid cells and emphasize the requirement of erythroid-specific factors for their function.</div></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1868 4","pages":"Article 195116"},"PeriodicalIF":3.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145087956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

RNA-protein interaction techniques - A historical and comparative analysis rna -蛋白质相互作用技术-历史和比较分析。

IF 3.1 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2025-12-01 Epub Date: 2025-09-11 DOI: 10.1016/j.bbagrm.2025.195115

Sourabh Chakrabarty , Sayan Roy , Soumyadip Sarkar , Kusum K. Singh

{"title":"RNA-protein interaction techniques - A historical and comparative analysis","authors":"Sourabh Chakrabarty , Sayan Roy , Soumyadip Sarkar , Kusum K. Singh","doi":"10.1016/j.bbagrm.2025.195115","DOIUrl":"10.1016/j.bbagrm.2025.195115","url":null,"abstract":"<div><div>RNAs intricately orchestrate a myriad of molecular and cellular processes. This includes mRNAs which serve as the essential blueprints for protein synthesis and the non-coding RNAs which act as versatile regulators, influencing gene expression, RNA stability, and even protein function. Over the past few decades, a diverse array of RNA- and protein-centric methodologies have emerged to discern and elucidate the identities of RNA binding proteins (RBPs) and RNAs engaged in RNA-Protein interactions (RPI). The selection of an appropriate method is paramount, given the distinctive advantages and limitations inherent to each technique, in order to effectively address specific biological inquiries. This review spans the spectrum of techniques employed in RNA-Protein interaction studies, ranging from time-honored methods like Electrophoretic Mobility Shift Assay (EMSA) to contemporary approaches such as CRISPR-based RNA-Protein interaction profiling (CBRIP). This review aims not only to list methods but also to provide historical background, discuss the strengths and weaknesses of each approach, and highlight their current applications. Furthermore, it consolidates methodologies tailored to characterize RNA-protein interactions based on their distinct purposes.</div></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1868 4","pages":"Article 195115"},"PeriodicalIF":3.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Heterogeneity of Acute Myeloid Leukemia patients explored through single-cell and single-sample gene regulatory networks 通过单细胞和单样本基因调控网络探讨急性髓系白血病患者的异质性。

IF 3.1 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2025-12-01 Epub Date: 2025-11-04 DOI: 10.1016/j.bbagrm.2025.195119

Leandro Fernandes, Edoardo Saccenti

{"title":"Heterogeneity of Acute Myeloid Leukemia patients explored through single-cell and single-sample gene regulatory networks","authors":"Leandro Fernandes, Edoardo Saccenti","doi":"10.1016/j.bbagrm.2025.195119","DOIUrl":"10.1016/j.bbagrm.2025.195119","url":null,"abstract":"<div><div>Acute myeloid leukaemia (AML) is a genetically heterogeneous disease, driven by diverse mutations and epigenetic alterations that disrupt normal haematopoiesis. Understanding how this heterogeneity manifests at the gene regulatory level can provide insight into disease mechanisms and uncover potential targets for personalized treatment strategies.</div><div>In this study, single-cell RNA sequencing data from AML patients and healthy controls were used to infer patient gene regulatory networks (GRNs) for progenitor, monocyte, and dendritic cells. Consensus networks were constructed using four inference methods (ARACNE, CLR, MRNET, GENIE3). Additionally, single-sample single-cell networks were constructed using the LIONESS approach for all patients and cell types.</div><div>Dimensionality reduction applied to both network statistics and adjacency matrices of consensus networks revealed limited clustering, reflecting the biological heterogeneity of AML. Notably, dimensionality reduction and classification models based on single-cell networks achieved distinct patient clustering and perfect discrimination accuracy. This indicates that single-cell GRNs can capture patient-specific signatures of gene regulation.</div><div>Pathway enrichment analysis of highly connected and predictive genes highlighted distinct regulatory programs across cell types and individuals. These findings demonstrate the potential of GRNs from single-cell data to distinguish between patients and may serve as a foundation for the development of personalized biomarkers and therapeutics.</div></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1868 4","pages":"Article 195119"},"PeriodicalIF":3.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145460726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Effects of disease severity on RNA integrity measures in necrotising soft tissue infection as a possible source of research bias: An observational cohort study 疾病严重程度对坏死性软组织感染中RNA完整性测量的影响可能是研究偏倚的来源：一项观察性队列研究

IF 3.1 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2025-12-01 Epub Date: 2025-11-10 DOI: 10.1016/j.bbagrm.2025.195121

Julie Vinkel , Edoardo Saccenti , Bart Nijsse , Morten Hedetoft , Ole Hyldegaard

{"title":"Effects of disease severity on RNA integrity measures in necrotising soft tissue infection as a possible source of research bias: An observational cohort study","authors":"Julie Vinkel , Edoardo Saccenti , Bart Nijsse , Morten Hedetoft , Ole Hyldegaard","doi":"10.1016/j.bbagrm.2025.195121","DOIUrl":"10.1016/j.bbagrm.2025.195121","url":null,"abstract":"<div><div>RNA sequencing is increasingly being employed in clinical studies. During data pre-processing, samples are typically excluded from further analysis based on quality metrics that assess the integrity of the intermediate genomic product. RNA degradation may occur during sample handling as well as necrosis, affecting tissues in people with necrotising soft tissue infections (NSTIs).</div><div>RNA integrity measured with RNA Quality Number (RQN) and Transcript Integrity Number (TIN) in infected tissue samples may be lower in severe cases of NSTI.</div><div>We analysed whole blood and infected tissue samples from 95 individuals with acute NSTI and evaluated RNA integrity using RQN and TIN. Using linear models, we examined their relationships with age, BMI, RNA quantity, Sequential Organ Failure Assessment (SOFA) score, plasma lactate level (blood), and tissue type (infected tissue).</div><div>In infected tissue samples, we discovered that for every 5-point increase in SOFA score, the RQN increased by 0.19 points, 95 % CI [0.15, 1.80], <em>p</em> = 0.022, but there was no influence on the TIN. In blood, we observed no associations between RQN and SOFA or raised lactate levels, nor between TIN and SOFA score or elevated lactate. In both tissues, we discovered a link between age and RNA integrity measurements, and that RQN was dependent on the RNA quantity extracted from samples.</div><div>We advocate using numerous integrity measures to evaluate RNA integrity. Samples should not be removed based on any integrity measures in data pre-processing. The biological and technological implications of eliminating samples should be assessed using the integrity metrics as covariates.</div></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1868 4","pages":"Article 195121"},"PeriodicalIF":3.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145508088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Identification of a novel p65-p68 loop: A crucial determinant for p68 gene regulation in oncogenesis 新的p65-p68环的鉴定：肿瘤发生中p68基因调控的关键决定因素

IF 3.1 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2025-12-01 Epub Date: 2025-11-06 DOI: 10.1016/j.bbagrm.2025.195120

Mrinal K. Ghosh , Sunny Kumar , Veenita Khare , Siddik Sarkar , Shaheda Tabassum , Malini Basu

{"title":"Identification of a novel p65-p68 loop: A crucial determinant for p68 gene regulation in oncogenesis","authors":"Mrinal K. Ghosh , Sunny Kumar , Veenita Khare , Siddik Sarkar , Shaheda Tabassum , Malini Basu","doi":"10.1016/j.bbagrm.2025.195120","DOIUrl":"10.1016/j.bbagrm.2025.195120","url":null,"abstract":"<div><div>DEAD-box RNA helicase DDX5 (p68), located on chromosome 17, specifically at the 17q23.3 region), is overexpressed in most of the cancers, including colorectal cancer (CRC) and glioma, thereby gaining prominence as a potential biomarker. There is a paucity of research on the mechanisms of p68 gene regulation at the genetic level. RelA, (p65), belonging to the NF-κB signaling pathway plays a diversified role in accelerating oncogenesis. Here, we report for the first time a novel transcriptional positive feedback mechanism between p65 and p68 that drives oncogenesis in CRC and glioma. Using bioinformatics analysis, chromatin immunoprecipitation (ChIP), and luciferase reporter assays, we identified functional NF-κB binding sites in the p68 promoter region and demonstrated that p65 upregulates p68 expression. Functionally, increased p68 expression was associated with enhanced proliferation, migration, and invasion, established through <em>in vitro</em> as well as <em>in vivo</em> studies in glioma and CRC. Furthermore, the pharmacological inhibition of IKK (outside of the loop) <em>via</em> Bay-11 leads to the suppression of the “p65-p68 loop” and their oncogenic phenotypes. However, the analysis of patient-derived tumor samples revealed a positive correlation between p65 and p68, underscoring their clinical relevance. Hence, our findings elucidate novel transcriptional feedback “p65–68 loop” and its therapeutic potential in CRC and glioma.</div></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1868 4","pages":"Article 195120"},"PeriodicalIF":3.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145465735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Expression of CMK2 is controlled by the general stress-response transcriptional factor Msn2 through a single STRE site in budding yeast 在出芽酵母中，CMK2的表达受一般应激反应转录因子Msn2通过一个单一的STRE位点控制。

IF 3.1 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2025-12-01 Epub Date: 2025-08-13 DOI: 10.1016/j.bbagrm.2025.195107

Linghuo Jiang , Yiying Gu , Liudan Wei , Jinrong Feng , Lingxin Pan , Xiufan Liao , Yiping Mo , Chunyu Wei

{"title":"Expression of CMK2 is controlled by the general stress-response transcriptional factor Msn2 through a single STRE site in budding yeast","authors":"Linghuo Jiang , Yiying Gu , Liudan Wei , Jinrong Feng , Lingxin Pan , Xiufan Liao , Yiping Mo , Chunyu Wei","doi":"10.1016/j.bbagrm.2025.195107","DOIUrl":"10.1016/j.bbagrm.2025.195107","url":null,"abstract":"<div><div>Mammalian calcium/calmodulin-dependent protein kinase II (CaMKII) is a memory molecule in the brain, and regulates fatty acids and lipid metabolism. As a yeast homolog of CaMKII, Cmk2 is a negative feed-back regulator of calcium signaling in <em>Saccharomyces cerevisiae</em>. Previous systemic studies have shown that 42 transcription factors (TFs) are involved in the control of <em>CMK2</em> expression under various conditions other than calcium stress, but only one, Crz1, is reported to directly regulate <em>CMK2</em> expression in response to calcium stress. Here, we show that other 26 TFs, Adr1, Aft2, Cad1, Cst6, Cup2, Dal81, Dal82, Flo8, Gcr2, Haa1, Hfi1, Msn2, Oaf1, Pho4, Ppr1, Rfx1, Rgm1, Rpn4, Sfp1, SIp3, Smp1, Spt10, Stp1, Sum1, Swi4 and Tup1, are involved in the positive control of <em>CMK2</em> transcription, with 10 of them being calcium stress-specific. In contrast, other four TFs, Hir2, Rph1, Sin3 and Uga3, negatively regulates <em>CMK2</em> transcription independent of calcium stress. Therefore, multiple TFs directly or indirectly control the transcription of <em>CMK2</em> in yeast cells. EMSA and ChIP analysis demonstrate that the general stress-responsive Msn2 directly controls the expression of <em>CMK2</em> through one STRE site, 5′ C<sub>−155</sub>CCCT 3′, in its promoter. Our genetic study indicates that Crz1 is epistatic to Msn2 in controlling <em>CMK2</em> expression and the calcium sensitivity of yeast cells in response to calcium stress. This work provides important clues to the study on the regulation of CaMKII expression in mammalian cells.</div></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1868 4","pages":"Article 195107"},"PeriodicalIF":3.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144859964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

TET enzymes: Involvement in cancer development and therapeutical perspectives TET酶：参与癌症的发展和治疗前景。

IF 3.1 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2025-12-01 Epub Date: 2025-10-16 DOI: 10.1016/j.bbagrm.2025.195118

Tarik Aanniz , Meriem El Fessikh , Jihane Touhtouh , Sara Aboulaghras , Nasreddine El Omari , Asaad Khalid , Ashraf N. Abdalla , Mohammed Amanullah , Bey Hing Goh , Learn-Han Lee , Abdelhakim Bouyahya

{"title":"TET enzymes: Involvement in cancer development and therapeutical perspectives","authors":"Tarik Aanniz , Meriem El Fessikh , Jihane Touhtouh , Sara Aboulaghras , Nasreddine El Omari , Asaad Khalid , Ashraf N. Abdalla , Mohammed Amanullah , Bey Hing Goh , Learn-Han Lee , Abdelhakim Bouyahya","doi":"10.1016/j.bbagrm.2025.195118","DOIUrl":"10.1016/j.bbagrm.2025.195118","url":null,"abstract":"<div><div>The TET family of enzymes is essential for the dynamic regulation of DNA methylation and the epigenetic landscape of human genomes. Their ability to oxidize 5-methylcytosine (5mC) into various hydroxymethylated derivatives facilitates active DNA demethylation and serves as a critical regulatory mechanism in normal cellular processes. Dysregulation of TET proteins has been implicated in multiple types of cancer, highlighting their significance in tumorigenesis and their potential for therapeutic targeting. The functionality of TET proteins continues to be widely studied across various tissues and contexts. Their role as novel drug targets in cancer therapy is attracting increasing attention. Understanding how TET enzymes contribute to epigenetic alterations could provide new insights into cancer prevention and treatment, potentially extending the window of effective therapeutic intervention. This review aims to explore the diverse roles and regulatory mechanisms of TET proteins, examine how their dysregulation promotes cancer progression, and underscore the potential of TET enzymes as druggable targets for anticancer therapy.</div></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1868 4","pages":"Article 195118"},"PeriodicalIF":3.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145318950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 cAMP receptor protein, SyCRP1 acts as a transcriptional repressor of CO2-concentrating mechanism genes at high inorganic carbon levels in Synechocystis PCC 6803 聚囊藻（Synechocystis PCC 6803）中，cAMP受体蛋白SyCRP1作为高无机碳水平下co2富集机制基因的转录抑制因子。

IF 3.1 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2025-12-01 Epub Date: 2025-10-02 DOI: 10.1016/j.bbagrm.2025.195117

Suraj Chauhan , N. Prakash Prabhu , Martin Hagemann , Sue Lin-Chao , Jogadhenu S.S. Prakash

{"title":"The cAMP receptor protein, SyCRP1 acts as a transcriptional repressor of CO2-concentrating mechanism genes at high inorganic carbon levels in Synechocystis PCC 6803","authors":"Suraj Chauhan , N. Prakash Prabhu , Martin Hagemann , Sue Lin-Chao , Jogadhenu S.S. Prakash","doi":"10.1016/j.bbagrm.2025.195117","DOIUrl":"10.1016/j.bbagrm.2025.195117","url":null,"abstract":"<div><div>Cyanobacteria utilize a CO<sub>2</sub>-concentrating mechanism (CCM) to enhance photosynthetic efficiency by accumulating CO<sub>2</sub> around RuBisCO, a process crucial for adapting to fluctuating environmental CO<sub>2</sub> levels. While the upregulation of CCM genes under low inorganic carbon (C<sub>i</sub>) conditions is known, the precise C<sub>i</sub> sensing and regulatory mechanisms governing CCM gene expression remain incompletely understood. We show that a membrane-bound SyCRP1 senses high C<sub>i</sub> levels through cAMP binding to its low- and high-affinity sites. We demonstrate its interaction with membrane lipids and liposomes, and a subsequent reversal of its membrane localization upon cAMP binding. Comprehensive ChIP-seq analysis reveals direct binding of SyCRP1 to regulatory elements of core CCM genes. Our findings establish SyCRP1 as a key transcriptional repressor of these genes under high C<sub>i</sub> conditions, significantly advancing our understanding of the molecular mechanisms governing CCM genes' expression in cyanobacteria.</div></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1868 4","pages":"Article 195117"},"PeriodicalIF":3.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145226313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

RhoA functionally collaborates with HSPA1A to promote the migratory phenotype of cancer cells RhoA与HSPA1A在功能上协同促进癌细胞的迁移表型

IF 2.6 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2025-09-01 Epub Date: 2025-06-20 DOI: 10.1016/j.bbagrm.2025.195101

Sumaiya Nabi , Mohammad Amin Hajam , Umar Mushtaq , Aadil Manzoor Baba , Bashir Ahmad Malla , Firdous Ahmad Khanday , Nazir Ahmad Dar

{"title":"RhoA functionally collaborates with HSPA1A to promote the migratory phenotype of cancer cells","authors":"Sumaiya Nabi , Mohammad Amin Hajam , Umar Mushtaq , Aadil Manzoor Baba , Bashir Ahmad Malla , Firdous Ahmad Khanday , Nazir Ahmad Dar","doi":"10.1016/j.bbagrm.2025.195101","DOIUrl":"10.1016/j.bbagrm.2025.195101","url":null,"abstract":"<div><div>RhoA, a member of the GTPase family, plays a pivotal role in attaining a migratory phenotype, mainly by regulating cytoskeleton dynamics, cell adhesion and membrane protrusions. Although many upstream regulators and downstream effectors of RhoA have been identified, the discovery of new interacting partners continues to expand its interactome, providing fresh insights into its regulation and function. Co-immunoprecipitation and fluorescence microscopy were used to study the interaction, localization and morphological effects of HSPA1A and RhoA. The interaction was validated by modulating the protein expression through transfections and silencing approaches. Cell proliferation, migration and viability were assessed using MTT, a Boyden chamber and FACS assays, respectively. Our study identified HSPA1A, as an unexplored interacting partner of RhoA under physiological conditions. Functional analyses showed that the interaction between HSPA1A and RhoA enhances the migratory potential of cancer cells, induces G0/G1 cell cycle arrest and promotes a rounded cell morphology. Under HSPA1A transfection, increased RhoA protein levels were observed, while the silencing of HSPA1A resulted in decreased RhoA levels. This study highlights the critical role of HSPA1A-RhoA interaction in regulating cancer cell migration, morphology and cell cycle progression. These findings lay the groundwork for future research into its potential clinical applications.</div></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1868 3","pages":"Article 195101"},"PeriodicalIF":2.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144366089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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