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Perez I, Reyes-Nava NG, Pinales BE, Quintana AM. Overexpression of MMACHC Prevents Craniofacial Phenotypes Caused by Knockdown of znf143b. AMERICAN JOURNAL OF UNDERGRADUATE RESEARCH 2023; 20:77-84. [PMID: 38617190 PMCID: PMC11013955 DOI: 10.33697/ajur.2023.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
ZNF143 is a sequence-specific DNA binding protein that regulates the expression of protein-coding genes and small RNA molecules. In humans, ZNF143 interacts with HCFC1, a transcriptional cofactor, to regulate the expression of downstream target genes, including MMACHC, which encodes an enzyme involved in cobalamin (cbl) metabolism. Mutations in HCFC1 or ZNF143 cause an inborn error of cobalamin metabolism characterized by abnormal cbl metabolism, intellectual disability, seizures, and mild to moderate craniofacial abnormalities. However, the mechanisms by which ZNF143 mutations cause individual phenotypes are not completely understood. Defects in metabolism and craniofacial development are hypothesized to occur because of decreased expression of MMACHC. But recent results have called into question this mechanism as the cause for craniofacial development. Therefore, in the present study, we implemented a loss of function analysis to begin to uncover the function of ZNF143 in craniofacial development using the developing zebrafish. The knockdown of znf143b, one zebrafish ortholog of ZNF143, caused craniofacial phenotypes of varied severity, which included a shortened and cleaved Meckel's cartilage, partial loss of ceratobranchial arches, and a distorted ceratohyal. These phenotypes did not result from a defect in the number of total chondrocytes but were associated with a mild to moderate decrease in mmachc expression. Interestingly, expression of human MMACHC via endogenous transgene prevented the onset of craniofacial phenotypes associated with znf143b knockdown. Collectively, our data establishes that knockdown of znf143b causes craniofacial phenotypes that can be alleviated by increased expression of MMACHC.
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Affiliation(s)
- Isaiah Perez
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX
| | | | - Briana E. Pinales
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX
| | - Anita M. Quintana
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX
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Ye B, Shen W, Zhang C, Yu M, Ding X, Yin M, Wang Y, Guo X, Bai G, Lin K, Shi S, Li P, Zhang Y, Yu G, Zhao Z. The role of ZNF143 overexpression in rat liver cell proliferation. BMC Genomics 2022; 23:483. [PMID: 35780101 PMCID: PMC9250731 DOI: 10.1186/s12864-022-08714-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/21/2022] [Indexed: 11/10/2022] Open
Abstract
Background Zinc finger protein 143(ZNF143), a member of the Krüppel C2H2-type zinc finger protein family, is strongly associated with cell cycle regulation and cancer development. A recent study suggested that ZNF143 plays as a transcriptional activator that promotes hepatocellular cancer (HCC) cell proliferation and cell cycle transition. However, the exact biological role of ZNF143 in liver regeneration and normal liver cell proliferation has not yet been investigated. Methods In our study, we constructed a stable rat liver cell line (BRL-3A) overexpressing ZNF143 and then integrated RNA-seq and Cleavage Under Targets and Tagmentation (CUT&Tag) data to identify the mechanism underlying differential gene expression. Results Our results show that ZNF143 expression is upregulated during the proliferation phase of liver regeneration after 2/3 partial hepatectomy (PH). The cell counting kit-8 (CCK-8) assay, EdU staining and RNA-seq data analyses revealed that ZNF143 overexpression (OE) significantly inhibited BRL-3A cell proliferation and cell cycle progression. We then performed CUT&Tag assays and found that approximately 10% of ZNF143-binding sites (BSs) were significantly changed genome-wide by ZNF143 OE. However, CCCTC-binding factor (CTCF) binding to chromatin was not affected. Interestingly, the integration analysis of RNA-seq and CUT&Tag data showed that some of genes affected by ZNF143 differential BSs are in the center of each gene regulation module. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that these genes are critical in the maintenance of cell identity. Conclusion These results indicated that the expression level of ZNF143 in the liver is important for the maintenance of cell identity. ZNF143 plays different roles in HCC and normal liver cells and may be considered as a potential therapeutic target in liver disease. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08714-2.
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Affiliation(s)
- Bingyu Ye
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.,Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Wenlong Shen
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Chunyan Zhang
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Mengli Yu
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Xinru Ding
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Man Yin
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yahao Wang
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Xinjie Guo
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Ge Bai
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Kailin Lin
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.,Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Shu Shi
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Ping Li
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Yan Zhang
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Guoying Yu
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
| | - Zhihu Zhao
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China.
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Tine M, Kuhl H, Teske PR, Reinhardt R. Genome-wide analysis of European sea bass provides insights into the evolution and functions of single-exon genes. Ecol Evol 2021; 11:6546-6557. [PMID: 34141239 PMCID: PMC8207432 DOI: 10.1002/ece3.7507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/24/2021] [Accepted: 03/12/2021] [Indexed: 11/17/2022] Open
Abstract
Several studies have attempted to understand the origin and evolution of single-exon genes (SEGs) in eukaryotic organisms, including fishes, but few have examined the functional and evolutionary relationships between SEGs and multiple-exon gene (MEG) paralogs, in particular the conservation of promoter regions. Given that SEGs originate via the reverse transcription of mRNA from a "parental" MEGs, such comparisons may enable identifying evolutionarily-related SEG/MEG paralogs, which might fulfill equivalent physiological functions. Here, the relationship of SEG proportion with MEG count, gene density, intron count, and chromosome size was assessed for the genome of the European sea bass, Dicentrarchus labrax. Then, SEGs with an MEG parent were identified, and promoter sequences of SEG/MEG paralogs were compared, to identify highly conserved functional motifs. The results revealed a total count of 1,585 (8.3% of total genes) SEGs in the European sea bass genome, which was correlated with MEG count but not with gene density. The significant correlation of SEG content with the number of MEGs suggests that SEGs were continuously and independently generated over evolutionary time following species divergence through retrotranscription events, followed by tandem duplications. Functional annotation showed that the majority of SEGs are functional, as is evident from their expression in RNA-seq data used to support homology-based genome annotation. Differences in 5'UTR and 3'UTR lengths between SEG/MEG paralogs observed in this study may contribute to gene expression divergence between them and therefore lead to the emergence of new SEG functions. The comparison of nonsynonymous to synonymous changes (Ka/Ks) between SEG/MEG parents showed that 74 of them are under positive selection (Ka/Ks > 1; p = .0447). An additional fifteen SEGs with an MEG parent have a common promoter, which implies that they are under the influence of common regulatory networks.
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Affiliation(s)
- Mbaye Tine
- UFR des Sciences Agronomiques, de l'Aquaculture et des Technologies Alimentaires (S2ATA)Université Gaston Berger (UGB)Saint‐LouisSenegal
- Genome Centre at the Max‐Planck Institute for Plant Breeding ResearchKölnGermany
| | - Heiner Kuhl
- Department of Ecophysiology and AquacultureLeibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB)BerlinGermany
| | - Peter R. Teske
- Department of ZoologyCentre for Ecological Genomics and Wildlife ConservationUniversity of JohannesburgJohannesburgSouth Africa
| | - Richard Reinhardt
- Genome Centre at the Max‐Planck Institute for Plant Breeding ResearchKölnGermany
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Huning L, Kunkel GR. The ubiquitous transcriptional protein ZNF143 activates a diversity of genes while assisting to organize chromatin structure. Gene 2020; 769:145205. [PMID: 33031894 DOI: 10.1016/j.gene.2020.145205] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 10/23/2022]
Abstract
Zinc Finger Protein 143 (ZNF143) is a pervasive C2H2 zinc-finger transcriptional activator protein regulating the efficiency of eukaryotic promoter regions. ZNF143 is able to activate transcription at both protein coding genes and small RNA genes transcribed by either RNA polymerase II or RNA polymerase III. Target genes regulated by ZNF143 are involved in an array of different cellular processes including both cancer and development. Although a key player in regulating eukaryotic genes, the molecular mechanism by with ZNF143 binds and activates genes transcribed by two different polymerases is still relatively unknown. In addition to its role as a transcriptional regulator, recent genomics experiments have implicated ZNF143 as a potential co-factor involved in chromatin looping and establishing higher order structure within the genome. This review focuses primarily on possible activation mechanisms of promoters by ZNF143, with less emphasis on the role of ZNF143 in cancer and development, and its function in establishing higher order chromatin contacts within the genome.
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Affiliation(s)
- Laura Huning
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
| | - Gary R Kunkel
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.
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Castro VL, Quintana AM. The role of HCFC1 in syndromic and non-syndromic intellectual disability. ACTA ACUST UNITED AC 2020; 8. [PMID: 34164576 DOI: 10.18103/mra.v8i6.2122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mutations in the HCFC1 gene are associated with cases of syndromic (cblX) and non-syndromic intellectual disability. Syndromic individuals present with severe neurological defects including intractable epilepsy, facial dysmorphia, and intellectual disability. Non-syndromic individuals have also been described and implicate a role for HCFC1 during brain development. The penetrance of phenotypes and the presence of an overall syndrome is associated with the location of the mutation within the HCFC1 protein. Thus, one could hypothesize that the positioning of HCFC1 mutations lead to different neurological phenotypes that include but are not restricted to intellectual disability. The HCFC1 protein is comprised of multiple domains that function in cellular proliferation/metabolism. Several reports of HCFC1 disease variants have been identified, but a comprehensive review of each variant and its associated phenotypes has not yet been compiled. Here we perform a detailed review of HCFC1 function, model systems, variant location, and accompanying phenotypes to highlight current knowledge and the future status of the field.
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Affiliation(s)
- Victoria L Castro
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968
| | - Anita M Quintana
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968
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Ye B, Yang G, Li Y, Zhang C, Wang Q, Yu G. ZNF143 in Chromatin Looping and Gene Regulation. Front Genet 2020; 11:338. [PMID: 32318100 PMCID: PMC7154149 DOI: 10.3389/fgene.2020.00338] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 03/20/2020] [Indexed: 01/02/2023] Open
Abstract
ZNF143, a human homolog of the transcriptional activator Staf, is a C2H2-type protein consisting of seven zinc finger domains. As a transcription factor (TF), ZNF143 is sequence specifically binding to chromatin and activates the expression of protein-coding and non-coding genes on a genome scale. Although it is ubiquitous expressed, its expression in cancer cells and tissues is usually higher than that in normal cells and tissues. Therefore, abnormal expression of ZNF143 is related to cancer cell survival, proliferation, differentiation, migration, and invasion, suggesting that new small molecules can be designed by targeting ZNF143 as it may be a good potential biomarker and therapeutic target for related cancers. However, the mechanism on how ZNF143 regulates its targeting gene remains unclear. Recently, with the development of chromatin conformation capture (3C) and its derivatives, and high-throughput sequencing technology, new findings have been obtained in the study of ZNF143. Pioneering studies have showed that ZNF143 binds directly to promoters and contributes to chromatin interactions connecting promoters to distal regulatory elements, such as enhancers. Further, it has proved that ZNF143 is involved in CCCTC-binding factor (CTCF) in establishing the conserved chromatin loops by cooperating with cohesin and other partners. These results indicate that ZNF143 is a key loop formation factor. In addition, we report ZNF143 is dynamically bound to chromatin during the cell cycle demonstrated that it is a potential mitotic bookmarking factor. It may be associated with CTCF for mitosis-to-G1 phase transition and chromatin loop re-establishment in early G1 phase. In the future, researchers could further clarify the fine mechanism of ZNF143 in mediating chromatin loops with the help of CUT&RUN (CUT&Tag) and Cut-C technology. Thus, in this review, we summarize the research progress of TF ZNF143 in detail and also predict the potential functions of ZNF143 in cell fate and identity based on our recent discoveries.
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Affiliation(s)
- Bingyu Ye
- State Key Laboratory of Cell Differentiation and Regulation, Henan Normal University, Xinxiang, China.,Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,College of Life Sciences, Henan Normal University, Xinxiang, China.,Institute of Biomedical Science, Henan Normal University, Xinxiang, China.,Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), Henan Normal University, Xinxiang, China
| | - Ganggang Yang
- State Key Laboratory of Cell Differentiation and Regulation, Henan Normal University, Xinxiang, China.,Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,College of Life Sciences, Henan Normal University, Xinxiang, China.,Institute of Biomedical Science, Henan Normal University, Xinxiang, China.,Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), Henan Normal University, Xinxiang, China
| | - Yuanmeng Li
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Chunyan Zhang
- State Key Laboratory of Cell Differentiation and Regulation, Henan Normal University, Xinxiang, China.,Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,College of Life Sciences, Henan Normal University, Xinxiang, China.,Institute of Biomedical Science, Henan Normal University, Xinxiang, China.,Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), Henan Normal University, Xinxiang, China
| | - Qiwen Wang
- State Key Laboratory of Cell Differentiation and Regulation, Henan Normal University, Xinxiang, China.,Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,College of Life Sciences, Henan Normal University, Xinxiang, China.,Institute of Biomedical Science, Henan Normal University, Xinxiang, China.,Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), Henan Normal University, Xinxiang, China
| | - Guoying Yu
- State Key Laboratory of Cell Differentiation and Regulation, Henan Normal University, Xinxiang, China.,Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,College of Life Sciences, Henan Normal University, Xinxiang, China.,Institute of Biomedical Science, Henan Normal University, Xinxiang, China.,Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), Henan Normal University, Xinxiang, China
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