Structures and biological functions of zinc finger proteins and their roles in hepatocellular carcinoma

Li, Xinxin; Han, Mengzhen; Zhang, Hongwei; Liu, Furong; Pan, Yonglong; Zhu, Jinghan; Liao, Zhibin; Chen, Xiaoping; Zhang, Bixiang

doi:10.1186/s40364-021-00345-1

Cited by 46 publications

(30 citation statements)

References 151 publications

(128 reference statements)

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“…Our detected TFs were classified into three groups including TF classes with 1–10 TFs such as β-sheet, lg-fold, other α-Helix classes; TF classes with 10–20 TFs such as winged helix–turn–helix, helix–turn-helix, zipper-type; and TF classes with more than 20 TFs such as zinc-coordinating. Zinc finger proteins, the most abundant and structurally diverse groups of protein in nature, act as TFs and function in different cellular processes, including cell proliferation [ 60 , 61 , 62 ]. B-cell lymphoma/leukemia 11B (BCL11B) is one member of the large family of zinc finger proteins [ 61 ].…”

Section: Discussionmentioning

confidence: 99%

Gene Networks and Pathways Involved in LPS-Induced Proliferative Response of Bovine Endometrial Epithelial Cells

Najafi

Guo

Andersson

et al. 2022

Genes

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Lipopolysaccharide (LPS) is a component of the outer membrane of Gram-negative bacteria involved in the pathogenic processes leading to mastitis and metritis in animals such as dairy cattle. LPS causes cell proliferation associated with endometrium inflammation. Former in vitro studies have demonstrated that LPS induces an intense stimulation of the proliferation of a pure population of bovine endometrial epithelial cells. In a follow-up transcriptomic study based on RNA-sequencing data obtained after 24 h exposure of primary bovine endometrial epithelial cells to 0, 2, and 8 μg/mL LPS, 752 and 727 differentially expressed genes (DEGs) were detected between the controls and LPS-treated samples that encode proteins known to be associated with either proliferation or apoptosis, respectively. The present bioinformatic analysis was performed to decipher the gene networks involved to obtain a deeper understanding of the mechanisms underlying the proliferative and apoptosis processes. Our findings have revealed 116 putative transcription factors (TFs) and the most significant number of interactions between these TFs and DEGs belong to NFKβ1, TP53, STAT1, and HIF1A. Moreover, our results provide novel insights into the early signaling and metabolic pathways in bovine endometrial epithelial cells associated with the innate immune response and cell proliferation to Escherichia coli-LPS infection. The results further indicated that LPS challenge elicited a strong transcriptomic response, leading to potent activation of pro-inflammatory pathways that are associated with a marked endometrial cancer, Toll-like receptor, NFKβ, AKT, apoptosis, and MAPK signaling pathways. This effect may provide a mechanistic explanation for the relationship between LPS and cell proliferation.

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Section: Discussionmentioning

confidence: 99%

Gene Networks and Pathways Involved in LPS-Induced Proliferative Response of Bovine Endometrial Epithelial Cells

Najafi

Guo

Andersson

et al. 2022

Genes

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“…A deficiency in zinc would cause the onset of or failure to regulate these few named diseases out of the several ones that are dependent on the proper functioning of zinc fingers to stabilize the protein folds that may then decide the fate of the tumor or disease of concern. In regards to this, the drugs that are being designed for the treatments of these diseases target specific ZNFs to restore the normal functioning or halt the abnormal expression of the core proteins expressing the disease [32].…”

Section: Zinc In Zinc Finger Proteins (Znf)mentioning

confidence: 99%

Zinc Metabolism: A Review with Regard to Zn Finger Proteins, DNA Methylation and p53; In Reference to its Deficiency Syndromes and Tracing its Immunological as Well as Epigenetic Relations

Abbas¹

2022

ijcsrr

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Epigenetics is the branch of biology that studies the effects of environment on genetics and vice versa. It is the connecting link between genotype and phenotype of an individual, and can be widely influenced by the nutrition and availability of certain essential micronutrients, in this review, zinc. Although a trace element, zinc is essential to the body as a core component of more than 300 proteins and enzymes, which when functioning normally impart structural and mechanical capacities to the body tissues and fluids. Zinc is ubiquitous to all parts of the body and regulates various metabolic and biological processes such as cell proliferation, apoptosis, tumorigenesis, along with the regular working of fetal and adult organs. The role of zinc-finger proteins is crucial to impart stability to a protein's folds and in turn render it functional to play its role in gene expression to serve as oncogenes or tumor suppressor genes. Zinc deficiency is a common occurrence in various parts of the world and is generally due to inadequate intake through the diet but may also manifest itself in an inheritable form. The effects of low zinc on a cellular level can be seen through a diminishing immunity, increased oxidative stress, reduced functionality of the p53 protein leading to tumor formation, incorrect DNA methylation. While phenotypically, zinc deficit can be both congenital and acquired. Some such diseases discussed here are irritable bowel syndrome, acrodermatitis enteropathica, thymic atrophy, celiac disease and preterm birth. In this review, the focus is on the aspect of zinc availability to cells as an epigenetic modulator/regulator and the subsequent consequences arising due to imbalance of zinc in the cell.

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“…These IPR domains belonged to zinc finger RING-type, zinc finger PHD-type, zinc finger FYVE/PHDtype (FYVE: Fab 1 (yeast orthologue of PIKfyve), YOTB, Vac 1 (vesicle transport protein), and EEA1), homeoboxlike domain superfamily, WD40-repeat-containing domain, SANT/Myb (SANT: Swi3, Ada2, N-Cor, and TFIIIB) domain, zinc finger, and C3HC4 RING-type. Zinc finger motifs function as part of DNA-binding and protein-protein interaction domains (Li et al, 2022). They form a large regulatory network that senses and responds to different environmental stimuli.…”

Section: Tfs and Regulatorsmentioning

confidence: 99%

Alkaloid production and response to natural adverse conditions in Peganum harmala : in silico transcriptome analyses

Jazayeri¹,

Pooralinaghi²,

Navarrete³

et al. 2022

bta

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Peganum harmala is a valuable wild plant that grows and survives under adverse conditions and produces pharmaceutical alkaloid metabolites. Using different assemblers to develop a transcriptome improves the quality of assembled transcriptome. In this study, a concrete and accurate method for detecting stress-responsive transcripts by comparing stress-related gene ontology (GO) terms and public domains was designed. An integrated transcriptome for P. harmala including 42 656 coding sequences was created by merging de novo assembled transcriptomes. Around 35 000 transcripts were annotated with more than 90% resemblance to three closely related species of Citrus, which confirmed the robustness of the assembled transcriptome; 4853 stress-responsive transcripts were identified. CYP82 involved in alkaloid biosynthesis showed a higher number of transcripts in P. harmala than in other plants, indicating its diverse alkaloid biosynthesis attributes. Transcription factors (TFs) and regulatory elements with 3887 transcripts comprised 9% of the transcriptome. Among the TFs of the integrated transcriptome, cystein2/histidine2 (C2H2) and WD40 repeat families were the most abundant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) MAPK (mitogen-activated protein kinase) signaling map and the plant hormone signal transduction map showed the highest assigned genes to these pathways, suggesting their potential stress resistance. The P. harmala whole-transcriptome survey provides important resources and paves the way for functional and comparative genomic studies on this plant to discover stress-tolerance-related markers and response mechanisms in stress physiology, phytochemistry, ecology, biodiversity, and evolution. P. harmala can be a potential model for studying adverse environmental cues and metabolite biosynthesis and a major source for the production of various alkaloids.

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Structures and biological functions of zinc finger proteins and their roles in hepatocellular carcinoma

Cited by 46 publications

References 151 publications

Gene Networks and Pathways Involved in LPS-Induced Proliferative Response of Bovine Endometrial Epithelial Cells

Gene Networks and Pathways Involved in LPS-Induced Proliferative Response of Bovine Endometrial Epithelial Cells

Zinc Metabolism: A Review with Regard to Zn Finger Proteins, DNA Methylation and p53; In Reference to its Deficiency Syndromes and Tracing its Immunological as Well as Epigenetic Relations

Alkaloid production and response to natural adverse conditions in Peganum harmala : in silico transcriptome analyses

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