Biochimica et Biophysica Acta-Gene Regulatory Mechanisms最新文献

{"title":"Damaged collagen detected by collagen hybridizing peptide as efficient diagnosis marker for early hepatic fibrosis","authors":"Ping Tao ,&nbsp;Jinfang Liu ,&nbsp;Yuan Li ,&nbsp;Tao Zhang ,&nbsp;Fangzhou Wang ,&nbsp;Lei Chang ,&nbsp;Chonghui Li ,&nbsp;Xinlan Ge ,&nbsp;Tao Zuo ,&nbsp;Shichun Lu ,&nbsp;Yuanyuan Ruan ,&nbsp;Zhimin Yang ,&nbsp;Ping Xu","doi":"10.1016/j.bbagrm.2023.194928","DOIUrl":"10.1016/j.bbagrm.2023.194928","url":null,"abstract":"<div><p>Liver fibrosis is characterized by excessive synthesis and deposition of extracellular matrix (ECM) in liver tissues. However, it still has been lacking of early detection and diagnosis methods. The collagen hybridizing peptide (CHP) is a novel synthetic peptide that enables detection of collagen damage and tissue remodeling. Here, we showed that obvious CHP-positive staining could be detected in the liver while given CCl₄ for only 3 days, which was significantly enhanced while given CCl₄ for 7 days. However, H&amp;E staining showed no significant changes in fibrous tissue, and sirius red-positive staining could only be observed while given CCl₄<span> for 14 days. Moreover, CHP-positive staining enhanced initially at portal area which further extended into the hepatic lobule, which was increased more significantly than sirius red-positive staining in the model of 10 and 14 days. Further proteomic<span><span><span> analysis of CHP-positive staining revealed that pathways associated with ECM remodeling were significantly increased, while retinol metabolism was downregulated. Meanwhile, proteins enriched in cellular </span>gene transcription and </span>signal transduction<span> involved in fibrogenesis were also upregulated, suggesting that fibrosis occurred in CHP-positive staining. Our study provided evidence that CHP could detect the collagen damage in liver, which might be an efficient indicator for the diagnosis of liver fibrosis at a very early stage.</span></span></span></p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194928"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9536210","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}

{"title":"METTL3 activates PERK-eIF2α dependent coelomocyte apoptosis by targeting the endoplasmic reticulum degradation-related protein SEL1L in echinoderms","authors":"Dongdong Li ,&nbsp;Ming Guo ,&nbsp;Zhimeng Lv ,&nbsp;Yina Shao ,&nbsp;Weikang Liang ,&nbsp;Chenghua Li","doi":"10.1016/j.bbagrm.2023.194927","DOIUrl":"10.1016/j.bbagrm.2023.194927","url":null,"abstract":"<div><p><span>N6-methyladenosine (m6A) plays an important role in regulating many physiological and disease processes in vertebrates, in which methyltransferase-like 3 (METTL3) is the best-known m6A methyltransferase. However, the functional roles of invertebrate METTL3 have not yet been highlighted. In this study, we found that METTL3 from </span><span><em>Apostichopus japonicus</em></span> (AjMETTL3) was significantly induced in coelomocytes accompanied by higher levels of m6A modification in response to <span><em>Vibrio splendidus</em></span> challenge. Overexpression or silencing of <em>AjMETTL3</em> in coelomocytes increased or decreased the m6A levels and promoted or inhibited <em>V. splendidus</em><span>-induced coelomocyte apoptosis, respectively. To further explore the molecular mechanism of AjMETTL3-mediated coelomic immunity, m6A-seq analysis revealed that the endoplasmic reticulum-related degradation (ERAD) pathway was significantly enriched, in which suppressor/enhancer of Lin-12-like (</span><em>AjSEL1L)</em> was suggested to be a target of AjMETTL3 in a negative regulatory manner. Functional analysis revealed that the increased AjMETTL3 reduced the stability of <em>AjSEL1L</em> mRNA by targeting the m6A modification site of 2004 bp-GGACA-2008 bp. The decreased AjSEL1L was further confirmed to be involved in AjMETTL3-mediated coelomocyte apoptosis. Mechanistically, the inhibited <em>AjSEL1L</em><span> increased the transcription of AjOS9 and Ajp97 in the EARD pathway to promote ubiquitin protein accumulation and ER stress, which further activated AjPERK-AjeIF2α pathway dependent coelomocyte apoptosis, but not the AjIRE1 or AjATF6 pathway. Taken together, our results supported invertebrate METTL3-mediated coelomocyte apoptosis by regulating the PERK-eIF2α pathway.</span></p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194927"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9543957","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}

{"title":"Formation of aggresomes with hydrogel-like characteristics by proteasome inhibition","authors":"Seo Hyeong Park ,&nbsp;Sang-Eun Lee ,&nbsp;Jun Hyoung Jeon ,&nbsp;Jung Hoon Lee ,&nbsp;Eisuke Itakura ,&nbsp;Sunghoe Chang ,&nbsp;Won Hoon Choi ,&nbsp;Min Jae Lee","doi":"10.1016/j.bbagrm.2023.194932","DOIUrl":"10.1016/j.bbagrm.2023.194932","url":null,"abstract":"<div><p><span><span>The spatiotemporal sequestration of misfolded proteins is a mechanism by which cells counterbalance proteome </span>homeostasis<span> upon exposure to various stress stimuli. Chronic inhibition of proteasomes results in a large, juxtanuclear, membrane-less inclusion, known as the </span></span>aggresome<span>. Although the molecular mechanisms driving its formation, clearance, and pathophysiological implications are continuously being uncovered, the biophysical aspects of aggresomes remain largely uncharacterized. Using fluorescence recovery after photobleaching and liquid droplet disruption assays, we found that the aggresomes are a homogeneously blended condensates with liquid-like properties similar to droplets formed via liquid–liquid phase separation. However, unlike fluidic liquid droplets, aggresomes have more viscosity and hydrogel-like characteristics. We also observed that the inhibition of aggresome formation using microtubule-disrupting agents resulted in less soluble and smaller cytoplasmic speckles, which was associated with marked cytotoxicity. Therefore, the aggresome appears to be cytoprotective and serves as a temporal reservoir for dysfunctional proteasomes and substrates that need to be degraded. Our results suggest that the aggresome assembles through distinct and potentially sequential processes of energy-dependent retrograde transportation and spontaneous condensation into a hydrogel.</span></p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194932"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9914451","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}

{"title":"Iron restriction increases the expression of a cytotoxic cysteine proteinase TvCP2 by a novel mechanism of tvcp2 mRNA alternative polyadenylation in Trichomonas vaginalis","authors":"Luis Alberto Rivera-Rivas,&nbsp;Rossana Arroyo","doi":"10.1016/j.bbagrm.2023.194935","DOIUrl":"10.1016/j.bbagrm.2023.194935","url":null,"abstract":"<div><p><span><em>Trichomonas vaginalis</em></span><span> TvCP2 (TVAG_057000) is a cytotoxic cysteine proteinase (CP) expressed under iron-limited conditions. This work aimed to identify one of the mechanisms of </span><em>tvcp2</em><span> gene expression regulation by iron at the posttranscriptional level. We checked </span><em>tvcp2</em><span> mRNA stability under both iron-restricted (IR) and high iron (HI) conditions in the presence of actinomycin D. Greater stability of the </span><em>tvcp2</em> mRNA under the IR than in HI conditions was observed, as expected. <em>In silico</em><span> analysis of the 3′ regulatory region showed the presence of two putative polyadenylation signals in the </span><em>tvcp2</em><span> transcript. By 3′-RACE assays, we demonstrated the existence of two isoforms of the </span><em>tvcp2</em><span> mRNA with different 3′-UTR that resulted in more TvCP2 protein under IR than in HI conditions detected by WB<span> assays. Additionally, we searched for homologs of the trichomonad polyadenylation machinery by an </span></span><em>in silico</em> analysis in the genome database, TrichDB. 16 genes that encode proteins that could be part of the trichomonad polyadenylation machinery were found. qRT-PCR assays showed that most of these genes were positively regulated by iron. Thus, our results show the presence of alternative polyadenylation as a novel iron posttranscriptional regulatory mechanism in <em>T. vaginalis</em> for the <em>tvcp2</em> gene expression.</p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194935"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9914455","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}

{"title":"The N-degron pathway: From basic science to therapeutic applications","authors":"Ah Jung Heo ,&nbsp;Su Bin Kim ,&nbsp;Yong Tae Kwon ,&nbsp;Chang Hoon Ji","doi":"10.1016/j.bbagrm.2023.194934","DOIUrl":"10.1016/j.bbagrm.2023.194934","url":null,"abstract":"<div><p><span><span>The N-degron pathway is a degradative system in which single N-terminal (Nt) amino acids regulate the half-lives of proteins and other biological materials. These determinants, called N-degrons, are recognized by N-recognins that link them to the ubiquitin (Ub)-proteasome system (UPS) or autophagy-lysosome system (ALS). In the UPS, the Arg/N-degron pathway targets the Nt-arginine (Nt-Arg) and other N-degrons to assemble Lys48 (K48)-linked Ub chains by UBR box N-recognins for proteasomal </span>proteolysis. In the ALS, Arg/N-degrons are recognized by the N-recognin p62/SQSTSM-1/Sequestosome-1 to induce </span><em>cis</em>-degradation of substrates and <em>trans</em>-degradation of various cargoes such as protein aggregates and subcellular organelles. This crosstalk between the UPS and ALP involves reprogramming of the Ub code. Eukaryotic cells developed diverse ways to target all 20 principal amino acids for degradation. Here we discuss the components, regulation, and functions of the N-degron pathways, with an emphasis on the basic mechanisms and therapeutic applications of Arg/N-degrons and N-recognins.</p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194934"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9536217","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}

{"title":"Post-translational regulation of proto-oncogene ZBTB7A expression by p53 status in cancer cells: HSP90-dependent stabilization vs. p53-KLHL20-ubiquitin proteasomal degradation","authors":"Seo-Hyun Choi,&nbsp;Su-Yeon Cho,&nbsp;Sun Young Park,&nbsp;Man-Wook Hur","doi":"10.1016/j.bbagrm.2023.194931","DOIUrl":"10.1016/j.bbagrm.2023.194931","url":null,"abstract":"<div><p><span><span>ZBTB7A overexpressed in many human cancers is a major oncogenic driver. ZBTB7A promotes tumorigenesis by regulating transcription of the genes involved in cell survival and proliferation, apoptosis, invasion, and migration/metastasis. One unresolved issue is the mechanism underlying the aberrant overexpression of ZBTB7A in cancer cells. Interestingly, inhibition of HSP90 decreased ZBTB7A expression in a variety of human cancer cells. ZBTB7A interacts with and is stabilized by HSP90. Inhibition of HSP90 by 17-AAG resulted in p53-dependent </span>proteolysis<span> of ZBTB7A via increased p53 expression and upregulation of the CUL3-dependent E3 ubiquitin ligase<span>, KLHL20. Down-regulation of ZBTB7A resulted in the derepression of a major negative regulator of cell cycle progression, </span></span></span><em>p21/CDKN1A</em>. We discovered a new function of p53 regulating ZBTB7A expression through KLHL20-E3 ligase and proteasomal protein degradation system.</p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194931"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9559349","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}

{"title":"Rho-dependent transcription termination is the dominant mechanism in Mycobacterium tuberculosis","authors":"Ezaz Ahmad ,&nbsp;Anirban Mitra ,&nbsp;Wareed Ahmed ,&nbsp;Varsha Mahapatra ,&nbsp;Shubhada R. Hegde ,&nbsp;Claudia Sala ,&nbsp;Stewart T. Cole ,&nbsp;Valakunja Nagaraja","doi":"10.1016/j.bbagrm.2023.194923","DOIUrl":"10.1016/j.bbagrm.2023.194923","url":null,"abstract":"<div><p><span><span>Intrinsic and Rho-dependent transcription termination mechanisms regulate gene expression and recycle </span>RNA polymerase in bacteria. Both the modes are well studied in </span><em>Escherichia coli</em><span>, and a few other organisms. The understanding of Rho function is limited in most other bacteria including mycobacteria. Here, we highlight the dominance of Rho-dependent termination in mycobacteria and validate Rho as a key regulatory factor. The lower abundance of intrinsic terminators, high cellular levels of Rho, and its genome-wide association with a majority of transcriptionally active genes indicate the pronounced role of Rho-mediated termination in </span><span><em>Mycobacterium tuberculosis</em></span> (<em>Mtb</em><span>). Rho modulates the termination of RNA synthesis<span> for both protein-coding and stable RNA genes in </span></span><em>Mtb</em><span><span>. Concordantly, the depletion of Rho in mycobacteria impact its growth and enhances the transcription read-through at 3′ ends of the transcription units. We demonstrate that MtbRho is catalytically active in the presence of RNA with varied secondary structures. These properties suggest an evolutionary adaptation of Rho as the efficient and preponderant mode </span>of transcription termination in mycobacteria.</span></p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194923"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9897408","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}

{"title":"“MiR-7 controls cholesterol biosynthesis through posttranscriptional regulation of DHCR24 expression”","authors":"Mario Fernández-de Frutos ,&nbsp;Virginia Pardo-Marqués ,&nbsp;Marta Torrecilla-Parra ,&nbsp;Patricia Rada ,&nbsp;Ana Pérez-García ,&nbsp;Yolanda Martín-Martín ,&nbsp;Gema de la Peña ,&nbsp;Ana Gómez ,&nbsp;Ana Toledano-Zaragoza ,&nbsp;Diego Gómez-Coronado ,&nbsp;María José Casarejos ,&nbsp;José M. Solís ,&nbsp;Noemí Rotllan ,&nbsp;Óscar Pastor ,&nbsp;María Dolores Ledesma ,&nbsp;Ángela M. Valverde ,&nbsp;Rebeca Busto ,&nbsp;Cristina M. Ramírez","doi":"10.1016/j.bbagrm.2023.194938","DOIUrl":"10.1016/j.bbagrm.2023.194938","url":null,"abstract":"<div><p><span><span><span><span>Dysregulation of cholesterol homeostasis is associated with several pathologies including cardiovascular diseases and neurological disorders such as Alzheimer's disease (AD). </span>MicroRNAs<span> (miRNAs) have emerged as key post-transcriptional regulators of cholesterol metabolism. We previously established the role of miR-7 in regulating insulin resistance and </span></span>amyloidosis, which represents a common pathological feature between type 2 diabetes and AD. We show here an additional metabolic function of miR-7 in </span>cholesterol biosynthesis<span>. We found that miR-7 blocks the last steps of the cholesterol biosynthetic pathway </span></span><em>in vitro</em> by targeting relevant genes including DHCR24 and SC5D posttranscriptionally. Intracranial infusion of miR-7 on an adeno-associated viral vector reduced the expression of DHCR24 in the brain of wild-type mice, supporting <em>in vivo</em> miR-7 targeting. We also found that cholesterol regulates endogenous levels of miR-7 <em>in vitro</em><span>, correlating with transcriptional regulation through SREBP2 binding to its promoter region. In parallel to SREBP2 inhibition, the levels of miR-7 and hnRNPK (the host gene of miR-7) were concomitantly reduced in brain in a mouse model of Niemann Pick type C1 disease and in murine fatty liver, which are both characterized by intracellular cholesterol accumulation. Taken together, the results establish a novel regulatory feedback loop by which miR-7 modulates cholesterol homeostasis at the posttranscriptional level, an effect that could be exploited for therapeutic interventions against prevalent human diseases.</span></p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194938"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9898423","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}

{"title":"RelB represses miR-193a-5p expression to promote the phenotypic transformation of vascular smooth muscle cells in aortic aneurysm","authors":"Yisi Liu ,&nbsp;Xiaoxiang Tian ,&nbsp;Dan Liu ,&nbsp;Xiaolin Zhang ,&nbsp;Chenghui Yan ,&nbsp;Yaling Han","doi":"10.1016/j.bbagrm.2023.194926","DOIUrl":"10.1016/j.bbagrm.2023.194926","url":null,"abstract":"<div><p>Aortic aneurysm (AA) is a potentially fatal disease with the possibility of rupture, causing high mortality rates with no effective drugs for the treatment of AA. The mechanism of AA, as well as its therapeutic potential to inhibit aneurysm expansion, has been minimally explored. Small non-coding RNA (miRNAs and miRs) is emerging as a new fundamental regulator of gene expression. This study aimed to explore the role and mechanism of miR-193a-5p in abdominal aortic aneurysms (AAA). In AAA vascular tissue and Angiotensin II (Ang II)-treated vascular smooth muscle cells (VSMCs), the expression of miR-193a-5 was determined using real-time quantitative PCR (RT-qPCR). Western blotting was used to detect the effects of miR-193a-5p on PCNA, CCND1, CCNE1, and CXCR4. To detect the effect of miR-193a-5p on the proliferation and migration of VSMCs, CCK-8, and EdU immunostaining, flow cytometry, wound healing, and Transwell Chamber analysis were performed. In vitro results suggest that overexpression of miR-193a-5p inhibited the proliferation and migration of VSMCs, and its inhibition aggravated their proliferation and migration. In VSMCs, miR-193a-5p mediated proliferation by regulating CCNE1 and CCND1 genes and migration by regulating CXCR4. Further, in the Ang II-induced abdominal aorta of mice, the expression of miR-193a-5p was reduced and significantly downregulated in the serum of patients with aortic aneurysm (AA). In vitro studies confirmed that Ang II-induced downregulation of miR-193a-5p in VSMCs by upregulation of the expression of the transcriptional repressor RelB in the promoter region. This study may provide new intervention targets for the prevention and treatment of AA.</p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194926"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9913915","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}

{"title":"PKI: A bioinformatics method of quantifying the importance of nodes in gene regulatory network via a pseudo knockout index","authors":"Yijuan Wang ,&nbsp;Chao Liu ,&nbsp;Xu Qiao ,&nbsp;Xianhua Han ,&nbsp;Zhi-Ping Liu","doi":"10.1016/j.bbagrm.2023.194911","DOIUrl":"10.1016/j.bbagrm.2023.194911","url":null,"abstract":"<div><h3>Background</h3><p>Gene regulatory network<span> (GRN) is a model that characterizes the complex relationships between genes and thereby provides an informatics environment to measure the importance of nodes. The evaluation of important nodes in a GRN can effectively refer to their functional implications severing as key players in particular biological processes<span>, such as master regulator and driver gene. Currently, it is mainly based on network topological parameters and focuses only on evaluating a single node individually. However, genes and products play their functions by interacting with each other. It is worth noting that the effects of gene combinations in GRN are not simply additive. Key combinations discovery is of significance in revealing gene sets with important functions. Recently, with the development of single-cell RNA-sequencing (scRNA-seq) technology, we can quantify gene expression profiles of individual cells that provide the potential to identify crucial nodes in gene regulations regarding specific condition, e.g., stem cell differentiation.</span></span></p></div><div><h3>Results</h3><p><span>In this paper, we propose a bioinformatics method, called Pseudo Knockout Importance (PKI), to quantify the importance of node and node sets in a specific GRN structure using time-course scRNA-seq data. First, we construct ordinary differential equations to approach the gene regulations during cell differentiation. Then we design gene pseudo knockout experiments and define PKI score evaluation criteria based on the coefficient of determination. The importance of nodes can be described as the influence on the ODE system of removing variables. For key gene combinations, PKI is derived as a combinatorial optimization problem of quantifying the </span><em>in silico</em><span> gene knockout effects.</span></p></div><div><h3>Conclusions</h3><p><span>Here, we focus our analyses on the specific GRN of embryonic stem cells with time series gene expression profile. To verify the effectiveness and advantage of PKI method, we compare its node importance rankings with other twelve kinds of centrality-based methods, such as degree and Latora closeness. For key node combinations, we compare the results with the method based on minimum dominant set. Moreover, the famous combinations of transcription factors in </span>induced pluripotent stem cell are also employed to verify the vital gene combinations identified by PKI. These results demonstrate the reliability and superiority of the proposed method.</p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194911"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9541644","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}