Gene最新文献

{"title":"Matrix metalloproteinases: Master regulators of tissue morphogenesis","authors":"P. Sreesada ,&nbsp;Vandana ,&nbsp;Bhagath Krishnan ,&nbsp;R. Amrutha ,&nbsp;Yash Chavan ,&nbsp;Hasanath Alfia ,&nbsp;Anjali Jyothis ,&nbsp;Parvathy Venugopal,&nbsp;Rajaguru Aradhya,&nbsp;Prashanth Suravajhala,&nbsp;Bipin G. Nair","doi":"10.1016/j.gene.2024.148990","DOIUrl":"10.1016/j.gene.2024.148990","url":null,"abstract":"<div><div>The matrix metalloproteinases (MMPs) are a class of zinc proteases that aid in breaking most of the extracellular matrix’s (ECM) constituents. Additionally, MMPs play a part in processing elements that affect inflammation, cell development and proliferation, and many more. <em>In vivo</em> genetic study of the Drosophila MMPs Mmp1 and Mmp2 reveals they are essential for tissue remodeling but not embryonic development. The canonical and conserved MMP domain organization is present in both fly MMPs. Because Mmp2 appeared to be membrane-anchored and Mmp1 appeared to be released, the pericellular localization of Drosophila MMPs has been used to classify them. This suggests that the protein’s localization is the critical distinction in this small MMP family. The signal sequence, the propeptide, the catalytic domain, and the hemopexin-like domain are among the numerous domains found in MMPs. Following secretion from the extracellular environment to the endoplasmic reticulum, the pre-domain, also known as the signal sequence, serves to direct MMP production. MMPs of the secretory and membrane types (MT-MMPs) are two groups of MMPs that have been widely recognized. Subgroups of MMPs are categorized based on their structure and function. While analysis of the intracellular activity of human MMPs is challenging because the human genome contains around 23 distinct MMPs with overlapping functions, only two MMPs, dMMP1 and dMMP2, are encoded by the <em>Drosophila melanogaster</em> genome. On the other hand, the balance between MMPs and the family members are implicated in various pathophysiology/progression of diseases, but whether or not the mechanisms of MMP inhibition are not clearly understood as master regulators. In this review, we outline the role of MMPs as master regulators of tissue morphogenesis.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142406318","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":"Molecular characterization of PANoptosis-related genes as novel signatures for peripheral nerve injury based on time-series transcriptome sequencing","authors":"Yuan Dai ,&nbsp;Minghao Shao ,&nbsp;Linli Li ,&nbsp;Hailong Li ,&nbsp;Tingwei Lu ,&nbsp;Feizhou Lyu","doi":"10.1016/j.gene.2024.148995","DOIUrl":"10.1016/j.gene.2024.148995","url":null,"abstract":"<div><div>Programmed cell death (PCD) pathways play pivotal roles in the development and progression of peripheral nerve injury (PNI). PANoptosis, as a novel form of PCD pathway with key features of pyroptosis, apoptosis and necroptosis, is implicated in the pathogenesis of multiple neurologic diseases. This study aimed to identify PANoptosisrelated biomarkers and characterize their molecular roles and immune landscape in PNI. PANoptosis-related genes (PRGs) were retrieved from Reactome pathway database and previous literatures. Differentially expressed PANoptosis-related genes (DEPRGs) were identified based on a time-series transcriptome sequencing dataset. DEPRGs were predicted to be enriched in inflammatory response, inflammatory complex, PCD and NOD-like receptor signaling pathway through GO, KEGG, Reactome and GSEA analysis. Hub genes, including Ripk3, Pycard and Il18, were then recognized through PPI network and multiple algorithms. The molecular regulatory mechanisms of hub genes were elucidated by transcription factor network and competing endogenous RNA network. Moreover, the immune cell landscape of hub genes was analyzed. Eventually, the expression levels of hub genes were verified through external dataset and animal model. Ripk3, Pycard and Il18 were remarkably upregulated in PNI samples, which were in consistent with the results of bioinformatic analysis. This study uncovered the molecular characterization of PANoptosis-related genes in PNI and illustrated the novel PANoptosis biomarker for PNI.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142406319","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":"Retraction notice to “TRIM59 knockdown blocks cisplatin resistance in A549/DDP cells through regulating PTEN/AKT/HK2” [GENE 747 (2020) 144553]","authors":"Rong He,&nbsp;Hongxu Liu","doi":"10.1016/j.gene.2024.148986","DOIUrl":"10.1016/j.gene.2024.148986","url":null,"abstract":"","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142406320","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":"Identification of SUMOylation-related signature genes associated with immune infiltration in ulcerative colitis through bioinformatics analysis and experimental validation","authors":"Ying Long ,&nbsp;Feihong Huang ,&nbsp;Juan Zhang ,&nbsp;Jinxiu Zhang ,&nbsp;Ruoxi Cheng ,&nbsp;Liye Zhu ,&nbsp;Qiuling Chen ,&nbsp;Dan Yang ,&nbsp;Xiaoping Pan ,&nbsp;Wenfang Yang ,&nbsp;Mengbin Qin ,&nbsp;Jiean Huang","doi":"10.1016/j.gene.2024.148996","DOIUrl":"10.1016/j.gene.2024.148996","url":null,"abstract":"<div><h3>Objective</h3><div>Ulcerative colitis (UC) is a chronic inflammatory disorder challenging to diagnose clinically. We focused on identifying and validating SUMOylation-related signature genes in UC and their association with immune infiltration.</div></div><div><h3>Methods</h3><div>Five eligible gene expression profiles were selected from the Gene Expression Omnibus (GEO) database and merged into a single dataset comprising 260 UC patients and 76 healthy controls (HC). Differentially expressed genes (DEGs) were identified, and these were intersected with SUMOylation-related genes to obtain differentially expressed SUMOylation-related genes (DESRGs). Next, we identify the signature genes and validate them through comprehensive analyses employing GO, KEGG, GSVA, Lasso-cox regression, ROC curves, and clustering analysis. The infiltrating immune cells were analyzed using the CIBERSORT algorithm and Pearson correlation analysis. Finally, in vitro and in vivo experiments validated the identified signature genes.</div></div><div><h3>Results</h3><div>PALMD, THRB, MAGED1, PARP1, and SLC16A1 were identified. Next, an excellent predictive model for UC was established and distinct subgroups of patients associated with SUMOylation were identified. Moreover, the NF-κB signaling pathway likely plays a pivotal role in the regulation of SUMOylation in UC. Additionally, we validated that the alterations in PALMD, THRB, and MAGED1 expression in LPS-induced Caco-2 cells concurred with our bioinformatics findings, particularly demonstrating statistically significant differences in PALMD and THRB expression. Finally, in a DSS-induced mouse colitis model, we observed a significant upregulation of PALMD expression. <em>Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation.</em></div></div><div><h3>Conclusion</h3><div>This study comprehensively elucidates the biological roles of SUMOylation-related genes in UC, identifying PALMD, MAGED1, THRB, PARP1, and SLC16A1 as signature genes that represent promising biomarkers for UC diagnosis and prognosis.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142462441","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":"Host repair polymorphisms and H. pylori genes in gastric disease outcomes: Who are the guardian and villains?","authors":"Morgana Maria de Oliveira Barboza ,&nbsp;Reginaldo Ferreira da Costa ,&nbsp;João Paulo Por Deus Gomes ,&nbsp;Rommel Mário Rodríguez Burbano ,&nbsp;Paulo Goberlânio de Barros Silva ,&nbsp;Silvia Helena Barem Rabenhorst","doi":"10.1016/j.gene.2024.148977","DOIUrl":"10.1016/j.gene.2024.148977","url":null,"abstract":"<div><div>Gastric cancer (GC) is the fourth-leading cause of cancer-related mortality. The intestinal subtype of GC comes after the <em>cascade of Correa</em>, presenting <em>H. pylori</em> infection as the major etiological factor. One of the main mechanisms proposed for the progression from a more benign gastric lesion to cancer is DNA damage caused by chronic inflammation. Polymorphisms in DNA repair genes can lead to an imbalance of host DNA damage and repair, contributing to the development of GC. From there, we evaluated the risk of polymorphisms in DNA repair system genes in progressive gastric diseases and their association with the <em>H. pylori</em> genotype. This study included 504 patients from two public hospitals in Brazil’s north and northeast regions. The samples were classified into active and inactive gastritis, metaplasia, and GC. Polymorphisms in the DNA repair genes <em>MLH1</em>-93G &gt; A, <em>APE1</em> 2197 T &gt; G, <em>XRCC1</em> 28,152 G &gt; A, <em>MGMT</em> 533 A &gt; G, and <em>XRCC3</em> 18,067C &gt; T were investigated by RFLP-PCR and <em>H. pylori</em> genotype by PCR. Statistical analyses were conducted using EPINFO 7.0., SNPSTAT, and CART software. The <em>XRCC1</em> (GA) polymorphic allele stood out because it was associated with a lower risk of more severe gastric disease progression. Haplotypes of <em>XRCC1</em> (GA) associated with some genotypes of <em>MGMT</em>, <em>XRCC3</em>, <em>MLH1</em>, and <em>APE1</em> also showed protection against the progression of gastric diseases. <em>XRCC3</em> (CT) showed a decreased risk of gastric disease progression in women, while a risk 1.3x to GC was observed in the <em>MLH1</em> (A) polymorphic allele. The interaction between <em>H. pylori</em> genes and the host showed that the <em>H. pylori cagE</em> gene was the most important virulence factor associated with a worse clinical outcome, even overlapping with the <em>XRCC1</em> polymorphism, where the <em>MLH1</em> polymorphism response varied according to <em>vacA</em> alleles. Our results show the relevance of <em>XRCC1</em> G &gt; A for genome integrity, sex influence, and interaction between <em>H. pylori</em> virulence factors and <em>XRCC1</em> and <em>MLH1</em> genotypes for gastric lesion outcomes in Brazilian populations.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142400003","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":"Uncovering the effects of non-lethal oxidative stress on replication initiation in Escherichia coli","authors":"Jiaxin Qiao ,&nbsp;Dongdong Du ,&nbsp;Yao Wang ,&nbsp;Lingjun Xi ,&nbsp;Weiwei Zhu ,&nbsp;Morigen","doi":"10.1016/j.gene.2024.148992","DOIUrl":"10.1016/j.gene.2024.148992","url":null,"abstract":"<div><div>Cell cycle adaptability assists bacteria in response to adverse stress. The effect of oxidative stress on replication initiation in <em>Escherichia coli</em> remains unclear. This work examined the impact of exogenous oxidant and genetic mutation-mediated oxidative stress on replication initiation. We found that 0–0.5 mM H₂O₂ suppresses <em>E. coli</em> replication initiation in a concentration-dependent manner but does not lead to cell death. Deletion of antioxidant enzymes SodA-SodB, KatE, or AhpC results in delayed replication initiation. The antioxidant N-acetylcysteine (NAC) promotes replication initiation in Δ<em>katE</em> and Δ<em>sodA</em>Δ<em>sodB</em> mutants. We then explored the factors that mediate the inhibition of replication initiation by oxidative stress. MutY, a base excision repair DNA glycosylase, resists inhibition of replication initiation by H₂O₂. Lon protease deficiency eliminates inhibition of replication initiation mediated by exogenous H₂O₂ exposure but not by <em>katE</em> or <em>sodA</em>-<em>sodB</em> deletion. The absence of <em>clpP</em> and <em>hslV</em> further delays replication initiation in the Δ<em>ktaE</em> mutant, whereas <em>hflK</em> deletion promotes replication initiation in the Δ<em>katE</em> and Δ<em>sodA</em>Δ<em>sodB</em> mutants. In conclusion, non-lethal oxidative stress inhibits replication initiation, and AAA+ proteases are involved and show flexible regulation in <em>E. coli</em>.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142400005","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":"Effects of Carrier’s sex on the outcome of embryos and pregnancies in 412 couples undergoing preimplantation genetic testing for structural rearrangements","authors":"Hu Tan,&nbsp;Qianwen Huang,&nbsp;Dun Liu,&nbsp;Li Huang,&nbsp;Chuangqi Chen,&nbsp;Fang Wang,&nbsp;Mei Dong,&nbsp;Huinan Weng,&nbsp;Xiulan Zhu,&nbsp;Xiqian Zhang,&nbsp;Fenghua Liu","doi":"10.1016/j.gene.2024.148989","DOIUrl":"10.1016/j.gene.2024.148989","url":null,"abstract":"<div><h3>Study design</h3><div>To ascertain whether the carrier’s sex affects the outcome of embryos and pregnancies in couples undergoing preimplantation genetic testing for structural rearrangements (PGT-SR).</div></div><div><h3>Methods</h3><div>This retrospective study comprised 412 couples with reciprocal translocations (RecT), Robertsonian translocations (RobT), or inversions (INV) between January 2017 and October 2022. We applied next-generation sequencing (NGS) on 2588 embryos after trophectoderm (TE) biopsy.</div></div><div><h3>Results</h3><div>Genetically transferable blastocyst rate was higher in the male carrier group (34.0 % vs 31.7 %, <em>P</em> = 0.013) relative to the female carrier group whereas other embryo and pregnancy outcomes remained similar. Further analysis revealed that this result was primarily due to the alteration of segregation patterns in the RobT subgroup, in which the proportion of alternate segregation was higher (84.3 % vs 66.4 %, <em>P</em> &lt; 0.001) in male carriers compared with female carriers. In the RecT subgroup, the genetically transferable blastocyst rate between male and female carriers was similar although the segregation models also changed, such that the frequency of the adjacent-1 segregation pattern was higher in male carriers than in female carriers (42.5 % vs 34.7 %, <em>P</em> = 0.002). In addition, interchromosomal effect (ICE) did not differ between male and female carriers although ICE was lower in male carriers of the RobT subgroup (pure ICE: 35.50 % vs 44.30 %, <em>P</em> = 0.14; total ICE: 35.50 % vs 40.30 %, <em>P</em> = 0.32) and higher in male carriers of the INV subgroup (pure ICE: 42.3 % vs 37.20 %, <em>P</em> = 0.33; total ICE: 40.90 % vs 36.00 %, <em>P</em> = 0.36).</div></div><div><h3>Conclusions</h3><div>The carrier’s sex was closely associated with the genetically transferable embryo rate in couples undergoing PGT-SR, principally resulted from the change in segregation pattern in the RobT subgroup but not in the RecT and INV subgroups.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389544","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":"Evidence for high-risk pollutants and emerging microbial contaminants at two major bathing ghats of the river Ganga using high-resolution mass spectrometry and metagenomics","authors":"Durgesh Narain Singh ,&nbsp;Parul Pandey ,&nbsp;Vijay Shankar Singh ,&nbsp;Anil Kumar Tripathi","doi":"10.1016/j.gene.2024.148991","DOIUrl":"10.1016/j.gene.2024.148991","url":null,"abstract":"<div><div>An efficient wastewater treatment plant is imperative to limit the entry of emerging pollutants (EPs) and emerging microbial contaminants (EMCs) in the river ecosystem. The detection of emerging EPs in aquatic environments is challenging due to complex sample preparation methods, and the need for sophisticated accurate analytical tools. In Varanasi (India), the river Ganga holds immense significance as a holy river but is consistently polluted with municipal (MWW) and hospital wastewater (HWW). We developed an efficient method for untargeted detection of EPs in the water samples using High-resolution mass spectrometry (HRMS), and identified 577 and 670 chemicals (or chemical components) in the water samples from two major bathing ghats, Assi Ghat (AG) and Dashashwamedh Ghat (DG), respectively. The presence of EPs of different categories <em>viz</em> chemicals from research labs, diagnostic labs, lifestyle and industrial chemicals, toxins, flavor and food additives indicated the unsafe disposal of MWW and HWW or inefficient wastewater treatment plants (WWTPs). Besides, shotgun metagenomic analysis depicted the presence of bacteria associated with MWW <em>viz Cloacibacterium normanse</em>, <em>Sphaerotilus natans</em> (sewage fungi), <em>E. coli</em>, and <em>Prevotella.</em> Also, the presence of human pathogens <em>Arcobacter</em>, <em>Polynucleobacter</em>, <em>Pseudomonas</em>, <em>Klebsiella</em>, <em>Aeromonas</em>, <em>Acinetobacter</em>, <em>Vibrio</em>, and <em>Campylobacter</em> suggests the discharge of HWW. EPs are linked to the development, and transmission of antimicrobial resistance (AMR). Occurrence of antibiotic resistance genes (ARGs), plasmid-borne β-lactamases, aminoglycoside transferases, and ARGs associated with integrons, transposons and plasmids <em>viz mcr</em>-3 gene that confer resistance to colistin, the last resort of antibiotics confirmed the presence of emerging microbial contaminants. Subsequent genome reconstruction studies showed the presence of uncultivable ARB and transmission of ARGs through horizontal gene transfer. This study can be used to monitor the health of aquatic bodies as well as the efficiency of WWTPs and raise an urgent need for efficient WWTPs to safeguard the river, Ganga.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142400002","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 expression and function of Gpnmb in lymphatic endothelial cells.","authors":"Trinity A Kronk, Ernesto Solorzano, Gabrielle T Robinson, Joshua Castor, Hope C Ball, Fayez F Safadi","doi":"10.1016/j.gene.2024.148993","DOIUrl":"https://doi.org/10.1016/j.gene.2024.148993","url":null,"abstract":"<p><p>The lymphatic system functions in fluid homeostasis, lipid absorption and the modulation of the immune response. The role of Gpnmb (osteoactivin), an established osteoinductive molecule with newly identified anti-inflammatory properties, has not been studied in lymphangiogenesis. Here, we demonstrate that Gpnmb increases lymphatic endothelial cell (LEC) migration and lymphangiogenesis marker gene expression in vitro by enhancing pro-autophagic gene expression, while no changes were observed in cell proliferation or viability. In addition, cellular spreading and cytoskeletal reorganization was not altered following Gpnmb treatment. We show that systemic Gpnmb overexpression in vivo leads to increases in lymphatic tubule number per area. Overall, data presented in this study suggest Gpnmb is a positive modulator of lymphangiogenesis.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142400004","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":"Syntenic lncRNA locus exhibits DNA regulatory functions with sequence evolution","authors":"Gyan Ranjan ,&nbsp;Vinod Scaria ,&nbsp;Sridhar Sivasubbu","doi":"10.1016/j.gene.2024.148988","DOIUrl":"10.1016/j.gene.2024.148988","url":null,"abstract":"<div><div>Syntenic long non-coding RNAs (lncRNAs) often show limited sequence conservation across species, prompting concern in the field. This study delves into functional signatures of syntenic lncRNAs between humans and zebrafish. Syntenic lncRNAs are highly expressed in zebrafish, with ∼90 % located near protein-coding genes, either in sense or antisense orientation. During early zebrafish development and in human embryonic stem cells (H1-hESC), syntenic lncRNA loci are enriched with <em>cis</em>-regulatory repressor signatures, influencing the expression of development-associated genes. In later zebrafish developmental stages and specific human cell lines, these syntenic lncRNA loci function as enhancers or transcription start sites (TSS) for protein-coding genes. Analysis of transposable elements (TEs) in syntenic lncRNA sequences revealed intriguing patterns: human lncRNAs are enriched in simple repeat elements, while their zebrafish counterparts show enrichment in LTR elements. This sequence evolution likely arises from post-rearrangement mutations that enhance DNA elements or <em>cis</em>-regulatory functions. It may also contribute to vertebrate innovation by creating novel transcription factor binding sites within the locus. This study highlights the conserved functionality of syntenic lncRNA loci through DNA elements, emphasizing their conserved roles across species despite sequence divergence.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389546","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}