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The regulatory interplay between miRNA and DNA methylation orchestrates vital ovarian functions and associated traits in PCOS. miRNA 和 DNA 甲基化之间的调控相互作用协调着多囊卵巢综合征的重要卵巢功能和相关特征。
IF 2.6 3区 生物学
Gene Pub Date : 2024-12-14 DOI: 10.1016/j.gene.2024.149165
Snehal Bhingardeve, Pooja Sagvekar, Sadhana Desai, Vijay Mangoli, Richa Jagtap, Srabani Mukherjee
{"title":"The regulatory interplay between miRNA and DNA methylation orchestrates vital ovarian functions and associated traits in PCOS.","authors":"Snehal Bhingardeve, Pooja Sagvekar, Sadhana Desai, Vijay Mangoli, Richa Jagtap, Srabani Mukherjee","doi":"10.1016/j.gene.2024.149165","DOIUrl":"https://doi.org/10.1016/j.gene.2024.149165","url":null,"abstract":"<p><p>Polycystic ovary syndrome (PCOS) is the leading cause of amenorrhea and anovulatory infertility in women of reproductive age. Both gene polymorphisms and tissue-specific epigenetic alterations, which determine gene transcription and translation dynamics in disease-states, strongly influence PCOS development. Particularly, promoter-proximal DNA methylation and microRNA expression changes show strong associations with follicular defects, suggesting post-transcriptional dysregulation of localized gene networks. Our recent methylome study and other studies, posit DNA methylation as a regulator of microRNA expression in PCOS. Here, we identified microRNAs, potentially regulated by DNA methylation, and investigated whether their altered expression influences target gene expression in the PCOS ovary. Using granulosa cell samples of women with PCOS and age-BMI matched controls, we evaluated the transcript levels of 14 microRNAs participating in different ovarian processes and assessed their CpG-DNA methylation levels. For 9 of these microRNAs, which revealed differential methylation consistent with their gene hypomethylation or hypermethylation profiles, we evaluated the expression of their predicted, proteincoding target transcripts. Our data indicated that microRNA hypermethylation and decreased transcription of miR-10b-5p, miR-127-3p, miR-5189, miR-410-3p and miR23a-3p were consistent with the upregulation of PTEN, MMP13, OLR1, TET3 and APAF1 in PCOS. Conversely, microRNA hypomethylation and increased expression of miR-140-5p, miR-182-3p, miR-200b-5p and miR-3687 were consistent with downregulation of FZD6, LRP6, ZEB1 and LDLR. However, these observations need robust validations in larger study cohorts complemented with functional and mechanistic studies. Overall, our study indicates that altered microRNA expression as a consequence of DNA methylation changes, may contribute to metabolic and reproductive dysfunction in PCOS.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":" ","pages":"149165"},"PeriodicalIF":2.6,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142835158","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
Association of R3HDM1 variants with growth and meat quality traits in Qinchuan cattle and its role in lipid accumulation. R3HDM1变异与秦川牛生长和肉质性状的关系及其在脂质积累中的作用
IF 2.6 3区 生物学
Gene Pub Date : 2024-12-14 DOI: 10.1016/j.gene.2024.149177
Miaoli Wang, Wentao Zhang, Chuang Li, Chenyang Liu, Xiaoping He, Ziyi Zhang, Gong Cheng
{"title":"Association of R3HDM1 variants with growth and meat quality traits in Qinchuan cattle and its role in lipid accumulation.","authors":"Miaoli Wang, Wentao Zhang, Chuang Li, Chenyang Liu, Xiaoping He, Ziyi Zhang, Gong Cheng","doi":"10.1016/j.gene.2024.149177","DOIUrl":"https://doi.org/10.1016/j.gene.2024.149177","url":null,"abstract":"<p><p>The R3H domain containing 1 (R3HDM1) gene has emerged as a candidate influencing residual feed intake and beef yield. Despite this, the genetic variation of R3HDM1 and its effects on beef cattle remain unexplored. This study identified four single nucleotide polymorphisms (SNPs) in the R3HDM1 gene of Qinchuan cattle, with the g.61695680 T > C SNP significantly associated with chest depth and backfat thickness. The g.61695680 T > C synonymous mutation significantly altered the RNA secondary structure and stability of R3HDM1. RNA interference experiments demonstrated that R3HDM1 knockdown reduced adipogenesis and lipid accumulation in bovine preadipocytes by modulating key adipogenic factors such as CEBPβ (P < 0.05), ACCα (P < 0.05), and ATGL (P < 0.01). These findings suggest that the g.61695680 T > C variants within R3HDM1 could serve as valuable molecular markers for selecting improved Qinchuan cattle, thus enhancing genetic selection strategies for beef production.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":" ","pages":"149177"},"PeriodicalIF":2.6,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142835155","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
Cell elongation and altered phytohormone levels play a role in establishing distyly in Averrhoa carambola. 细胞伸长和植物激素水平的改变在 Averrhoa carambola 的雌雄同株中起了作用。
IF 2.6 3区 生物学
Gene Pub Date : 2024-12-14 DOI: 10.1016/j.gene.2024.149167
Wubaiyu Lin, Si Qin, Siyu Chen, Lianhuan Xu, Zirui Yang, Xinyun Lin, Junwen Zhai, Hui Ren, Zehuang Zhang, Shasha Wu
{"title":"Cell elongation and altered phytohormone levels play a role in establishing distyly in Averrhoa carambola.","authors":"Wubaiyu Lin, Si Qin, Siyu Chen, Lianhuan Xu, Zirui Yang, Xinyun Lin, Junwen Zhai, Hui Ren, Zehuang Zhang, Shasha Wu","doi":"10.1016/j.gene.2024.149167","DOIUrl":"https://doi.org/10.1016/j.gene.2024.149167","url":null,"abstract":"<p><p>The flowers of distylous plants exhibit two distinct morphologies that facilitate precise pollen transfer. Averrhoa carambola, a woody plant characterized by distyly, has an unclear molecular regulatory mechanism underlying this trait. Its prolonged flowering period and substantial flower production render it an excellent model for investigating the distylous syndrome. This study aims to elucidate the mechanism of distyly in A. carambola and to identify the regulatory genes. The long-style cultivar 'Daguo Tianyangtao 1' and the short-style cultivar 'Daguo Tianyangtao 3' were selected as models for this investigation. We examined phenotypic characteristics, anatomical structures, and endogenous hormone content associated with distyly. Transcriptomic data were utilized to pinpoint candidate genes involved in the regulation of distyly, followed by a bioinformatics analysis these genes. The results indicate that variations in cell elongation contribute to the differential heights of stigmas and anthers in A. carambola, thereby resulting in the distylous syndrome. Auxins, Gibberellin A3 (GA<sub>3</sub>), Gibberellin A4 (GA<sub>4</sub>), and brassinolide (BL) were found to influence elongation of styles, whereas Gibberellin A1 (GA<sub>1</sub>) and GA<sub>4</sub> affected filament elongation. Transcriptome sequencing analysis identified 34 hormone-related differentially expressed genes (DEGs) and 16 cell development-related DEGs in different morphs of pistils, and 29 hormone-related DEGs and 22 cell development-related DEGs were identified in different morphs of stamens. Four candidate genes-AcaBRU1, AcaPRE1, AcaXTH2, and AcaEXPA11-were found to possess conserved motifs characteristic of their respective families. Consequently, various plant hormones modulate the expression of response genes, leading to differences in elongation of style and filament cells between different flower types of A. carambola, thereby promoting the distylous syndrome. This study provides a theoretical basis for understanding the mechanisms of distyly formation in woody plants.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":" ","pages":"149167"},"PeriodicalIF":2.6,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142835156","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
CARM1-induced lncRNA NEAT1 synchronously activates MYCN and GalNAcT-I to accelerate the progression of neuroblastoma. CARM1诱导的lncRNA NEAT1可同步激活MYCN和GalNAcT-I,从而加速神经母细胞瘤的进展。
IF 2.6 3区 生物学
Gene Pub Date : 2024-12-14 DOI: 10.1016/j.gene.2024.149164
Zhigang Hu, Weili Xu, Huiming Wang, Meng Li, Juan Wang, Chi Sun, Xiaofeng Yang
{"title":"CARM1-induced lncRNA NEAT1 synchronously activates MYCN and GalNAcT-I to accelerate the progression of neuroblastoma.","authors":"Zhigang Hu, Weili Xu, Huiming Wang, Meng Li, Juan Wang, Chi Sun, Xiaofeng Yang","doi":"10.1016/j.gene.2024.149164","DOIUrl":"10.1016/j.gene.2024.149164","url":null,"abstract":"<p><strong>Purpose: </strong>Long non-coding RNAs (lncRNAs) play important roles in progression of neuroblastoma (NB). LncRNA nuclear paraspeckle assembly transcript 1 (NEAT1) has been shown to affect the development of multiple tumors. However, the effect of NEAT1 on NB remain unclear. In this study, the new mechanisms whereby how NEAT1 influences tumor progression in NB was investigated.</p><p><strong>Methods: </strong>RT-qPCR, western blot, bioinformatics, cell growth, Transwell, and flow cytometric analyses were performed to determine how NEAT1 synchronously regulates the miR-873-5p/MYCN proto-oncogene(MYCN) and miR-873-5p/polypeptide N-acetylgalactosaminyltransferase 1(GalNAcT-I) axes to accelerate the progression of NB. NB-bearing animal models were established to evaluate the function of NEAT1 in NB. The relationships between transcription factor coactivatorassociated arginine methyltransferase 1 (CARM1) and NEAT1, NEAT1 and miR-873-5p, miR-873-5p and GalNacT-I or MYCN, were verified using luciferase reporter gene assay, respectively.</p><p><strong>Results: </strong>Our study revealed elevated levels of NEAT1 expression in NB cells and tissues which was associated with an advanced pathological stage and poor prognostic outcomes. According to in vitro gain- and loss- of function experiments, NEAT1 enhances progression of NB. NEAT1 silencing was found to inhibit NB proliferation in vivo. Mechanistically, to achieve upstream regulation, epigenetic downregulation of NEAT1 was achieved via the inhibition of CARM1. NEAT1 was found to positively regulate MYCN and GalNAcT-I levels as a competitive sponge of miR-873-5p.</p><p><strong>Conclusion: </strong>Activity of the lncRNA NEAT1 can be triggered via CARM1, which synchronously promotes NB development via the miR-873-5p/MYCN and miR-873-5p/GalNAcT-I axes. These findings shed light on the novel molecular mechanisms underlying NB progression.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":" ","pages":"149164"},"PeriodicalIF":2.6,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142828040","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
Rapid detection and differentiation of less common non-tuberculous mycobacteria using an in-house line probe assay.
IF 2.6 3区 生物学
Gene Pub Date : 2024-12-13 DOI: 10.1016/j.gene.2024.149163
Nafiseh Izadi, Mojtaba Sankian, Zahra Meshkat, Ehsan Aryan
{"title":"Rapid detection and differentiation of less common non-tuberculous mycobacteria using an in-house line probe assay.","authors":"Nafiseh Izadi, Mojtaba Sankian, Zahra Meshkat, Ehsan Aryan","doi":"10.1016/j.gene.2024.149163","DOIUrl":"10.1016/j.gene.2024.149163","url":null,"abstract":"","PeriodicalId":12499,"journal":{"name":"Gene","volume":" ","pages":"149163"},"PeriodicalIF":2.6,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142828042","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
Evaluation of zma-miR408 and its target genes function on maize (Zea mays) leaf growth response to cold stress by VIGS-based STTM approach. 基于 VIGS 的 STTM 方法评估 zma-miR408 及其靶基因对玉米(Zea mays)叶片生长冷胁迫响应的功能。
IF 2.6 3区 生物学
Gene Pub Date : 2024-12-12 DOI: 10.1016/j.gene.2024.149161
Burak Akgul, Fatma Aydinoglu
{"title":"Evaluation of zma-miR408 and its target genes function on maize (Zea mays) leaf growth response to cold stress by VIGS-based STTM approach.","authors":"Burak Akgul, Fatma Aydinoglu","doi":"10.1016/j.gene.2024.149161","DOIUrl":"10.1016/j.gene.2024.149161","url":null,"abstract":"<p><p>miR408 is a conserved plant miRNA family that is known to regulate genes involved in copper metabolism. However, the function of miR408 in maize leaf growth regulation under cold stress isn't defined. In this study, endogenous maize miR408 was transiently silenced by using virus-induced gene silencing (VIGS) combined with short tandem target mimic (STTM) approaches. To this end, STTM-miR408a/b was designed, synthesized, and applied to maize seedlings. Subsequently, STTM-miR408a/b (STTM) and mock-treated (M) seedlings were subjected to cold stress (C) and the growth response of the seedlings was monitored. Finally, STTM-miR408a/b-treatment successfully downregulated the expression of endogenous mir408a/b and upregulated their putative targets Basic Blue Protein (BBP) and Blue Copper Protein (BCP) antagonistically in the STTM and STTM_C groups compared to M and M_C groups. On the other hand, their putative target Laccase (LAC22) gene was upregulated in the STTM group compared to the M group, but there were no significant expression differences between the M_C and STTM_C groups. The elongation rate of the STTM-miR408a/b-treated second and third leaves was reduced by 10% and 19% resulting in 19% and 11% shortening, respectively. Furthermore, the activity of catalase (CAT) and glutathione reductase (GR) was decreased by 57% in STTM, M_C, and STTM_C, and 29% and 28% in the M_C and STTM_C groups and ascorbate peroxidase (APX) was increased by 15% in M_C and STTM_C groups, respectively. These findings illuminated the maize leaf growth response to cold via regulation of expression of miR408 and its target genes and antioxidant system.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":" ","pages":"149161"},"PeriodicalIF":2.6,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142824146","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
From ancestor to pathogen: Expansion and evolutionary adaptations of multidrug resistance causing MFS efflux pumps in mycobacteria. 从祖先到病原体:分枝杆菌中引起多药耐药性的 MFS 外排泵的扩展和进化适应。
IF 2.6 3区 生物学
Gene Pub Date : 2024-12-12 DOI: 10.1016/j.gene.2024.149160
Garima Singh, Yusuf Akhter
{"title":"From ancestor to pathogen: Expansion and evolutionary adaptations of multidrug resistance causing MFS efflux pumps in mycobacteria.","authors":"Garima Singh, Yusuf Akhter","doi":"10.1016/j.gene.2024.149160","DOIUrl":"10.1016/j.gene.2024.149160","url":null,"abstract":"<p><p>Multidrug resistance (MDR) in Mycobacterium tuberculosis (Mtb) is a growing threat. Efflux pumps, particularly those belonging to the Major Facilitator Superfamily (MFS), play a key role in MDR. This study investigated MFS transporters across Mycobacterium spp. to understand their evolution and role in drug resistance. We conducted a proteome-wide analysis of MFS proteins in Mtb, Mycobacterium smegmatis (non-pathogenic), and Mycobacterium canettii (closely related ancestor of Mtb). Mtb, known for its MDR, possessed the highest abundance of MFS drug efflux pumps, while Mycobacterium smegmatis had the least. This suggests a link between MFS drug efflux pump abundance and MDR phenotypes. Interestingly, Mycobacterium canettii displayed an intermediate level, possibly indicating the presence of these pumps before the emergence of Mtb as a pathogen. Further analysis of Mtb proteome revealed 31 putative MFS transporters and 3 proteins from expanded MFS subfamilies. Phylogenetic analysis categorized them into thirteen distinct families based on structural features. These findings highlight the potential importance of MFS transporters in MDR and the pathogenicity of Mtb. Overall, this study highlights the evolutionary role of MFS transporters in bacterial adaptation to antibiotics. The observed correlation between efflux pump abundance and MDR suggests MFS transporters as promising targets for future anti-tuberculosis therapies. Further research on specific transporter functions within MFS subfamilies can pave the way for novel therapeutic strategies.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":" ","pages":"149160"},"PeriodicalIF":2.6,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142824163","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
Deciphering new insights into copy number variations as drivers of genomic diversity and adaptation in farm animal species.
IF 2.6 3区 生物学
Gene Pub Date : 2024-12-11 DOI: 10.1016/j.gene.2024.149159
C S Celus, Sheikh Firdous Ahmad, Munish Gangwar, Subodh Kumar, Amit Kumar
{"title":"Deciphering new insights into copy number variations as drivers of genomic diversity and adaptation in farm animal species.","authors":"C S Celus, Sheikh Firdous Ahmad, Munish Gangwar, Subodh Kumar, Amit Kumar","doi":"10.1016/j.gene.2024.149159","DOIUrl":"https://doi.org/10.1016/j.gene.2024.149159","url":null,"abstract":"<p><p>The basis of all improvement in (re)production performance of animals and plants lies in the genetic variation. The underlying genetic variation can be further explored through investigations using molecular markers including single nucleotide polymorphism (SNP) and microsatellite, and more recently structural variants like copy number variations (CNVs). Unlike SNPs, CNVs affect a larger proportion of the genome, making them more impactful vis-à-vis variation at the phenotype level. They significantly contribute to genetic variation and provide raw material for natural and artificial selection for improved performance. CNVs are characterized as unbalanced structural variations that arise from four major mechanisms viz., non-homologous end joining (NHEJ), non-allelic homologous recombination (NAHR), fork stalling, and template switching (FoSTeS), and retrotransposition. Various detection methods have been developed to identify CNVs, including molecular techniques and massively parallel sequencing. Next-generation sequencing (NGS)/ high-throughput sequencing offers higher resolution and sensitivity, but challenges remain in delineating CNVs in regions with repetitive sequences or high GC content. High-throughput sequencing technologies utilize different methods based on read-pair, split-read, read depth, and assembly approaches (or their combination) to detect CNVs. Read-pair based methods work by mapping discordant reads, while the read-depth approach works on detecting the correlation between read depth and copy number of genetic segments or a gene. Split-read methods involve mapping segments of reads to different locations on the genome, while assembly methods involve comparing contigs to a reference or de novo sequencing. Similar to other marker-trait association studies, CNV-association studies are not uncommon in humans and farm animals. Soon, extensive studies will be needed to deduce the unique evolutionary trajectories and underlying molecular mechanisms for targeted genetic improvements in different farm animal species. The present review delineates the importance of CNVs in genetic studies, their generation along with programs and principles to efficiently identify them, and finally throw light on the existing literature on studies in farm animal species vis-à-vis CNVs.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":" ","pages":"149159"},"PeriodicalIF":2.6,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142822135","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 repression of the lipolytic inhibitor G0s2 enhancers affects lipid metabolism.
IF 2.6 3区 生物学
Gene Pub Date : 2024-12-10 DOI: 10.1016/j.gene.2024.149162
Ziqi Li, Sha Zeng, Qinjiao Du, Xiaokai Li, Qiuyue Chen, Songling Zhang, Xun Zhou, Haohuan Li, Anan Jiang, Xun Wang, Peng Shang, Mingzhou Li, Keren Long
{"title":"The repression of the lipolytic inhibitor G0s2 enhancers affects lipid metabolism.","authors":"Ziqi Li, Sha Zeng, Qinjiao Du, Xiaokai Li, Qiuyue Chen, Songling Zhang, Xun Zhou, Haohuan Li, Anan Jiang, Xun Wang, Peng Shang, Mingzhou Li, Keren Long","doi":"10.1016/j.gene.2024.149162","DOIUrl":"10.1016/j.gene.2024.149162","url":null,"abstract":"<p><p>The G0/G1 switch gene 2 (G0s2) is a selective inhibitor of adipose triglyceride lipase (ATGL) which is the rate-limiting enzyme for triglycerides (TGs) hydrolysis in adipocytes, and regulates the mobilization of TGs in adipocytes and hepatocytes. The expression and functional disorders of G0S2 are associated with various metabolic diseases and related pathological states, such as obesity and metabolic syndrome and non-alcoholic fatty liver disease (NAFLD). However, the extent to which the transcriptional regulatory mechanisms mediated by the interaction between the G0s2 gene promoter and enhancer regions are involved remains unknown. Here, through the analysis of epigenomic data (H3K27ac, H3K4me1, and DHS-seq) and luciferase reporter assays, we identified three active enhancers of G0s2 in 3 T3-L1 adipocytes. Subsequently, using the dCas9-KRAB system for epigenetic inhibition of G0S2-En2, -En4, and -En5 revealed the functional role of these enhancers in regulating G0s2 expression and lipid droplet biosynthesis. Additionally, transcriptome analyses revealed that inhibition of G0S2-En5 downregulated pathways associated with lipid metabolism and lipid biosynthesis. Furthermore, overexpression of transcription factors (TFs) and motif mutation experiments identified that PPARG and RXRA regulate the activity of G0S2-En5. Taken together, we identified functional enhancers regulating G0s2 expression and elucidated the important role of the G0S2-En5 in lipid droplet biogenesis.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":" ","pages":"149162"},"PeriodicalIF":2.6,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142817711","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
Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in petunia and identification of the putative candidate member involved in floral volatile benzenoids/phenylpropanoids metabolism.
IF 2.6 3区 生物学
Gene Pub Date : 2024-12-10 DOI: 10.1016/j.gene.2024.149150
Chao Zhang, Lingli Jiang, Jieyu Qian, Guo Yu, Hongsheng Qing, Li Li, Jianxin Fu
{"title":"Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in petunia and identification of the putative candidate member involved in floral volatile benzenoids/phenylpropanoids metabolism.","authors":"Chao Zhang, Lingli Jiang, Jieyu Qian, Guo Yu, Hongsheng Qing, Li Li, Jianxin Fu","doi":"10.1016/j.gene.2024.149150","DOIUrl":"10.1016/j.gene.2024.149150","url":null,"abstract":"<p><p>The basic helix-loop-helix (bHLH) family, a prominent group of transcription factors, is involved in plant growth, development, and secondary metabolic processes. Petunia (Petunia hybrida), a beloved and widely cultivated garden flower, boasts a diverse array of varieties, some of which exude a captivating fragrance that has garnered immense popularity. The aromatic allure of petunias primarily stems from the presence of volatile benzenoids/phenylpropanoids, the principal floral scent compounds. But whether bHLH transcription factors regulate petunia floral scent compound synthesis is not clear. In this study, we sought to screen the putative candidate member of bHLH which can be involved in the biosynthesis of benzenoids/phenylpropanoids by examining 63 members of the petunia bHLH gene family. Phylogenetic analysis of the 63 petunia bHLH proteins them into 16 subgroups. Almost all bHLH members contained alkaline/helix-loop-helix domains. Based on the reported RNA sequencing data of P. hybrida 'Mitchell', 30 assembled sequences were mapped to the bHLH genes of P. axillaris. Further qRT-PCR assays suggested that PhbHLH19 might be the putative candidate member in the biosynthesis of benzenoids/phenylpropanoids. PhbHLH19 showed higher expression levels in the petal limb but was lowly expressed at the bud stage, with a rapid increase in the expression level when flowers opened. The expression of PhbHLH19 displayed a significant positive correlation with that of PhPAL2, and the yeast one-hybrid assay verified that PhbHLH19 can bind to the promoter of PhPAL2. Moreover, a dual-luciferase assay proved the transcriptional activation of PhbHLH19 on PhPAL2. These findings suggested that PhbHLH19 might be a putative candidate in the regulation of benzenoid/phenylpropanoid synthesis by activating PhPAL2 expression.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":" ","pages":"149150"},"PeriodicalIF":2.6,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142817707","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
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