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Chen Y, Zhao J, Zhong C, Kang Y, Xiong Z, Huang J, Li Z, Liu Q, Shi D, Li X, Wang J, Li H. Enhancer Enh483 regulates myoblast proliferation and differentiation of buffalo myoblasts by targeting FAXC. Cell Tissue Res 2024:10.1007/s00441-024-03944-0. [PMID: 39688691 DOI: 10.1007/s00441-024-03944-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Accepted: 12/02/2024] [Indexed: 12/18/2024]
Abstract
A detailed understanding of the precise regulatory mechanisms governing buffalo skeletal muscle is crucial for improving meat quality and yield. Proper skeletal muscle fate decisions necessitate the accurate regulation of key enhancers. This study screened nine potential enhancers linked to muscle development by analysing ATAC-seq data from buffalo myoblasts during the proliferative and differentiative phases. The enhancer activity of these candidates was confirmed in buffalo myoblasts, C2C12, and human skeletal muscle myoblasts using a dual-luciferase reporter system. The CRISPRi system and RT-qPCR were used to test the effects of 9 candidate enhancers on buffalo myoblasts. The active enhancer, Enh483, was selected based on its significant impact. Upon successful inhibition of Enh483 using CRISPRi, decreases in the expression of buffalo myogenic proliferation marker genes (PCNA, CyclinD1, and CDK2) were observed via RT-qPCR and Western blot. Subsequent proliferation assays using CCK-8 and EdU confirmed the promotive effect of Enh483 on buffalo myogenic cell proliferation. Following a 5-day differentiation induction period, changes in the expression of differentiation marker genes (MyoD1, MyoG, and MyHC) were analysed using RT-qPCR and Western blot. Additionally, fused myotube numbers were quantified, and the impact of Enh483 on buffalo myogenic cell differentiation was assessed through immunofluorescence. Our findings indicate that Enh483 facilitates buffalo myogenic cell differentiation. Further interaction analysis utilising 3C-PCR revealed a direct association between Enh483 and the FAXC promoter. In summary, the results from this study lay a foundational framework for deciphering the intricate regulatory mechanisms underpinning buffalo muscle development.
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Affiliation(s)
- Yaling Chen
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Jiahui Zhao
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Cuiwei Zhong
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Yujin Kang
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Zhaocheng Xiong
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Jieping Huang
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Zhipeng Li
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Qingyou Liu
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Deshun Shi
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Xinxin Li
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Jian Wang
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China
| | - Hui Li
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530005, China.
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Werner A, Kanhere A, Wahlestedt C, Mattick JS. Natural antisense transcripts as versatile regulators of gene expression. Nat Rev Genet 2024; 25:730-744. [PMID: 38632496 DOI: 10.1038/s41576-024-00723-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2024] [Indexed: 04/19/2024]
Abstract
Long non-coding RNAs (lncRNAs) are emerging as a major class of gene products that have central roles in cell and developmental biology. Natural antisense transcripts (NATs) are an important subset of lncRNAs that are expressed from the opposite strand of protein-coding and non-coding genes and are a genome-wide phenomenon in both eukaryotes and prokaryotes. In eukaryotes, a myriad of NATs participate in regulatory pathways that affect expression of their cognate sense genes. Recent developments in the study of NATs and lncRNAs and large-scale sequencing and bioinformatics projects suggest that whether NATs regulate expression, splicing, stability or translation of the sense transcript is influenced by the pattern and degrees of overlap between the sense-antisense pair. Moreover, epigenetic gene regulatory mechanisms prevail in somatic cells whereas mechanisms dependent on the formation of double-stranded RNA intermediates are prevalent in germ cells. The modulating effects of NATs on sense transcript expression make NATs rational targets for therapeutic interventions.
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Affiliation(s)
| | | | | | - John S Mattick
- University of New South Wales, Sydney, New South Wales, Australia
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Chen J, Liu K, Vadas MA, Gamble JR, McCaughan GW. The Role of the MiR-181 Family in Hepatocellular Carcinoma. Cells 2024; 13:1289. [PMID: 39120319 PMCID: PMC11311592 DOI: 10.3390/cells13151289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the fourth-leading cause of cancer-related death worldwide. Due to the high mortality rate in HCC patients, discovering and developing novel systemic treatment options for HCC is a vital unmet medical need. Among the numerous molecular alterations in HCCs, microRNAs (miRNAs) have been increasingly recognised to play critical roles in hepatocarcinogenesis. We and others have recently revealed that members of the microRNA-181 (miR-181) family were up-regulated in some, though not all, human cirrhotic and HCC tissues-this up-regulation induced epithelial-mesenchymal transition (EMT) in hepatocytes and tumour cells, promoting HCC progression. MiR-181s play crucial roles in governing the fate and function of various cells, such as endothelial cells, immune cells, and tumour cells. Previous reviews have extensively covered these aspects in detail. This review aims to give some insights into miR-181s, their targets and roles in modulating signal transduction pathways, factors regulating miR-181 expression and function, and their roles in HCC.
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Affiliation(s)
- Jinbiao Chen
- Liver Injury and Cancer Program, Cancer Innovations Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Ken Liu
- Liver Injury and Cancer Program, Cancer Innovations Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW 2050, Australia
| | - Mathew A. Vadas
- Vascular Biology Program, Healthy Ageing Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia; (M.A.V.); (J.R.G.)
| | - Jennifer R. Gamble
- Vascular Biology Program, Healthy Ageing Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia; (M.A.V.); (J.R.G.)
| | - Geoffrey W. McCaughan
- Liver Injury and Cancer Program, Cancer Innovations Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW 2050, Australia
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Mian Y, Wang L, Keikhosravi A, Guo K, Misteli T, Arda HE, Finn EH. Cell type- and transcription-independent spatial proximity between enhancers and promoters. Mol Biol Cell 2024; 35:ar96. [PMID: 38717453 PMCID: PMC11244156 DOI: 10.1091/mbc.e24-02-0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/12/2024] [Accepted: 04/29/2024] [Indexed: 06/07/2024] Open
Abstract
Cell type-specific enhancers are critically important for lineage specification. The mechanisms that determine cell-type specificity of enhancer activity, however, are not fully understood. Most current models for how enhancers function invoke physical proximity between enhancer elements and their target genes. Here, we use an imaging-based approach to examine the spatial relationship of cell type-specific enhancers and their target genes with single-cell resolution. Using high-throughput microscopy, we measure the spatial distance from target promoters to their cell type-specific active and inactive enhancers in individual pancreatic cells derived from distinct lineages. We find increased proximity of all promoter-enhancer pairs relative to non-enhancer pairs separated by similar genomic distances. Strikingly, spatial proximity between enhancers and target genes was unrelated to tissue-specific enhancer activity. Furthermore, promoter-enhancer proximity did not correlate with the expression status of target genes. Our results suggest that promoter-enhancer pairs exist in a distinctive chromatin environment but that genome folding is not a universal driver of cell-type specificity in enhancer function.
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Affiliation(s)
- Yasmine Mian
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Li Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Adib Keikhosravi
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Konnie Guo
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - H. Efsun Arda
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Elizabeth H. Finn
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104
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Liu D, Wang W, Wu Y, Qiu Y, Zhang L. LINC00887 Acts as an Enhancer RNA to Promote Medullary Thyroid Carcinoma Progression by Binding with FOXQ1. Curr Cancer Drug Targets 2024; 24:519-533. [PMID: 38804344 DOI: 10.2174/0115680096258716231026063704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 05/29/2024]
Abstract
BACKGROUND Medullary thyroid carcinoma (MTC) is a rare but aggressive endocrine malignancy that originates from the parafollicular C cells of the thyroid gland. Enhancer RNAs (eRNAs) are non-coding RNAs transcribed from enhancer regions, which are critical regulators of tumorigenesis. However, the roles and regulatory mechanisms of eRNAs in MTC remain poorly understood. This study aims to identify key eRNAs regulating the malignant phenotype of MTC and to uncover transcription factors involved in the regulation of key eRNAs. METHODS GSE32662 and GSE114068 were used for the identification of differentially expressed genes, eRNAs, enhancers and enhancer-regulated genes in MTC. Metascape and the transcription factor affinity prediction method were used for gene function enrichment and transcription factor prediction, respectively. qRT-PCR was used to detect gene transcription levels. ChIP-qPCR was used to assess the binding of histone H3 lysine 27 acetylation (H3K27ac)-enriched regions to anti- H3K27ac. RIP-qPCR was used to detect the binding between FOXQ1 and LINC00887. CCK8 and Transwell were performed to measure the proliferation and invasion of MTC cells, respectively. Intracellular reactive oxygen species (ROS) levels were quantified using a ROS assay kit. RESULTS Four eRNAs (H1FX-AS1, LINC00887, MCM3AP-AS1 and A1BG-AS1) were screened, among which LINC00887 was the key eRNA promoting the proliferation and invasion of MTC cells. A total of 135 genes controlled by LINC00887-regulated enhancers were identified; among them, BCL2, PRDX1, SFTPD, TPO, GSS, RAD52, ZNF580, and ZFP36L1 were significantly enriched in the "ROS metabolic process" term. As a transcription factor regulating genes enriched in the "ROS metabolic process" term, FOXQ1 could recruit LINC00887. Overexpression of FOXQ1 restored LINC00887 knockdown-induced downregulation of GSS and ZFP36L1 transcription in MTC cells. Additionally, FOXQ1 overexpression counteracted the inhibitory effects of LINC00887 knockdown on the proliferation and invasion of MTC cells and the promotion of intracellular ROS accumulation induced by LINC00887 knockdown. CONCLUSION LINC00887 was identified as a key eRNA promoting the malignant phenotype of MTC cells. The involvement of FOXQ1 was essential for LINC00887 to play a pro-tumorigenic role in MTC. Our findings suggest that the FOXQ1/LINC00887 axis is a potential therapeutic target for MTC.
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Affiliation(s)
- Daxiang Liu
- Department of Otolaryngology & Head and Neck Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050035, China
| | - Wenjing Wang
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050035 , China
| | - Yanzhao Wu
- Department of Otolaryngology & Head and Neck Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050035, China
| | - Yongle Qiu
- Department of Stomatology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050035 , China
| | - Lan Zhang
- Department of Otolaryngology & Head and Neck Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050035, China
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Dobrica MO, Varghese CS, Harris JM, Ferguson J, Magri A, Arnold R, Várnai C, Parish JL, McKeating JA. CTCF regulates hepatitis B virus cccDNA chromatin topology. J Gen Virol 2024; 105. [PMID: 38175123 DOI: 10.1099/jgv.0.001939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024] Open
Abstract
Hepatitis B Virus (HBV) is a small DNA virus that replicates via an episomal covalently closed circular DNA (cccDNA) that serves as the transcriptional template for viral mRNAs. The host protein, CCCTC-binding factor (CTCF), is a key regulator of cellular transcription by maintaining epigenetic boundaries, nucleosome phasing, stabilisation of long-range chromatin loops and directing alternative exon splicing. We previously reported that CTCF binds two conserved motifs within Enhancer I of the HBV genome and represses viral transcription, however, the underlying mechanisms were not identified. We show that CTCF depletion in cells harbouring cccDNA-like HBV molecules and in de novo infected cells resulted in an increase in spliced transcripts, which was most notable in the abundant SP1 spliced transcript. In contrast, depletion of CTCF in cell lines with integrated HBV DNA had no effect on the abundance of viral transcripts and in line with this observation there was limited evidence for CTCF binding to viral integrants, suggesting that CTCF-regulation of HBV transcription is specific to episomal cccDNA. Analysis of HBV chromatin topology by Assay for Transposase Accessible Chromatin Sequencing (ATAC-Seq) revealed an accessible region spanning Enhancers I and II and the basal core promoter (BCP). Mutating the CTCF binding sites within Enhancer I resulted in a dramatic rearrangement of chromatin accessibility where the open chromatin region was no longer detected, indicating loss of the phased nucleosome up- and down-stream of the HBV enhancer/BCP. These data demonstrate that CTCF functions to regulate HBV chromatin conformation and nucleosomal positioning in episomal maintained cccDNA, which has important consequences for HBV transcription regulation.
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Affiliation(s)
- Mihaela Olivia Dobrica
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Present address: Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Christy Susan Varghese
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | | | - Jack Ferguson
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Present address: Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Andrea Magri
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Roland Arnold
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Csilla Várnai
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Joanna L Parish
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- National Institute for Health and Care Research (NIHR) Birmingham Biomedical Research Centre, Oxford, UK
| | - Jane A McKeating
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
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