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Wu J, Zhou Y, Zhao D, Xu R, Wang J, Lin H, Ding Z, Zou Y. Engineered mouse H1 promoter mutants with superior RNA polymerase III activity. Biochem Biophys Rep 2024; 39:101795. [PMID: 39175666 PMCID: PMC11340601 DOI: 10.1016/j.bbrep.2024.101795] [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: 05/05/2024] [Revised: 07/11/2024] [Accepted: 07/18/2024] [Indexed: 08/24/2024] Open
Abstract
Vectors incorporating the human H1 (hH1) promoter are being applied for RNA interference (RNAi) experiments and genome editing. Although extensive studies have been conducted on the hH1 promoter, our understanding of the mouse H1 promoter remains limited. In this study, we predicted the 163 bp mouse H1 (mH1) promoter and 84 bp mouse H1 core (mH1 core) promoter through global alignment and detected its RNA polymerase II (Pol II) and III activities through the expression of the EGFP and the abundance of artificial sequence, which were generally slightly weaker than those of the hH1 promoter. Furthermore, to boost its Pol III activity, we engineered various promoter mutants by introducing mutations or systematically swapping elements. Surprisingly, the Pol II activity of mH1 core mut5 with AT stretch was at least 2-fold greater than that of the wild type, making it a potential candidate for target protein expression purposes. Fortunately, the Pol III activities of mH1 mut1 and mH1 core mut5 were at least 1.5 times stronger than those of the parental promoters in human and mouse cell lines on account of AT stretch, as did the mH1 mut4 with AT stretch and proximal sequence element (PSE) and TATA box insertion mutations. We highly recommend these three promoters as valuable supplements to the type 3 Pol III promoter toolbox.
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Affiliation(s)
- Jiaying Wu
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Yufei Zhou
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai, 200032, China
| | - Di Zhao
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai, 200032, China
| | - Ran Xu
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai, 200032, China
- Shanghai Geriatric Medical Center, Shanghai, 201104, China
| | - Jienan Wang
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai, 200032, China
| | - Hong Lin
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai, 200032, China
| | - Zhiwen Ding
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai, 200032, China
- Departments of Cardiology, Qingpu Branch of Zhongshan Hospital, Fudan University, Shanghai, 218120, China
| | - Yunzeng Zou
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai, 200032, China
- Departments of Cardiology, Qingpu Branch of Zhongshan Hospital, Fudan University, Shanghai, 218120, China
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2
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Sharma AL, Tyagi P, Khumallambam M, Tyagi M. Cocaine-induced DNA-PK relieves RNAP II pausing by promoting TRIM28 phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.19.608673. [PMID: 39229050 PMCID: PMC11370412 DOI: 10.1101/2024.08.19.608673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Drug abuse continues to pose a significant challenge in HIV control efforts. In our investigation, we discovered that cocaine not only upregulates the expression of DNA-dependent protein kinase (DNA-PK) but also augments DNA-PK activation by enhancing its phosphorylation at S2056. Moreover, DNA-PK phosphorylation triggers the translocation of DNA-PK into the nucleus. The finding that cocaine promotes nuclear translocation of DNA-PK further validates our observation of enhanced DNA-PK recruitment at the HIV long terminal repeat (LTR) following cocaine exposure. By activating and facilitating the nuclear translocation of DNA-PK, cocaine effectively orchestrates multiple stages of HIV transcription, thereby promoting HIV replication. Additionally, our study indicates that cocaine-induced DNA-PK promotes hyper-phosphorylation of RNA polymerase II (RNAP II) carboxyl-terminal domain (CTD) at Ser5 and Ser2 sites, enhancing both initiation and elongation phases, respectively, of HIV transcription. Cocaine's enhancement of transcription initiation and elongation is further supported by its activation of cyclin-dependent kinase 7 (CDK7) and subsequent phosphorylation of CDK9, thereby promoting positive transcriptional elongation factor b (P-TEFb) activity. We demonstrate for the first time that cocaine, through DNA-PK activation, promotes the specific phosphorylation of TRIM28 at Serine 824 (p-TRIM28, S824). This modification converts TRIM28 from a transcriptional inhibitor to a transactivator for HIV transcription. Additionally, we observe that phosphorylation of TRIM28 (p-TRIM28, S824) promotes the transition from the pausing phase to the elongation phase of HIV transcription, thereby facilitating the production of full-length HIV genomic transcripts. This finding corroborates the observed enhanced RNAP II CTD phosphorylation at Ser2, a marker of transcriptional elongation, following cocaine exposure. Accordingly, upon cocaine treatment, we observed elevated recruitment of p-TRIM28-(S824) at the HIV LTR. Overall, our results have unraveled the intricate molecular mechanisms underlying cocaine-induced HIV transcription and gene expression. These findings hold promise for the development of highly targeted therapeutics aimed at mitigating the detrimental effects of cocaine in individuals living with HIV.
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Affiliation(s)
| | - Priya Tyagi
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Meenata Khumallambam
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Mudit Tyagi
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
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3
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Munshi R. How Transcription Factor Clusters Shape the Transcriptional Landscape. Biomolecules 2024; 14:875. [PMID: 39062589 PMCID: PMC11274464 DOI: 10.3390/biom14070875] [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: 06/01/2024] [Revised: 07/14/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
In eukaryotic cells, gene transcription typically occurs in discrete periods of promoter activity, interspersed with intervals of inactivity. This pattern deviates from simple stochastic events and warrants a closer examination of the molecular interactions that activate the promoter. Recent studies have identified transcription factor (TF) clusters as key precursors to transcriptional bursting. Often, these TF clusters form at chromatin segments that are physically distant from the promoter, making changes in chromatin conformation crucial for promoter-TF cluster interactions. In this review, I explore the formation and constituents of TF clusters, examining how the dynamic interplay between chromatin architecture and TF clustering influences transcriptional bursting. Additionally, I discuss techniques for visualizing TF clusters and provide an outlook on understanding the remaining gaps in this field.
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Affiliation(s)
- Rahul Munshi
- Joseph Henry Laboratories of Physics and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
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4
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Kupkova K, Shetty SJ, Hoffman EA, Bekiranov S, Auble DT. Genome-scale chromatin binding dynamics of RNA Polymerase II general transcription machinery components. EMBO J 2024; 43:1799-1821. [PMID: 38565951 PMCID: PMC11066129 DOI: 10.1038/s44318-024-00089-2] [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: 08/02/2023] [Revised: 02/20/2024] [Accepted: 02/28/2024] [Indexed: 04/04/2024] Open
Abstract
A great deal of work has revealed, in structural detail, the components of the preinitiation complex (PIC) machinery required for initiation of mRNA gene transcription by RNA polymerase II (Pol II). However, less-well understood are the in vivo PIC assembly pathways and their kinetics, an understanding of which is vital for determining how rates of in vivo RNA synthesis are established. We used competition ChIP in budding yeast to obtain genome-scale estimates of the residence times for five general transcription factors (GTFs): TBP, TFIIA, TFIIB, TFIIE and TFIIF. While many GTF-chromatin interactions were short-lived ( < 1 min), there were numerous interactions with residence times in the range of several minutes. Sets of genes with a shared function also shared similar patterns of GTF kinetic behavior. TFIIE, a GTF that enters the PIC late in the assembly process, had residence times correlated with RNA synthesis rates. The datasets and results reported here provide kinetic information for most of the Pol II-driven genes in this organism, offering a rich resource for exploring the mechanistic relationships between PIC assembly, gene regulation, and transcription.
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Affiliation(s)
- Kristyna Kupkova
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
- Center for Public Health Genomics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - Savera J Shetty
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - Elizabeth A Hoffman
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - David T Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA.
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5
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Sonsungsan P, Suratanee A, Buaboocha T, Chadchawan S, Plaimas K. Identification of Salt-Sensitive and Salt-Tolerant Genes through Weighted Gene Co-Expression Networks across Multiple Datasets: A Centralization and Differential Correlation Analysis. Genes (Basel) 2024; 15:316. [PMID: 38540375 PMCID: PMC10970189 DOI: 10.3390/genes15030316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/18/2024] [Accepted: 02/24/2024] [Indexed: 06/14/2024] Open
Abstract
Salt stress is a significant challenge that severely hampers rice growth, resulting in decreased yield and productivity. Over the years, researchers have identified biomarkers associated with salt stress to enhance rice tolerance. However, the understanding of the mechanism underlying salt tolerance in rice remains incomplete due to the involvement of multiple genes. Given the vast amount of genomics and transcriptomics data available today, it is crucial to integrate diverse datasets to identify key genes that play essential roles during salt stress in rice. In this study, we propose an integration of multiple datasets to identify potential key transcription factors. This involves utilizing network analysis based on weighted co-expression networks, focusing on gene-centric measurement and differential co-expression relationships among genes. Consequently, our analysis reveals 86 genes located in markers from previous meta-QTL analysis. Moreover, six transcription factors, namely LOC_Os03g45410 (OsTBP2), LOC_Os07g42400 (OsGATA23), LOC_Os01g13030 (OsIAA3), LOC_Os05g34050 (OsbZIP39), LOC_Os09g29930 (OsBIM1), and LOC_Os10g10990 (transcription initiation factor IIF), exhibited significantly altered co-expression relationships between salt-sensitive and salt-tolerant rice networks. These identified genes hold potential as crucial references for further investigation into the functions of salt stress response in rice plants and could be utilized in the development of salt-resistant rice cultivars. Overall, our findings shed light on the complex genetic regulation underlying salt tolerance in rice and contribute to the broader understanding of rice's response to salt stress.
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Affiliation(s)
- Pajaree Sonsungsan
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Apichat Suratanee
- Department of Mathematics, Faculty of Applied Science, King Mongkut’s University of Technology North Bangkok, Bangkok 10800, Thailand;
| | - Teerapong Buaboocha
- Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Supachitra Chadchawan
- Center of Excellence in Environment and Plant Physiology (CEEPP), Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kitiporn Plaimas
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Advanced Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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6
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Yuan T, Wu L, Li S, Zheng J, Li N, Xiao X, Zhang H, Fei T, Xie L, Zuo Z, Li D, Huang P, Feng H, Cao Y, Yan N, Wei X, Shi L, Sun Y, Wei W, Sun Y, Zuo E. Deep learning models incorporating endogenous factors beyond DNA sequences improve the prediction accuracy of base editing outcomes. Cell Discov 2024; 10:20. [PMID: 38378648 PMCID: PMC10879117 DOI: 10.1038/s41421-023-00624-1] [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: 05/30/2023] [Accepted: 11/09/2023] [Indexed: 02/22/2024] Open
Abstract
Adenine base editors (ABEs) and cytosine base editors (CBEs) enable the single nucleotide editing of targeted DNA sites avoiding generation of double strand breaks, however, the genomic features that influence the outcomes of base editing in vivo still remain to be characterized. High-throughput datasets from lentiviral integrated libraries were used to investigate the sequence features affecting base editing outcomes, but the effects of endogenous factors beyond the DNA sequences are still largely unknown. Here the base editing outcomes of ABE and CBE were evaluated in mammalian cells for 5012 endogenous genomic sites and 11,868 genome-integrated target sequences, with 4654 genomic sites sharing the same target sequences. The comparative analyses revealed that the editing outcomes of ABE and CBE at endogenous sites were substantially different from those obtained using genome-integrated sequences. We found that the base editing efficiency at endogenous target sites of both ABE and CBE was influenced by endogenous factors, including epigenetic modifications and transcriptional activity. A deep-learning algorithm referred as BE_Endo, was developed based on the endogenous factors and sequence information from our genomic datasets, and it yielded unprecedented accuracy in predicting the base editing outcomes. These findings along with the developed computational algorithms may facilitate future application of BEs for scientific research and clinical gene therapy.
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Affiliation(s)
- Tanglong Yuan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Leilei Wu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Shiyan Li
- Bio-Med Big Data Center, Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jitan Zheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi, China
| | - Nana Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiao Xiao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Haihang Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Tianyi Fei
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Long Xie
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Zhenrui Zuo
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Di Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi, China
| | | | - Hu Feng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Yaqi Cao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Nana Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Xinming Wei
- Epigenic Therapeutics, Inc., Shanghai, China
| | - Lei Shi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Yongsen Sun
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Wu Wei
- Bio-Med Big Data Center, Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- Lingang Laboratory, Shanghai, China.
| | - Yidi Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
| | - Erwei Zuo
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China.
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7
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Archuleta SR, Goodrich JA, Kugel JF. Mechanisms and Functions of the RNA Polymerase II General Transcription Machinery during the Transcription Cycle. Biomolecules 2024; 14:176. [PMID: 38397413 PMCID: PMC10886972 DOI: 10.3390/biom14020176] [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: 12/21/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Central to the development and survival of all organisms is the regulation of gene expression, which begins with the process of transcription catalyzed by RNA polymerases. During transcription of protein-coding genes, the general transcription factors (GTFs) work alongside RNA polymerase II (Pol II) to assemble the preinitiation complex at the transcription start site, open the promoter DNA, initiate synthesis of the nascent messenger RNA, transition to productive elongation, and ultimately terminate transcription. Through these different stages of transcription, Pol II is dynamically phosphorylated at the C-terminal tail of its largest subunit, serving as a control mechanism for Pol II elongation and a signaling/binding platform for co-transcriptional factors. The large number of core protein factors participating in the fundamental steps of transcription add dense layers of regulation that contribute to the complexity of temporal and spatial control of gene expression within any given cell type. The Pol II transcription system is highly conserved across different levels of eukaryotes; however, most of the information here will focus on the human Pol II system. This review walks through various stages of transcription, from preinitiation complex assembly to termination, highlighting the functions and mechanisms of the core machinery that participates in each stage.
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Affiliation(s)
| | - James A. Goodrich
- Department of Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309, USA;
| | - Jennifer F. Kugel
- Department of Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309, USA;
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8
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Rasouli M, Safari F, Sobhani N, Alavi M, Roudi R. Regulation of Cellular-Signaling Pathways by Mammalian Proteins Containing Bacterial EPIYA or EPIYA-Like Motifs Predicted to be Phosphorylated. DNA Cell Biol 2024; 43:74-84. [PMID: 38153368 DOI: 10.1089/dna.2023.0350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023] Open
Abstract
The effector proteins of several pathogenic bacteria contain the Glu-Pro-Ile-Tyr-Ala (EPIYA) motif or other similar motifs. The EPIYA motif is delivered into the host cells by type III and IV secretion systems, through which its tyrosine residue undergoes phosphorylation by host kinases. These motifs atypically interact with a wide range of Src homology 2 (SH2) domain-containing mammalian proteins through tyrosine phosphorylation, which leads to the perturbation of multiple signaling cascades, the spread of infection, and improved bacterial colonization. Interestingly, it has been reported that EPIYA (or EPIYA-like) motifs exist in mammalian proteomes and regulate mammalian cellular-signaling pathways, leading to homeostasis and disease pathophysiology. It is possible that pathogenic bacteria have exploited EPIYA (or EPIYA-like) motifs from mammalian proteins and that the mammalian EPIYA (or EPIYA-like) motifs have evolved to have highly specific interactions with SH2 domain-containing proteins. In this review, we focus on the regulation of mammalian cellular-signaling pathways by mammalian proteins containing these motifs.
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Affiliation(s)
- Mohammad Rasouli
- Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran
| | - Fatemeh Safari
- Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran
| | - Navid Sobhani
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mana Alavi
- Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran
| | - Raheleh Roudi
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology, Stanford University, Stanford, California, USA
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9
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Uemura K, Ohyama T. Physical Peculiarity of Two Sites in Human Promoters: Universality and Diverse Usage in Gene Function. Int J Mol Sci 2024; 25:1487. [PMID: 38338773 PMCID: PMC10855393 DOI: 10.3390/ijms25031487] [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: 12/08/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/12/2024] Open
Abstract
Since the discovery of physical peculiarities around transcription start sites (TSSs) and a site corresponding to the TATA box, research has revealed only the average features of these sites. Unsettled enigmas include the individual genes with these features and whether they relate to gene function. Herein, using 10 physical properties of DNA, including duplex DNA free energy, base stacking energy, protein-induced deformability, and stabilizing energy of Z-DNA, we clarified for the first time that approximately 97% of the promoters of 21,056 human protein-coding genes have distinctive physical properties around the TSS and/or position -27; of these, nearly 65% exhibited such properties at both sites. Furthermore, about 55% of the 21,056 genes had a minimum value of regional duplex DNA free energy within TSS-centered ±300 bp regions. Notably, distinctive physical properties within the promoters and free energies of the surrounding regions separated human protein-coding genes into five groups; each contained specific gene ontology (GO) terms. The group represented by immune response genes differed distinctly from the other four regarding the parameter of the free energies of the surrounding regions. A vital suggestion from this study is that physical-feature-based analyses of genomes may reveal new aspects of the organization and regulation of genes.
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Affiliation(s)
- Kohei Uemura
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan;
| | - Takashi Ohyama
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan;
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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10
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Duan M, Song S, Wasserman H, Lee PH, Liu KJ, Gordân R, He Y, Mao P. High UV damage and low repair, but not cytosine deamination, stimulate mutation hotspots at ETS binding sites in melanoma. Proc Natl Acad Sci U S A 2024; 121:e2310854121. [PMID: 38241433 PMCID: PMC10823218 DOI: 10.1073/pnas.2310854121] [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: 06/27/2023] [Accepted: 11/20/2023] [Indexed: 01/21/2024] Open
Abstract
Noncoding mutation hotspots have been identified in melanoma and many of them occur at the binding sites of E26 transformation-specific (ETS) proteins; however, their formation mechanism and functional impacts are not fully understood. Here, we used UV (Ultraviolet) damage sequencing data and analyzed cyclobutane pyrimidine dimer (CPD) formation, DNA repair, and CPD deamination in human cells at single-nucleotide resolution. Our data show prominent CPD hotspots immediately after UV irradiation at ETS binding sites, particularly at sites with a conserved TTCCGG motif, which correlate with mutation hotspots identified in cutaneous melanoma. Additionally, CPDs are repaired slower at ETS binding sites than in flanking DNA. Cytosine deamination in CPDs to uracil is suggested as an important step for UV mutagenesis. However, we found that CPD deamination is significantly suppressed at ETS binding sites, particularly for the CPD hotspot on the 5' side of the ETS motif, arguing against a role for CPD deamination in promoting ETS-associated UV mutations. Finally, we analyzed a subset of frequently mutated promoters, including the ribosomal protein genes RPL13A and RPS20, and found that mutations in the ETS motif can significantly reduce the promoter activity. Thus, our data identify high UV damage and low repair, but not CPD deamination, as the main mechanism for ETS-associated mutations in melanoma and uncover important roles of often-overlooked mutation hotspots in perturbing gene transcription.
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Affiliation(s)
- Mingrui Duan
- Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM87131
| | - Shenghan Song
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM87131
| | - Hana Wasserman
- Program in Computational Biology and Bioinformatics, Department of Biostatistics and Bioinformatics, Duke University, Durham, NC27708
| | - Po-Hsuen Lee
- Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM87131
| | - Ke Jian Liu
- Department of Pathology, Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY11794-7263
| | - Raluca Gordân
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC27708
- Department of Computer Science, Duke University, Durham, NC27708
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC27708
| | - Yi He
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM87131
| | - Peng Mao
- Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM87131
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11
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Liu X, Chen M, Qu X, Liu W, Dou Y, Liu Q, Shi D, Jiang M, Li H. Cis-Regulatory Elements in Mammals. Int J Mol Sci 2023; 25:343. [PMID: 38203513 PMCID: PMC10779164 DOI: 10.3390/ijms25010343] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
In cis-regulatory elements, enhancers and promoters with complex molecular interactions are used to coordinate gene transcription through physical proximity and chemical modifications. These processes subsequently influence the phenotypic characteristics of an organism. An in-depth exploration of enhancers and promoters can substantially enhance our understanding of gene regulatory networks, shedding new light on mammalian development, evolution and disease pathways. In this review, we provide a comprehensive overview of the intrinsic structural attributes, detection methodologies as well as the operational mechanisms of enhancers and promoters, coupled with the relevant novel and innovative investigative techniques used to explore their actions. We further elucidated the state-of-the-art research on the roles of enhancers and promoters in the realms of mammalian development, evolution and disease, and we conclude with forward-looking insights into prospective research avenues.
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Affiliation(s)
| | | | | | | | | | | | | | - Mingsheng Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, 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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12
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Chung K, Booth MJ. Sequence-independent, site-specific incorporation of chemical modifications to generate light-activated plasmids. Chem Sci 2023; 14:12693-12706. [PMID: 38020373 PMCID: PMC10646958 DOI: 10.1039/d3sc02761a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Plasmids are ubiquitous in biology, where they are used to study gene-function relationships and intricate molecular networks, and hold potential as therapeutic devices. Developing methods to control their function will advance their application in research and may also expedite their translation to clinical settings. Light is an attractive stimulus to conditionally regulate plasmid expression as it is non-invasive, and its properties such as wavelength, intensity, and duration can be adjusted to minimise cellular toxicity and increase penetration. Herein, we have developed a method to site-specifically introduce photocages into plasmids, by resynthesising one strand in a manner similar to Kunkel mutagenesis. Unlike alternative approaches to chemically modify plasmids, this method is sequence-independent at the site of modification and uses commercially available phosphoramidites. To generate our light-activated (LA) plasmids, photocleavable biotinylated nucleobases were introduced at specific sites across the T7 and CMV promoters on plasmids and bound to streptavidin to sterically block access. These LA-plasmids were then successfully used to control expression in both cell-free systems (T7 promoter) and mammalian cells (CMV promoter). These light-activated plasmids might be used to remotely control cellular activity and reduce off-target toxicity for future medical use. Our simple approach to plasmid modification might also be used to introduce novel chemical moieties for advanced function.
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Affiliation(s)
- Khoa Chung
- Department of Chemistry, University of Oxford Mansfield Road OX1 3TA Oxford UK
| | - Michael J Booth
- Department of Chemistry, University of Oxford Mansfield Road OX1 3TA Oxford UK
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
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13
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Kupkova K, Shetty SJ, Hoffman EA, Bekiranov S, Auble DT. Genome-scale chromatin interaction dynamic measurements for key components of the RNA Pol II general transcription machinery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550532. [PMID: 37546819 PMCID: PMC10402067 DOI: 10.1101/2023.07.25.550532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Background A great deal of work has revealed in structural detail the components of the machinery responsible for mRNA gene transcription initiation. These include the general transcription factors (GTFs), which assemble at promoters along with RNA Polymerase II (Pol II) to form a preinitiation complex (PIC) aided by the activities of cofactors and site-specific transcription factors (TFs). However, less well understood are the in vivo PIC assembly pathways and their kinetics, an understanding of which is vital for determining on a mechanistic level how rates of in vivo RNA synthesis are established and how cofactors and TFs impact them. Results We used competition ChIP to obtain genome-scale estimates of the residence times for five GTFs: TBP, TFIIA, TFIIB, TFIIE and TFIIF in budding yeast. While many GTF-chromatin interactions were short-lived (< 1 min), there were numerous interactions with residence times in the several minutes range. Sets of genes with a shared function also shared similar patterns of GTF kinetic behavior. TFIIE, a GTF that enters the PIC late in the assembly process, had residence times correlated with RNA synthesis rates. Conclusions The datasets and results reported here provide kinetic information for most of the Pol II-driven genes in this organism and therefore offer a rich resource for exploring the mechanistic relationships between PIC assembly, gene regulation, and transcription. The relationships between gene function and GTF dynamics suggest that shared sets of TFs tune PIC assembly kinetics to ensure appropriate levels of expression.
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Affiliation(s)
- Kristyna Kupkova
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
- Center for Public Health Genomics, University of Virginia Health System, Charlottesville, VA 22908
| | - Savera J. Shetty
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
| | - Elizabeth A. Hoffman
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
| | - David T. Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
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14
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Chiliński M, Lipiński J, Agarwal A, Ruan Y, Plewczynski D. Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions. Sci Rep 2023; 13:11693. [PMID: 37474564 PMCID: PMC10359366 DOI: 10.1038/s41598-023-38865-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/16/2023] [Indexed: 07/22/2023] Open
Abstract
There have been multiple attempts to predict the expression of the genes based on the sequence, epigenetics, and various other factors. To improve those predictions, we have decided to investigate adding protein-specific 3D interactions that play a significant role in the condensation of the chromatin structure in the cell nucleus. To achieve this, we have used the architecture of one of the state-of-the-art algorithms, ExPecto, and investigated the changes in the model metrics upon adding the spatially relevant data. We have used ChIA-PET interactions that are mediated by cohesin (24 cell lines), CTCF (4 cell lines), and RNAPOL2 (4 cell lines). As the output of the study, we have developed the Spatial Gene Expression (SpEx) algorithm that shows statistically significant improvements in most cell lines. We have compared ourselves to the baseline ExPecto model, which obtained a 0.82 Spearman's rank correlation coefficient (SCC) score, and 0.85, which is reported by newer Enformer were able to obtain the average correlation score of 0.83. However, in some cases (e.g. RNAPOL2 on GM12878), our improvement reached 0.04, and in some cases (e.g. RNAPOL2 on H1), we reached an SCC of 0.86.
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Affiliation(s)
- Mateusz Chiliński
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662, Warsaw, Poland
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland
| | | | - Abhishek Agarwal
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
- Life Sciences Institute, Zhejiang University, Zhejiang, Hangzhou, China
| | - Dariusz Plewczynski
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662, Warsaw, Poland.
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland.
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15
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Dresch JM, Conrad RD, Klonaros D, Drewell RA. Investigating the sequence landscape in the Drosophila initiator core promoter element using an enhanced MARZ algorithm. PeerJ 2023; 11:e15597. [PMID: 37366427 PMCID: PMC10290830 DOI: 10.7717/peerj.15597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023] Open
Abstract
The core promoter elements are important DNA sequences for the regulation of RNA polymerase II transcription in eukaryotic cells. Despite the broad evolutionary conservation of these elements, there is extensive variation in the nucleotide composition of the actual sequences. In this study, we aim to improve our understanding of the complexity of this sequence variation in the TATA box and initiator core promoter elements in Drosophila melanogaster. Using computational approaches, including an enhanced version of our previously developed MARZ algorithm that utilizes gapped nucleotide matrices, several sequence landscape features are uncovered, including an interdependency between the nucleotides in position 2 and 5 in the initiator. Incorporating this information in an expanded MARZ algorithm improves predictive performance for the identification of the initiator element. Overall our results demonstrate the need to carefully consider detailed sequence composition features in core promoter elements in order to make more robust and accurate bioinformatic predictions.
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16
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Chiliński M, Lipiński J, Agarwal A, Ruan Y, Plewczynski D. Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.06.535849. [PMID: 37066361 PMCID: PMC10104055 DOI: 10.1101/2023.04.06.535849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
There have been multiple attempts to predict the expression of the genes based on the sequence, epigenetics, and various other factors. To improve those predictions, we have decided to investigate adding protein-specific 3D interactions that play a major role in the compensation of the chromatin structure in the cell nucleus. To achieve this, we have used the architecture of one of the state-of-the-art algorithms, ExPecto (J. Zhou et al., 2018), and investigated the changes in the model metrics upon adding the spatially relevant data. We have used ChIA-PET interactions that are mediated by cohesin (24 cell lines), CTCF (4 cell lines), and RNAPOL2 (4 cell lines). As the output of the study, we have developed the Spatial Gene Expression (SpEx) algorithm that shows statistically significant improvements in most cell lines.
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17
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Soliman SH, Cisneros WJ, Iwanaszko M, Aoi Y, Ganesan S, Walter M, Zeidner JM, Mishra RK, Kim EY, Wolinsky SM, Hultquist JF, Shilatifard A. Enhancing HIV-1 latency reversal through regulating the elongating RNA Pol II pause-release by a small-molecule disruptor of PAF1C. SCIENCE ADVANCES 2023; 9:eadf2468. [PMID: 36888719 PMCID: PMC9995073 DOI: 10.1126/sciadv.adf2468] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 02/03/2023] [Indexed: 05/03/2023]
Abstract
The polymerase-associated factor 1 complex (PAF1C) is a key, post-initiation transcriptional regulator of both promoter-proximal pausing and productive elongation catalyzed by RNA Pol II and is also involved in transcriptional repression of viral gene expression during human immunodeficiency virus-1 (HIV-1) latency. Using a molecular docking-based compound screen in silico and global sequencing-based candidate evaluation in vivo, we identified a first-in-class, small-molecule inhibitor of PAF1C (iPAF1C) that disrupts PAF1 chromatin occupancy and induces global release of promoter-proximal paused RNA Pol II into gene bodies. Transcriptomic analysis revealed that iPAF1C treatment mimics acute PAF1 subunit depletion and impairs RNA Pol II pausing at heat shock-down-regulated genes. Furthermore, iPAF1C enhances the activity of diverse HIV-1 latency reversal agents both in cell line latency models and in primary cells from persons living with HIV-1. In sum, this study demonstrates that efficient disruption of PAF1C by a first-in-class, small-molecule inhibitor may have therapeutic potential for improving current HIV-1 latency reversal strategies.
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Affiliation(s)
- Shimaa H. A. Soliman
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - William J. Cisneros
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Marta Iwanaszko
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sheetal Ganesan
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Miriam Walter
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jacob M. Zeidner
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Rama K. Mishra
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Eun-Young Kim
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Steven M. Wolinsky
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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18
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Welsh SA, Gardini A. Genomic regulation of transcription and RNA processing by the multitasking Integrator complex. Nat Rev Mol Cell Biol 2023; 24:204-220. [PMID: 36180603 PMCID: PMC9974566 DOI: 10.1038/s41580-022-00534-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2022] [Indexed: 11/09/2022]
Abstract
In higher eukaryotes, fine-tuned activation of protein-coding genes and many non-coding RNAs pivots around the regulated activity of RNA polymerase II (Pol II). The Integrator complex is the only Pol II-associated large multiprotein complex that is metazoan specific, and has therefore been understudied for years. Integrator comprises at least 14 subunits, which are grouped into distinct functional modules. The phosphodiesterase activity of the core catalytic module is co-transcriptionally directed against several RNA species, including long non-coding RNAs (lncRNAs), U small nuclear RNAs (U snRNAs), PIWI-interacting RNAs (piRNAs), enhancer RNAs and nascent pre-mRNAs. Processing of non-coding RNAs by Integrator is essential for their biogenesis, and at protein-coding genes, Integrator is a key modulator of Pol II promoter-proximal pausing and transcript elongation. Recent studies have identified an Integrator-specific serine/threonine-protein phosphatase 2A (PP2A) module, which targets Pol II and other components of the basal transcription machinery. In this Review, we discuss how the activity of Integrator regulates transcription, RNA processing, chromatin landscape and DNA repair. We also discuss the diverse roles of Integrator in development and tumorigenesis.
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19
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Nakadai T, Shimada M, Ito K, Cevher MA, Chu CS, Kumegawa K, Maruyama R, Malik S, Roeder RG. Two target gene activation pathways for orphan ERR nuclear receptors. Cell Res 2023; 33:165-183. [PMID: 36646760 PMCID: PMC9892517 DOI: 10.1038/s41422-022-00774-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 12/02/2022] [Indexed: 01/18/2023] Open
Abstract
Estrogen-related receptors (ERRα/β/γ) are orphan nuclear receptors that function in energy-demanding physiological processes, as well as in development and stem cell maintenance, but mechanisms underlying target gene activation by ERRs are largely unknown. Here, reconstituted biochemical assays that manifest ERR-dependent transcription have revealed two complementary mechanisms. On DNA templates, ERRs activate transcription with just the normal complement of general initiation factors through an interaction of the ERR DNA-binding domain with the p52 subunit of initiation factor TFIIH. On chromatin templates, activation by ERRs is dependent on AF2 domain interactions with the cell-specific coactivator PGC-1α, which in turn recruits the ubiquitous p300 and MED1/Mediator coactivators. This role of PGC-1α may also be fulfilled by other AF2-interacting coactivators like NCOA3, which is shown to recruit Mediator selectively to ERRβ and ERRγ. Importantly, combined genetic and RNA-seq analyses establish that both the TFIIH and the AF2 interaction-dependent pathways are essential for ERRβ/γ-selective gene expression and pluripotency maintenance in embryonic stem cells in which NCOA3 is a critical coactivator.
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Affiliation(s)
- Tomoyoshi Nakadai
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
- Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Miho Shimada
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Japan
| | - Keiichi Ito
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Murat Alper Cevher
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Chi-Shuen Chu
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Kohei Kumegawa
- Cancer Cell Diversity Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Reo Maruyama
- Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA.
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20
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Nayarisseri A, Bhrdwaj A, Khan A, Sharma K, Shaheen U, Selvaraj C, Khan MA, Abhirami R, Pravin MA, Shri GR, Raje D, Singh SK. Promoter–motif extraction from co-regulated genes and their relevance to co-expression using E. coli as a model. Brief Funct Genomics 2023; 22:204-216. [PMID: 37053503 DOI: 10.1093/bfgp/elac043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/29/2022] [Accepted: 10/26/2022] [Indexed: 02/04/2023] Open
Abstract
Abstract
Gene expression varies due to the intrinsic stochasticity of transcription or as a reaction to external perturbations that generate cellular mutations. Co-regulation, co-expression and functional similarity of substances have been employed for indoctrinating the process of the transcriptional paradigm. The difficult process of analysing complicated proteomes and biological switches has been made easier by technical improvements, and microarray technology has flourished as a viable platform. Therefore, this research enables Microarray to cluster genes that are co-expressed and co-regulated into specific segments. Copious search algorithms have been employed to ascertain diacritic motifs or a combination of motifs that are performing regular expression, and their relevant information corresponding to the gene patterns is also documented. The associated genes co-expression and relevant cis-elements are further explored by engaging Escherichia coli as a model organism. Various clustering algorithms have also been used to generate classes of genes with similar expression profiles. A promoter database ‘EcoPromDB’ has been developed by referring RegulonDB database; this promoter database is freely available at www.ecopromdb.eminentbio.com and is divided into two sub-groups, depending upon the results of co-expression and co-regulation analyses.
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Affiliation(s)
- Anuraj Nayarisseri
- Eminent Biosciences In silico Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
- LeGene Biosciences Pvt Ltd Bioinformatics Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Anushka Bhrdwaj
- Eminent Biosciences In silico Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Arshiya Khan
- Eminent Biosciences In silico Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Khushboo Sharma
- Eminent Biosciences In silico Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Uzma Shaheen
- Eminent Biosciences In silico Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
| | - Chandrabose Selvaraj
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Mohammad Aqueel Khan
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Rajaram Abhirami
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Muthuraja Arun Pravin
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Gurunathan Rubha Shri
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Dhanjay Raje
- Eminent Biosciences In silico Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
| | - Sanjeev Kumar Singh
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
- Department of Data Sciences, Centre of Biomedical Research , SGPGIMS Campus, Raebareli Rd, Lucknow 226014, India
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21
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Carter ZI, Jacobs RQ, Schneider DA, Lucius AL. Transient-State Kinetic Analysis of the RNA Polymerase II Nucleotide Incorporation Mechanism. Biochemistry 2023; 62:95-108. [PMID: 36525636 PMCID: PMC10069233 DOI: 10.1021/acs.biochem.2c00608] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Eukaryotic RNA polymerase II (Pol II) is an essential enzyme that lies at the core of eukaryotic biology. Due to its pivotal role in gene expression, Pol II has been subjected to a substantial number of investigations. We aim to further our understanding of Pol II nucleotide incorporation by utilizing transient-state kinetic techniques to examine Pol II single nucleotide addition on the millisecond time scale. We analyzed Saccharomyces cerevisiae Pol II incorporation of ATP or an ATP analog, Sp-ATP-α-S. Here we have measured the rate constants governing individual steps of the Pol II transcription cycle in the presence of ATP or Sp-ATP-α-S. These results suggest that Pol II catalyzes nucleotide incorporation by binding the next cognate nucleotide and immediately catalyzes bond formation and bond formation is either followed by a conformational change or pyrophosphate release. By comparing our previously published RNA polymerase I (Pol I) and Pol I lacking the A12 subunit (Pol I ΔA12) results that we collected under the same conditions with the identical technique, we show that Pol II and Pol I ΔA12 exhibit similar nucleotide addition mechanisms. This observation indicates that removal of the A12 subunit from Pol I results in a Pol II like enzyme. Taken together, these data further our collective understanding of Pol II's nucleotide incorporation mechanism and the evolutionary divergence of RNA polymerases across the three domains of life.
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Affiliation(s)
- Zachariah I Carter
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama35233, United States
| | - Ruth Q Jacobs
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama35233, United States
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama35233, United States
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama35233, United States
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22
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Subramanian S, George TP, George J, Thomas T. Ensemble learning based assessment of the role of transcription factors in gene expression. Comput Biol Med 2023; 152:106455. [PMID: 36566628 DOI: 10.1016/j.compbiomed.2022.106455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 11/29/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Cancer cells are formed when the associated, active genes fail to function the way they are meant to function. Multiple genes collectively control cell growth by activating a proper set of genes. Regulation of gene expression is controlled through the combined effort of multiple regulatory elements. Transcription of each gene is affected differently according to the combinatorial patterns of regulatory elements bound in the nearby regions. Identifying and analysing such patterns will give a better insight into the cell function. The main focus of this study is on developing a computational model to predict the functional role of transcriptional factors residing between divergent gene pairs. Acute Myeloid Leukaemia (AML) gene expression data from GEO and the two TFs EP300 and CTCF binding data calibrated in k562 cell line from ENCODE consortium are taken as a case study.
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Affiliation(s)
| | | | - Jeslin George
- Department of Statistical Sciences, Kannur University, India.
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23
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Moonen JR, Chappell J, Shi M, Shinohara T, Li D, Mumbach MR, Zhang F, Nair RV, Nasser J, Mai DH, Taylor S, Wang L, Metzger RJ, Chang HY, Engreitz JM, Snyder MP, Rabinovitch M. KLF4 recruits SWI/SNF to increase chromatin accessibility and reprogram the endothelial enhancer landscape under laminar shear stress. Nat Commun 2022; 13:4941. [PMID: 35999210 PMCID: PMC9399231 DOI: 10.1038/s41467-022-32566-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/05/2022] [Indexed: 12/14/2022] Open
Abstract
Physiologic laminar shear stress (LSS) induces an endothelial gene expression profile that is vasculo-protective. In this report, we delineate how LSS mediates changes in the epigenetic landscape to promote this beneficial response. We show that under LSS, KLF4 interacts with the SWI/SNF nucleosome remodeling complex to increase accessibility at enhancer sites that promote the expression of homeostatic endothelial genes. By combining molecular and computational approaches we discover enhancers that loop to promoters of KLF4- and LSS-responsive genes that stabilize endothelial cells and suppress inflammation, such as BMPR2, SMAD5, and DUSP5. By linking enhancers to genes that they regulate under physiologic LSS, our work establishes a foundation for interpreting how non-coding DNA variants in these regions might disrupt protective gene expression to influence vascular disease.
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Affiliation(s)
- Jan-Renier Moonen
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - James Chappell
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Minyi Shi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Tsutomu Shinohara
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Dan Li
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Maxwell R Mumbach
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Fan Zhang
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ramesh V Nair
- Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Joseph Nasser
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Daniel H Mai
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Shalina Taylor
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Lingli Wang
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ross J Metzger
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Howard Y Chang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jesse M Engreitz
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Michael P Snyder
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Marlene Rabinovitch
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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24
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Kochumon S, Jacob T, Koshy M, Al-Rashed F, Sindhu S, Al-Ozairi E, Al-Mulla F, Rosen ED, Ahmad R. Palmitate Potentiates Lipopolysaccharide-Induced IL-6 Production via Coordinated Acetylation of H3K9/H3K18, p300, and RNA Polymerase II. THE JOURNAL OF IMMUNOLOGY 2022; 209:731-741. [DOI: 10.4049/jimmunol.2100928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 06/08/2022] [Indexed: 01/04/2023]
Abstract
Abstract
IL-6 is elevated in obese individuals and participates in the metabolic dysfunction associated with that condition. However, the mechanisms that promote IL-6 expression in obesity are incompletely understood. Because elevated levels of palmitate and LPS have been reported in obesity, we investigated whether these agents interact to potentiate IL-6 production. In this study, we report that LPS induces higher levels of IL-6 in human monocytes in the presence of palmitate. Notably, the priming effect of palmitate is associated with enhanced p300 binding and transcription factor recruitment to Il6 promoter regions. Gene silencing of p300 blocks this action of palmitate. RNA polymerase II recruitment was also enhanced at the Il6 promoter in palmitate/LPS-exposed cells. Acetylation levels of H3K9 and H3K18 were increased in monocytes treated with palmitate. Moreover, LPS stimulation of palmitate-treated cells led to increased levels of the transcriptionally permissive acetylation marks H3K9/H3K18 in the Il6 promoter compared with LPS alone. The effect of palmitate on LPS-induced IL-6 production was suppressed by the inhibition of histone acetyltransferases. Conversely, histone deacetylase inhibitors trichostatin A or sodium butyrate can substitute for palmitate in IL-6 production. Esterification of palmitate with CoA was involved, whereas β-oxidation and ceramide biosynthesis were not required, for the induction of IL-6 and H3K9/H3K18 acetylation. Monocytes of obese individuals showed significantly higher H3K9/H3K18 acetylation and Il6 expression. Overall, our findings support a model in which increased levels of palmitate in obesity create a setting for LPS to potentiate IL-6 production via chromatin remodeling, enabling palmitate to contribute to metabolic inflammation.
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Affiliation(s)
- Shihab Kochumon
- *Immunology and Microbiology Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Texy Jacob
- *Immunology and Microbiology Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Merin Koshy
- *Immunology and Microbiology Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Fatema Al-Rashed
- *Immunology and Microbiology Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Sardar Sindhu
- *Immunology and Microbiology Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Ebaa Al-Ozairi
- †Medical Division, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Fahd Al-Mulla
- ‡Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Evan D. Rosen
- §Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA; and
- ¶Harvard Medical School, Boston, MA
| | - Rasheed Ahmad
- *Immunology and Microbiology Department, Dasman Diabetes Institute, Kuwait City, Kuwait
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25
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Peil K, Värv S, Ilves I, Kristjuhan K, Jürgens H, Kristjuhan A. Transcriptional regulator Taf14 binds DNA and is required for the function of transcription factor TFIID in the absence of histone H2A.Z. J Biol Chem 2022; 298:102369. [PMID: 35970389 PMCID: PMC9478928 DOI: 10.1016/j.jbc.2022.102369] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 11/16/2022] Open
Abstract
The transcriptional regulator Taf14 is a component of multiple protein complexes involved in transcription initiation and chromatin remodeling in yeast cells. Although Taf14 is not required for cell viability, it becomes essential in conditions where the formation of the transcription preinitiation complex is hampered. The specific role of Taf14 in mediating transcription initiation and preinitiation complex formation is unclear. Here, we explored its role in the general transcription factor IID by mapping Taf14 genetic and proteomic interactions and found that it was needed for the function of the complex if Htz1, the yeast homolog of histone H2A.Z, was absent from chromatin. Dissecting the functional domains of Taf14 revealed that the linker region between the YEATS and ET domains was required for cell viability in the absence of Htz1 protein. We further show that the linker region of Taf14 interacts with DNA. We propose that providing additional DNA binding capacity might be a general role of Taf14 in the recruitment of protein complexes to DNA and chromatin.
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Affiliation(s)
- Kadri Peil
- Institute of Molecular and Cell Biology, University of Tartu; Riia 23, Tartu 51010, Estonia
| | - Signe Värv
- Institute of Molecular and Cell Biology, University of Tartu; Riia 23, Tartu 51010, Estonia
| | - Ivar Ilves
- Institute of Technology, University of Tartu; Nooruse 1, Tartu 50411, Estonia
| | - Kersti Kristjuhan
- Institute of Molecular and Cell Biology, University of Tartu; Riia 23, Tartu 51010, Estonia
| | - Henel Jürgens
- Institute of Molecular and Cell Biology, University of Tartu; Riia 23, Tartu 51010, Estonia
| | - Arnold Kristjuhan
- Institute of Molecular and Cell Biology, University of Tartu; Riia 23, Tartu 51010, Estonia.
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26
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Morgan M, Shiekhattar R, Shilatifard A, Lauberth SM. It's a DoG-eat-DoG world-altered transcriptional mechanisms drive downstream-of-gene (DoG) transcript production. Mol Cell 2022; 82:1981-1991. [PMID: 35487209 PMCID: PMC9208299 DOI: 10.1016/j.molcel.2022.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/24/2022] [Accepted: 04/04/2022] [Indexed: 10/18/2022]
Abstract
The past decade has revolutionized our understanding of regulatory noncoding RNAs (ncRNAs). Among the most recently identified ncRNAs are downstream-of-gene (DoG)-containing transcripts that are produced by widespread transcriptional readthrough. The discovery of DoGs has set the stage for future studies to address many unanswered questions regarding the mechanisms that promote readthrough transcription, RNA processing, and the cellular functions of the unique transcripts. In this review, we summarize current findings regarding the biogenesis, function, and mechanisms regulating this exciting new class of RNA molecules.
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Affiliation(s)
- Marc Morgan
- Simpson Querrey Institute for Epigenetics and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ramin Shiekhattar
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Shannon M Lauberth
- Simpson Querrey Institute for Epigenetics and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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27
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Belk JA, Daniel B, Satpathy AT. Epigenetic regulation of T cell exhaustion. Nat Immunol 2022; 23:848-860. [PMID: 35624210 PMCID: PMC10439681 DOI: 10.1038/s41590-022-01224-z] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 04/06/2022] [Indexed: 12/15/2022]
Abstract
Chronic antigen stimulation during viral infections and cancer can lead to T cell exhaustion, which is characterized by reduced effector function and proliferation, and the expression of inhibitory immune checkpoint receptors. Recent studies have demonstrated that T cell exhaustion results in wholescale epigenetic remodeling that confers phenotypic stability to these cells and prevents T cell reinvigoration by checkpoint blockade. Here, we review foundational technologies to profile the epigenome at multiple scales, including mapping the locations of transcription factors and histone modifications, DNA methylation and three-dimensional genome conformation. We discuss how these technologies have elucidated the development and epigenetic regulation of exhausted T cells and functional implications across viral infection, cancer, autoimmunity and engineered T cell therapies. Finally, we cover emerging multi-omic and genome engineering technologies, current and upcoming opportunities to apply these to T cell exhaustion, and therapeutic opportunities for T cell engineering in the clinic.
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Affiliation(s)
- Julia A Belk
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Bence Daniel
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Ansuman T Satpathy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Parker Institute for Cancer Immunotherapy, Stanford University, Stanford, CA, USA.
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28
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Wiegard A, Kuzin V, Cameron DP, Grosser J, Ceribelli M, Mehmood R, Ballarino R, Valant F, Grochowski R, Karabogdan I, Crosetto N, Lindqvist A, Bizard AH, Kouzine F, Natsume T, Baranello L. Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1. Mol Cell 2021; 81:5007-5024.e9. [PMID: 34767771 DOI: 10.1016/j.molcel.2021.10.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/26/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022]
Abstract
As cells enter mitosis, chromatin compacts to facilitate chromosome segregation yet remains transcribed. Transcription supercoils DNA to levels that can impede further progression of RNA polymerase II (RNAPII) unless it is removed by DNA topoisomerase 1 (TOP1). Using ChIP-seq on mitotic cells, we found that TOP1 is required for RNAPII translocation along genes. The stimulation of TOP1 activity by RNAPII during elongation allowed RNAPII clearance from genes in prometaphase and enabled chromosomal segregation. Disruption of the TOP1-RNAPII interaction impaired RNAPII spiking at promoters and triggered defects in the post-mitotic transcription program. This program includes factors necessary for cell growth, and cells with impaired TOP1-RNAPII interaction are more sensitive to inhibitors of mTOR signaling. We conclude that TOP1 is necessary for assisting transcription during mitosis with consequences for growth and gene expression long after mitosis is completed. In this sense, TOP1 ensures that cellular memory is preserved in subsequent generations.
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Affiliation(s)
- Anika Wiegard
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Vladislav Kuzin
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Donald P Cameron
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Jan Grosser
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Michele Ceribelli
- Division of Pre-Clinical Innovation, NCATS, National Institutes of Health, Rockville, MD 20850, USA
| | - Rashid Mehmood
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden; Department of Software Engineering, University of Kotli, AJ&K, 45320 Kotli Azad Kashmir, Pakistan
| | - Roberto Ballarino
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Francesco Valant
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Radosław Grochowski
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
| | | | - Nicola Crosetto
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Arne Lindqvist
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Anna Helene Bizard
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Fedor Kouzine
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Toyoaki Natsume
- Department of Chromosome Science, National Institute of Genetics, Shizuoka 411-8540, Japan; Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Laura Baranello
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden.
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29
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Yu X, Qu C, Ke L, Tong Z, Li W. Step-by-Step Construction of Gene Co-Expression Network Analysis for Identifying Novel Biomarkers of Sepsis Occurrence and Progression. Int J Gen Med 2021; 14:6047-6057. [PMID: 34594129 PMCID: PMC8478343 DOI: 10.2147/ijgm.s328076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/10/2021] [Indexed: 12/23/2022] Open
Abstract
Background Sepsis is the leading cause of death in critically ill patients. Although it is well known that the immune system plays a key role in sepsis, exactly how it works remains unknown. Methods In our study, we used weighted gene co-expression network analysis (WGCNA) to screen out the immune-related genes that may play a critical role in the process of sepsis. Results A total of three sepsis-related hub genes were screened for further verification. Subsequent analysis of immune subtypes suggested their potential predictive effect in the clinic. Conclusion Our study shows that three immune-related genes CHMP1A, MED15 and MGAT1 are important biomarkers of sepsis. The screened genes may help to distinguish normal individuals from patients with different degrees of sepsis.
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Affiliation(s)
- Xianqiang Yu
- Medical School, Southeast University, Nanjing, People's Republic of China
| | - Cheng Qu
- Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, People's Republic of China
| | - Lu Ke
- Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, People's Republic of China
| | - Zhihui Tong
- Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, People's Republic of China
| | - Weiqin Li
- Medical School, Southeast University, Nanjing, People's Republic of China.,Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, People's Republic of China
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30
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Goszczynski DE, Tinetti PS, Choi YH, Hinrichs K, Ross PJ. Genome activation in equine in vitro-produced embryos. Biol Reprod 2021; 106:66-82. [PMID: 34515744 DOI: 10.1093/biolre/ioab173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/17/2021] [Accepted: 09/07/2021] [Indexed: 11/13/2022] Open
Abstract
Embryonic genome activation is a critical event in embryo development, in which the transcriptional program of the embryo is initiated. The timing and regulation of this process are species-specific. In vitro embryo production is becoming an important clinical and research tool in the horse; however, very little is known about genome activation in this species. The objective of this work was to identify the timing of genome activation, and the transcriptional networks involved, in in vitro-produced horse embryos. RNA-Seq was performed on oocytes and embryos at eight stages of development (MII, zygote, 2-cell, 4-cell, 8-cell, 16-cell, morula, blastocyst; n = 6 per stage, 2 from each of 3 mares). Transcription of seven genes was initiated at the 2-cell stage. The first substantial increase in gene expression occurred at the 4-cell stage (minor activation), followed by massive gene upregulation and downregulation at the 8-cell stage (major activation). An increase in intronic nucleotides, indicative of transcription initiation, was also observed at the 4-cell stage. Co-expression network analyses identified groups of genes that appeared to be regulated by common mechanisms. Investigation of hub genes and binding motifs enriched in the promoters of co-expressed genes implicated several transcription factors. This work represents, to the best of our knowledge, the first genomic evaluation of embryonic genome activation in horse embryos.
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Affiliation(s)
- D E Goszczynski
- Department of Animal Science, University of California, Davis, CA, USA
| | - P S Tinetti
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, USA
| | - Y H Choi
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, USA
| | - K Hinrichs
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, USA
| | - P J Ross
- Department of Animal Science, University of California, Davis, CA, USA
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31
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Petrenko N, Struhl K. Comparison of transcriptional initiation by RNA polymerase II across eukaryotic species. eLife 2021; 10:e67964. [PMID: 34515029 PMCID: PMC8463073 DOI: 10.7554/elife.67964] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 09/10/2021] [Indexed: 01/17/2023] Open
Abstract
The preinitiation complex (PIC) for transcriptional initiation by RNA polymerase (Pol) II is composed of general transcription factors that are highly conserved. However, analysis of ChIP-seq datasets reveals kinetic and compositional differences in the transcriptional initiation process among eukaryotic species. In yeast, Mediator associates strongly with activator proteins bound to enhancers, but it transiently associates with promoters in a form that lacks the kinase module. In contrast, in human, mouse, and fly cells, Mediator with its kinase module stably associates with promoters, but not with activator-binding sites. This suggests that yeast and metazoans differ in the nature of the dynamic bridge of Mediator between activators and Pol II and the composition of a stable inactive PIC-like entity. As in yeast, occupancies of TATA-binding protein (TBP) and TBP-associated factors (Tafs) at mammalian promoters are not strictly correlated. This suggests that within PICs, TFIID is not a monolithic entity, and multiple forms of TBP affect initiation at different classes of genes. TFIID in flies, but not yeast and mammals, interacts strongly at regions downstream of the initiation site, consistent with the importance of downstream promoter elements in that species. Lastly, Taf7 and the mammalian-specific Med26 subunit of Mediator also interact near the Pol II pause region downstream of the PIC, but only in subsets of genes and often not together. Species-specific differences in PIC structure and function are likely to affect how activators and repressors affect transcriptional activity.
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Affiliation(s)
- Natalia Petrenko
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
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32
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Mo JS, Chae SC. MicroRNA 452 regulates GTF2E1 expression in colorectal cancer cells. J Genet 2021. [PMID: 34553694 DOI: 10.1007/s12041-021-01312-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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33
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de Sousa LO, Oliveira LN, Naves RB, Pereira ALA, Santiago Freitas E Silva K, de Almeida Soares CM, de Sousa Lima P. The dual role of SrbA from Paracoccidioides lutzii: a hypoxic regulator. Braz J Microbiol 2021; 52:1135-1149. [PMID: 34148216 PMCID: PMC8382145 DOI: 10.1007/s42770-021-00527-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/12/2021] [Indexed: 11/26/2022] Open
Abstract
The fungus Paracoccidioides lutzii is one of the species of the Paracoccidioides genus, responsible for a neglected human mycosis, endemic in Latin America, the paracoccidioidomycosis (PCM). In order to survive in the host, the fungus overcomes a hostile environment under low levels of oxygen (hypoxia) during the infectious process. The hypoxia adaptation mechanisms are variable among human pathogenic fungi and worthy to be investigated in Paracoccidoides spp. Previous proteomic results identified that P. lutzii responds to hypoxia and it has a functional homolog of the SrbA transcription factor, a well-described hypoxic regulator. However, the direct regulation of genes by SrbA and the biological processes it governs while performing protein interactions have not been revealed yet. The goal of this study was to demonstrate the potential of SrbA targets genes in P. lutzii. In addition, to show the SrbA three-dimensional aspects as well as a protein interaction map and important regions of interaction with predicted targets. The results show that SrbA-regulated genes were involved with several biological categories, such as metabolism, energy, basal processes for cell maintenance, fungal morphogenesis, defense, virulence, and signal transduction. Moreover, in order to investigate the SrbA's role as a protein, we performed a 3D simulation and also a protein-protein network linked to this hypoxic regulator. These in silico analyses revealed relevant aspects regarding the biology of this pathogen facing hypoxia and highlight the potential of SrbA as an antifungal target in the future.
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Affiliation(s)
- Lorena Ordones de Sousa
- Unidade Universitária de Itapuranga, Câmpus Cora Coralina, Instituto Acadêmico de Ciências da Saúde e Biológicas, Universidade Estadual de Goiás, Itapuranga, Goiás, Brazil
| | - Lucas Nojosa Oliveira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Raphaela Barbosa Naves
- Unidade Universitária de Itapuranga, Câmpus Cora Coralina, Instituto Acadêmico de Ciências da Saúde e Biológicas, Universidade Estadual de Goiás, Itapuranga, Goiás, Brazil
| | - André Luiz Araújo Pereira
- Unidade Universitária de Itapuranga, Câmpus Cora Coralina, Instituto Acadêmico de Ciências da Saúde e Biológicas, Universidade Estadual de Goiás, Itapuranga, Goiás, Brazil
| | - Kleber Santiago Freitas E Silva
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Patrícia de Sousa Lima
- Unidade Universitária de Itapuranga, Câmpus Cora Coralina, Instituto Acadêmico de Ciências da Saúde e Biológicas, Universidade Estadual de Goiás, Itapuranga, Goiás, Brazil.
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Ajdary M, Farzan S, Razavi Y, Arabdolatabadi A, Haghparast A. Effects of Morphine on Serum Reproductive Hormone Levels and the Expression of Genes Involved in Fertility-related Pathways in Male Rats. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2021; 20:153-164. [PMID: 34400949 PMCID: PMC8170771 DOI: 10.22037/ijpr.2019.112119.13544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The effects of morphine on serum reproductive hormone levels and markers involved in fertility-related pathways were evaluated. A total of 30 male Wistar rats were divided into three groups (n = 10) and intraperitoneally administered the following substances for 20 days: two single daily doses of morphine (10 mg/kg; morphine group), saline (healthy saline), and intact group. After confirming the morphine dependence of the experimental groups, all the animals were sacrificed and their total testis tissue was extracted and stored at -80 °C until use. Male reproductive parameters (blood serum of testosterone, luteinizing hormone, and follicle-stimulating hormone) and using Q-PCR and western blot, we evaluated mRNA and protein expression of CREM, TBP, CREB1, HDAC1, and FOS involved in fertility-related pathways were analyzed and compared in the testis samples. The luteinizing hormone and testosterone levels were significantly lower in the morphine-administered group than in the saline and intact groups (P < 0.05). Moreover, the expressions of all five target genes were downregulated in the morphine group (P < 0.05). The protein expression of all five target proteins was downregulated in the morphine group (P < 0.05). We concluded that morphine could decrease the reproductive parameters in male rats.
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Affiliation(s)
- Marziyeh Ajdary
- Abadan Faculty of Medical Sciences, Abadan, Iran.,Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Sina Farzan
- Department of Anesthesiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Yasaman Razavi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Abbas Arabdolatabadi
- Young Researchers and Elite Club, Yazd Branch, Islamic Azad University, Yazd, Iran
| | - Abbas Haghparast
- Neuroscience Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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35
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Uruci S, Lo CSY, Wheeler D, Taneja N. R-Loops and Its Chro-Mates: The Strange Case of Dr. Jekyll and Mr. Hyde. Int J Mol Sci 2021; 22:ijms22168850. [PMID: 34445553 PMCID: PMC8396322 DOI: 10.3390/ijms22168850] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/04/2021] [Accepted: 08/12/2021] [Indexed: 12/22/2022] Open
Abstract
Since their discovery, R-loops have been associated with both physiological and pathological functions that are conserved across species. R-loops are a source of replication stress and genome instability, as seen in neurodegenerative disorders and cancer. In response, cells have evolved pathways to prevent R-loop accumulation as well as to resolve them. A growing body of evidence correlates R-loop accumulation with changes in the epigenetic landscape. However, the role of chromatin modification and remodeling in R-loops homeostasis remains unclear. This review covers various mechanisms precluding R-loop accumulation and highlights the role of chromatin modifiers and remodelers in facilitating timely R-loop resolution. We also discuss the enigmatic role of RNA:DNA hybrids in facilitating DNA repair, epigenetic landscape and the potential role of replication fork preservation pathways, active fork stability and stalled fork protection pathways, in avoiding replication-transcription conflicts. Finally, we discuss the potential role of several Chro-Mates (chromatin modifiers and remodelers) in the likely differentiation between persistent/detrimental R-loops and transient/benign R-loops that assist in various physiological processes relevant for therapeutic interventions.
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Affiliation(s)
- Sidrit Uruci
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
| | - Calvin Shun Yu Lo
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA;
| | - Nitika Taneja
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
- Correspondence:
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Baek I, Friedman LJ, Gelles J, Buratowski S. Single-molecule studies reveal branched pathways for activator-dependent assembly of RNA polymerase II pre-initiation complexes. Mol Cell 2021; 81:3576-3588.e6. [PMID: 34384542 DOI: 10.1016/j.molcel.2021.07.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/08/2021] [Accepted: 07/21/2021] [Indexed: 01/24/2023]
Abstract
RNA polymerase II (RNA Pol II) transcription reconstituted from purified factors suggests pre-initiation complexes (PICs) can assemble by sequential incorporation of factors at the TATA box. However, these basal transcription reactions are generally independent of activators and co-activators. To study PIC assembly under more realistic conditions, we used single-molecule microscopy to visualize factor dynamics during activator-dependent reactions in nuclear extracts. Surprisingly, RNA Pol II, TFIIF, and TFIIE can pre-assemble on enhancer-bound activators before loading into PICs, and multiple RNA Pol II complexes can bind simultaneously to create a localized cluster. Unlike TFIIF and TFIIE, TFIIH binding is singular and dependent on the basal promoter. Activator-tethered factors exhibit dwell times on the order of seconds. In contrast, PICs can persist on the order of minutes in the absence of nucleotide triphosphates, although TFIIE remains unexpectedly dynamic even after TFIIH incorporation. Our kinetic measurements lead to a new branched model for activator-dependent PIC assembly.
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Affiliation(s)
- Inwha Baek
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Larry J Friedman
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA.
| | - Stephen Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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Compe E, Egly JM. The Long Road to Understanding RNAPII Transcription Initiation and Related Syndromes. Annu Rev Biochem 2021; 90:193-219. [PMID: 34153211 DOI: 10.1146/annurev-biochem-090220-112253] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In eukaryotes, transcription of protein-coding genes requires the assembly at core promoters of a large preinitiation machinery containing RNA polymerase II (RNAPII) and general transcription factors (GTFs). Transcription is potentiated by regulatory elements called enhancers, which are recognized by specific DNA-binding transcription factors that recruit cofactors and convey, following chromatin remodeling, the activating cues to the preinitiation complex. This review summarizes nearly five decades of work on transcription initiation by describing the sequential recruitment of diverse molecular players including the GTFs, the Mediator complex, and DNA repair factors that support RNAPII to enable RNA synthesis. The elucidation of the transcription initiation mechanism has greatly benefited from the study of altered transcription components associated with human diseases that could be considered transcription syndromes.
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Affiliation(s)
- Emmanuel Compe
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch CEDEX, Commune Urbaine de Strasbourg, France; ,
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch CEDEX, Commune Urbaine de Strasbourg, France; , .,College of Medicine, National Taiwan University, Taipei 10051, Taiwan
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38
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Danielewski M, Matuszewska A, Szeląg A, Sozański T. The Impact of Anthocyanins and Iridoids on Transcription Factors Crucial for Lipid and Cholesterol Homeostasis. Int J Mol Sci 2021; 22:6074. [PMID: 34199904 PMCID: PMC8200123 DOI: 10.3390/ijms22116074] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/29/2021] [Accepted: 06/03/2021] [Indexed: 12/17/2022] Open
Abstract
Nutrition determines our health, both directly and indirectly. Consumed foods affect the functioning of individual organs as well as entire systems, e.g., the cardiovascular system. There are many different diets, but universal guidelines for proper nutrition are provided in the WHO healthy eating pyramid. According to the latest version, plant products should form the basis of our diet. Many groups of plant compounds with a beneficial effect on human health have been described. Such groups include anthocyanins and iridoids, for which it has been proven that their consumption may lead to, inter alia, antioxidant, cholesterol and lipid-lowering, anti-obesity and anti-diabetic effects. Transcription factors directly affect a number of parameters of cell functions and cellular metabolism. In the context of lipid and cholesterol metabolism, five particularly important transcription factors can be distinguished: liver X receptor (LXR), peroxisome proliferator-activated receptor-α (PPAR-α), peroxisome proliferator-activated receptor-γ (PPAR-γ), CCAAT/enhancer binding protein α (C/EBPα) and sterol regulatory element-binding protein 1c (SREBP-1c). Both anthocyanins and iridoids may alter the expression of these transcription factors. The aim of this review is to collect and systematize knowledge about the impact of anthocyanins and iridoids on transcription factors crucial for lipid and cholesterol homeostasis.
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Affiliation(s)
- Maciej Danielewski
- Department of Pharmacology, Wroclaw Medical University, Jana Mikulicza-Radeckiego 2, 50-345 Wroclaw, Poland; (A.M.); (A.S.); (T.S.)
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Huffines AK, Edwards YJK, Schneider DA. Spt4 Promotes Pol I Processivity and Transcription Elongation. Genes (Basel) 2021; 12:413. [PMID: 33809333 PMCID: PMC8000598 DOI: 10.3390/genes12030413] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 01/25/2023] Open
Abstract
RNA polymerases (Pols) I, II, and III collectively synthesize most of the RNA in a eukaryotic cell. Transcription by Pols I, II, and III is regulated by hundreds of trans-acting factors. One such protein, Spt4, has been previously identified as a transcription factor that influences both Pols I and II. Spt4 forms a complex with Spt5, described as the Spt4/5 complex (or DSIF in mammalian cells). This complex has been shown previously to directly interact with Pol I and potentially affect transcription elongation. The previous literature identified defects in transcription by Pol I when SPT4 was deleted, but the necessary tools to characterize the mechanism of this effect were not available at the time. Here, we use a technique called Native Elongating Transcript Sequencing (NET-seq) to probe for the global occupancy of Pol I in wild-type (WT) and spt4△ Saccharomyces cerevisiae (yeast) cells at single nucleotide resolution in vivo. Analysis of NET-seq data reveals that Spt4 promotes Pol I processivity and enhances transcription elongation through regions of the ribosomal DNA that are particularly G-rich. These data suggest that Spt4/5 may directly affect transcription elongation by Pol I in vivo.
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Affiliation(s)
| | | | - David A. Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham 720 20th Street South, Birmingham, AL 35294, USA; (A.K.H.); (Y.J.K.E.)
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40
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Falak N, Imran QM, Hussain A, Yun BW. Transcription Factors as the "Blitzkrieg" of Plant Defense: A Pragmatic View of Nitric Oxide's Role in Gene Regulation. Int J Mol Sci 2021; 22:E522. [PMID: 33430258 PMCID: PMC7825681 DOI: 10.3390/ijms22020522] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/30/2020] [Accepted: 01/05/2021] [Indexed: 12/24/2022] Open
Abstract
Plants are in continuous conflict with the environmental constraints and their sessile nature demands a fine-tuned, well-designed defense mechanism that can cope with a multitude of biotic and abiotic assaults. Therefore, plants have developed innate immunity, R-gene-mediated resistance, and systemic acquired resistance to ensure their survival. Transcription factors (TFs) are among the most important genetic components for the regulation of gene expression and several other biological processes. They bind to specific sequences in the DNA called transcription factor binding sites (TFBSs) that are present in the regulatory regions of genes. Depending on the environmental conditions, TFs can either enhance or suppress transcriptional processes. In the last couple of decades, nitric oxide (NO) emerged as a crucial molecule for signaling and regulating biological processes. Here, we have overviewed the plant defense system, the role of TFs in mediating the defense response, and that how NO can manipulate transcriptional changes including direct post-translational modifications of TFs. We also propose that NO might regulate gene expression by regulating the recruitment of RNA polymerase during transcription.
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Affiliation(s)
- Noreen Falak
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National University, Daegu 702-701, Korea; (N.F.); (Q.M.I.)
| | - Qari Muhammad Imran
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National University, Daegu 702-701, Korea; (N.F.); (Q.M.I.)
- Department of Medical Biochemistry and Biophysics, Umea University, 90187 Umea, Sweden
| | - Adil Hussain
- Department of Agriculture, Abdul Wali Khan University, Mardan, Khyber Pakhtunkhwa 23200, Pakistan;
| | - Byung-Wook Yun
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National University, Daegu 702-701, Korea; (N.F.); (Q.M.I.)
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41
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Grant PA, Winston F, Berger SL. The biochemical and genetic discovery of the SAGA complex. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194669. [PMID: 33338653 DOI: 10.1016/j.bbagrm.2020.194669] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022]
Abstract
One of the major advances in our understanding of gene regulation in eukaryotes was the discovery of factors that regulate transcription by controlling chromatin structure. Prominent among these discoveries was the demonstration that Gcn5 is a histone acetyltransferase, establishing a direct connection between transcriptional activation and histone acetylation. This breakthrough was soon followed by the purification of a protein complex that contains Gcn5, the SAGA complex. In this article, we review the early genetic and biochemical experiments that led to the discovery of SAGA and the elucidation of its multiple activities.
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Affiliation(s)
- Patrick A Grant
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, United States of America
| | - Fred Winston
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States of America.
| | - Shelley L Berger
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Department of Biology, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
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42
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Takahata S, Asanuma T, Mori M, Murakami Y. Construction and characterization of a zinc-inducible gene expression vector in fission yeast. Yeast 2020; 38:251-261. [PMID: 33245560 DOI: 10.1002/yea.3539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/07/2020] [Accepted: 11/16/2020] [Indexed: 11/08/2022] Open
Abstract
Gene expression vectors are useful and important tools that are commonly used in a variety of experiments, including expression of foreign genes, functional analysis of genes of interest and complementation experiments. In this study, a hybrid promoter, combining the adh1+ upstream activating sequence (UAS) of fission yeast and the GAL10 core promoter of budding yeast, was constructed to enable high level expression depending on the presence of zinc in culture medium for fission yeast. When the hybrid promoter was cloned on the multicopy plasmid, it was fully induced and repressed within 10 h in the presence and absence of zinc, respectively. The kinetics of induction and reduction were similar to those of the endogenous adh1+ mRNA. In contrast, native adh1+ promoter lost its tight repression in zinc-depleted condition when it was cloned on the plasmid. Because adh1+ UAS-specific transcription factors have not yet been identified, we identified UAS elements involved in zinc sensing by characterizing this hybrid promoter. We also found that the expression level increased by the TATA box mutation, GATAA, in the presence of zinc.
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Affiliation(s)
- Shinya Takahata
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Takahiro Asanuma
- Graduate School of Chemical Science and Engineering, Hokkaido University, Sapporo, Japan
| | - Miyuki Mori
- Graduate School of Chemical Science and Engineering, Hokkaido University, Sapporo, Japan
| | - Yota Murakami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
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43
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Cui G, Dong Q, Duan J, Zhang C, Liu X, He Q. NC2 complex is a key factor for the activation of catalase-3 transcription by regulating H2A.Z deposition. Nucleic Acids Res 2020; 48:8332-8348. [PMID: 32633757 PMCID: PMC7470962 DOI: 10.1093/nar/gkaa552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 06/05/2020] [Accepted: 06/19/2020] [Indexed: 12/16/2022] Open
Abstract
Negative cofactor 2 (NC2), including two subunits NC2α and NC2β, is a conserved positive/negative regulator of class II gene transcription in eukaryotes. It is known that NC2 functions by regulating the assembly of the transcription preinitiation complex. However, the exact role of NC2 in transcriptional regulation is still unclear. Here, we reveal that, in Neurospora crassa, NC2 activates catalase-3 (cat-3) gene transcription in the form of heterodimer mediated by histone fold (HF) domains of two subunits. Deletion of HF domain in either of two subunits disrupts the NC2α–NC2β interaction and the binding of intact NC2 heterodimer to cat-3 locus. Loss of NC2 dramatically increases histone variant H2A.Z deposition at cat-3 locus. Further studies show that NC2 recruits chromatin remodeling complex INO80C to remove H2A.Z from the nucleosomes around cat-3 locus, resulting in transcriptional activation of cat-3. Besides HF domains of two subunits, interestingly, C-terminal repression domain of NC2β is required not only for NC2 binding to cat-3 locus, but also for the recruitment of INO80C to cat-3 locus and removal of H2A.Z from the nucleosomes. Collectively, our findings reveal a novel mechanism of NC2 in transcription activation through recruiting INO80C to remove H2A.Z from special H2A.Z-containing nucleosomes.
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Affiliation(s)
- Guofei Cui
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qing Dong
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jiabin Duan
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Chengcheng Zhang
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiao Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Qun He
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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44
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Transcriptional cyclin-dependent kinases as the mediators of inflammation-a review. Gene 2020; 769:145200. [PMID: 33031895 DOI: 10.1016/j.gene.2020.145200] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/18/2020] [Accepted: 09/29/2020] [Indexed: 12/19/2022]
Abstract
Cyclin-dependent kinases (CDKs) belong to the serine/threonine kinase family, and their unique interactions with a variety of cyclin complexes influence its catalytic activity to ensure unimpaired cell cycle progression. In addition to their cell cycle regulatory roles, it is becoming increasingly clear that the CDKs can have multiple functional roles like transcription, epigenetic regulation, metabolism, stem cell self-renewal, neuronal functions, and in spermatogenesis. Further in addition, recent reports suggest that CDKs have a remarkable regulatory role in influencing the pro-inflammatory functions of various cytokines during the clinical inflammatory responses. CDKs initiate the inflammatory responses by triggering the activity of prominent pro-inflammatory transcription factors such as nuclear factor kappa B (NF-kB), signal transducer and activator of transcription 3 (STAT3), and activator protein 1 (AP-1). The transcriptional CDKs (tCDKs) is crucial for organizing various transcription events and associated processes such as RNA capping, splicing, 3' end formation, and chromatin remodeling. Although the in-depth mechanism of certain mammalian CDKs is explored with respect to inflammation, the role of other tCDKs or any synergistic play among the members still remains unexplored. Until today, there is only supportive and palliative care available most of the inflammatory disorders, and thus it is the right time to explore novel pharmacological targets. In this regard, we focus on the pathophysiological role of CDK7, CDK8 and CDK9 and their impact on the development of inflammatory disorders within the mammals. Additionally, we discuss the potential trends of having tCDKs as a therapeutic target for fine-tuning inflammatory disorders.
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Zicari S, Sharma AL, Sahu G, Dubrovsky L, Sun L, Yue H, Jada T, Ochem A, Simon G, Bukrinsky M, Tyagi M. DNA dependent protein kinase (DNA-PK) enhances HIV transcription by promoting RNA polymerase II activity and recruitment of transcription machinery at HIV LTR. Oncotarget 2020; 11:699-726. [PMID: 32133046 PMCID: PMC7041937 DOI: 10.18632/oncotarget.27487] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 01/29/2020] [Indexed: 01/24/2023] Open
Abstract
Despite reductions in mortality from the use of highly active antiretroviral therapy (HAART), the presence of latent or transcriptionally silent proviruses prevents HIV cure/eradication. We have previously reported that DNA-dependent protein kinase (DNA-PK) facilitates HIV transcription by interacting with the RNA polymerase II (RNAP II) complex recruited at HIV LTR. In this study, using different cell lines and peripheral blood mononuclear cells (PBMCs) of HIV-infected patients, we found that DNA-PK stimulates HIV transcription at several stages, including initiation, pause-release and elongation. We are reporting for the first time that DNA-PK increases phosphorylation of RNAP II C-terminal domain (CTD) at serine 5 (Ser5) and serine 2 (Ser2) by directly catalyzing phosphorylation and by augmenting the recruitment of the positive transcription elongation factor (P-TEFb) at HIV LTR. Our findings suggest that DNA-PK expedites the establishment of euchromatin structure at HIV LTR. DNA-PK inhibition/knockdown leads to the severe impairment of HIV replication and reactivation of latent HIV provirus. DNA-PK promotes the recruitment of Tripartite motif-containing 28 (TRIM28) at LTR and assists the release of paused RNAP II through TRIM28 phosphorylation. These results provide the mechanisms through which DNA-PK controls the HIV gene expression and, likely, can be extended to cellular gene expression, including during cell malignancy, where the role of DNA-PK has been well-established.
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Affiliation(s)
- Sonia Zicari
- Center for Translational Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA.,Section of Intercellular Interactions, Eunice-Kennedy National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.,Department of Pediatric Medicine, The Bambino Gesù Children's Hospital, Rome, Italy.,These authors contributed equally to this work
| | - Adhikarimayum Lakhikumar Sharma
- Center for Translational Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA.,These authors contributed equally to this work
| | - Geetaram Sahu
- Division of Infectious Diseases, Department of Medicine, George Washington University, Washington DC 20037, USA.,These authors contributed equally to this work
| | - Larisa Dubrovsky
- Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington DC 20037, USA
| | - Lin Sun
- Division of Infectious Diseases, Department of Medicine, George Washington University, Washington DC 20037, USA
| | - Han Yue
- Division of Infectious Diseases, Department of Medicine, George Washington University, Washington DC 20037, USA
| | - Tejaswi Jada
- Division of Infectious Diseases, Department of Medicine, George Washington University, Washington DC 20037, USA
| | - Alex Ochem
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Wernher and Beit Building (South), Observatory 7925, Cape Town, South Africa
| | - Gary Simon
- Division of Infectious Diseases, Department of Medicine, George Washington University, Washington DC 20037, USA
| | - Michael Bukrinsky
- Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington DC 20037, USA
| | - Mudit Tyagi
- Center for Translational Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA.,Division of Infectious Diseases, Department of Medicine, George Washington University, Washington DC 20037, USA.,Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington DC 20037, USA
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46
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Smith LIF, Huang V, Olah M, Trinh L, Liu Y, Hazell G, Conway-Campbell B, Zhao Z, Martinez A, Lefrançois-Martinez AM, Lightman S, Spiga F, Aguilera G. Involvement of CREB-regulated transcription coactivators (CRTC) in transcriptional activation of steroidogenic acute regulatory protein (Star) by ACTH. Mol Cell Endocrinol 2020; 499:110612. [PMID: 31604124 PMCID: PMC6899503 DOI: 10.1016/j.mce.2019.110612] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/06/2019] [Accepted: 10/04/2019] [Indexed: 12/20/2022]
Abstract
Studies in vivo have suggested the involvement of CREB-regulated transcription coactivator (CRTC)2 on ACTH-induced transcription of the key steroidogenic protein, Steroidogenic Acute Regulatory (StAR). The present study uses two ACTH-responsive adrenocortical cell lines, to examine the role of CRTC on Star transcription. Here we show that ACTH-induced Star primary transcript, or heteronuclear RNA (hnRNA), parallels rapid increases in nuclear levels of the 3 isoforms of CRTC; CRTC1, CRTC2 and CRTC3. Furthermore, ACTH promotes recruitment of CRTC2 and CRTC3 by the Star promoter and siRNA knockdown of either CRTC3 or CRTC2 attenuates the increases in ACTH-induced Star hnRNA. Using pharmacological inhibitors of PKA, MAP kinase and calcineurin, we show that the effects of ACTH on Star transcription and CRTC nuclear translocation depend predominantly on the PKA pathway. The data provides evidence that CRTC2 and CRTC3, contribute to activation of Star transcription by ACTH, and that PKA/CRTC-dependent pathways are part of the multifactorial mechanisms regulating Star transcription.
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Affiliation(s)
- Lorna I F Smith
- Section on Endocrine Physiology, Program on Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA; Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, UK.
| | - Victoria Huang
- Section on Endocrine Physiology, Program on Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Mark Olah
- Section on Endocrine Physiology, Program on Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Loc Trinh
- Section on Endocrine Physiology, Program on Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Ying Liu
- Section on Endocrine Physiology, Program on Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Georgina Hazell
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, UK
| | - Becky Conway-Campbell
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, UK
| | - Zidong Zhao
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, UK
| | - Antoine Martinez
- Génétique Reproduction & Développement, CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 63001, Clermont-Ferrand, France
| | - Anne-Marie Lefrançois-Martinez
- Génétique Reproduction & Développement, CNRS UMR 6293, Inserm U1103, Université Clermont Auvergne, 63001, Clermont-Ferrand, France
| | - Stafford Lightman
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, UK
| | - Francesca Spiga
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, UK
| | - Greti Aguilera
- Section on Endocrine Physiology, Program on Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
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Chen F, Zhou Q, Wu L, Li F, Liu B, Zhang S, Zhang J, Bao M, Liu G. Genome-wide identification and characterization of the ALOG gene family in Petunia. BMC PLANT BIOLOGY 2019; 19:600. [PMID: 31888473 PMCID: PMC6937813 DOI: 10.1186/s12870-019-2127-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 11/08/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND The ALOG (Arabidopsis LSH1 and Oryza G1) family of proteins, namely DUF640 (domain of unknown function 640) domain proteins, were found in land plants. Functional characterization of a few ALOG members in model plants such as Arabidopsis and rice suggested they play important regulatory roles in plant development. The information about its evolution, however, is largely limited, and there was no any report on the ALOG genes in Petunia, an important ornamental species. RESULTS The ALOG genes were identified in four species of Petunia including P. axillaris, P. inflata, P. integrifolia, and P. exserta based on the genome and/or transcriptome databases, which were further confirmed by cloning from P. hybrida 'W115' (Mitchel diploid), a popular laboratorial petunia line susceptible to genetic transformation. Phylogenetic analysis indicated that Petunia ALOG genes (named as LSHs according to their closest Arabidopsis homologs) were grouped into four clades, which can be further divided into eight groups, and similar exon-intron structure and motifs are reflected in the same group. The PhLSH genes of hybrid petunia 'W115' were mainly derived from P. axillaris. The qPCR analysis revealed distinct spatial expression patterns among them suggesting potentially functional diversification. Moreover, over-expressing PhLSH7a and PhLSH7b in Arabidopsis uncovered their functions in the development of both vegetative and reproductive organs. CONCLUSIONS Petunia genome includes 11 ALOG genes that can be divided into eight distinct groups, and they also show different expression patterns. Among these genes, PhLSH7b and PhLSH7a play significant roles in plant growth and development, especially in fruit development. Our results provide new insight into the evolution of ALOG gene family and have laid a good foundation for the study of petunia LSH gene in the future.
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Affiliation(s)
- Feng Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070 China
| | - Qin Zhou
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070 China
| | - Lan Wu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070 China
| | - Fei Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070 China
| | - Baojun Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070 China
| | - Shuting Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070 China
| | - Jiaqi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070 China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070 China
| | - Guofeng Liu
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, 510405 China
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Gryder BE, Pomella S, Sayers C, Wu XS, Song Y, Chiarella AM, Bagchi S, Chou HC, Sinniah RS, Walton A, Wen X, Rota R, Hathaway NA, Zhao K, Chen J, Vakoc CR, Shern JF, Stanton BZ, Khan J. Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma. Nat Genet 2019; 51:1714-1722. [PMID: 31784732 PMCID: PMC6886578 DOI: 10.1038/s41588-019-0534-4] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 10/23/2019] [Indexed: 12/31/2022]
Abstract
Core regulatory transcription factors (CR TFs) orchestrate the placement of super-enhancers (SEs) to activate transcription of cell-identity specifying gene networks, and are critical in promoting cancer. Here, we define the core regulatory circuitry of rhabdomyosarcoma and identify critical CR TF dependencies. These CR TFs build SEs that have the highest levels of histone acetylation, yet paradoxically the same SEs also harbor the greatest amounts of histone deacetylases. We find that hyperacetylation selectively halts CR TF transcription. To investigate the architectural determinants of this phenotype, we used absolute quantification of architecture (AQuA) HiChIP, which revealed erosion of native SE contacts, and aberrant spreading of contacts that involved histone acetylation. Hyperacetylation removes RNA polymerase II (RNA Pol II) from core regulatory genetic elements, and eliminates RNA Pol II but not BRD4 phase condensates. This study identifies an SE-specific requirement for balancing histone modification states to maintain SE architecture and CR TF transcription.
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Affiliation(s)
| | - Silvia Pomella
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Department of Oncohematology, Ospedale Pediatrico Bambino Gesù Research Institute, IRCCS, Rome, Italy
| | - Carly Sayers
- Pediatric Oncology Branch, CCR, NCI, NIH, Bethesda, MD, USA
| | - Xiaoli S Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Genetics Program, Stony Brook University, Stony Brook, NY, USA
| | - Young Song
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
| | - Anna M Chiarella
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Sukriti Bagchi
- Pediatric Oncology Branch, CCR, NCI, NIH, Bethesda, MD, USA
| | | | | | | | - Xinyu Wen
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rossella Rota
- Department of Oncohematology, Ospedale Pediatrico Bambino Gesù Research Institute, IRCCS, Rome, Italy
| | - Nathaniel A Hathaway
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Keji Zhao
- Systems Biology Center, NHLBI, NIH, Bethesda, MD, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, NIBIB, NIH, Bethesda, MD, USA
| | | | - Jack F Shern
- Pediatric Oncology Branch, CCR, NCI, NIH, Bethesda, MD, USA
| | - Benjamin Z Stanton
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- The Research Institute at Nationwide, Nationwide Children's Hospital, Columbus, OH, USA
| | - Javed Khan
- Genetics Branch, NCI, NIH, Bethesda, MD, USA.
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Mercatelli D, Scalambra L, Triboli L, Ray F, Giorgi FM. Gene regulatory network inference resources: A practical overview. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1863:194430. [PMID: 31678629 DOI: 10.1016/j.bbagrm.2019.194430] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 02/08/2023]
Abstract
Transcriptional regulation is a fundamental molecular mechanism involved in almost every aspect of life, from homeostasis to development, from metabolism to behavior, from reaction to stimuli to disease progression. In recent years, the concept of Gene Regulatory Networks (GRNs) has grown popular as an effective applied biology approach for describing the complex and highly dynamic set of transcriptional interactions, due to its easy-to-interpret features. Since cataloguing, predicting and understanding every GRN connection in all species and cellular contexts remains a great challenge for biology, researchers have developed numerous tools and methods to infer regulatory processes. In this review, we catalogue these methods in six major areas, based on the dominant underlying information leveraged to infer GRNs: Coexpression, Sequence Motifs, Chromatin Immunoprecipitation (ChIP), Orthology, Literature and Protein-Protein Interaction (PPI) specifically focused on transcriptional complexes. The methods described here cover a wide range of user-friendliness: from web tools that require no prior computational expertise to command line programs and algorithms for large scale GRN inferences. Each method for GRN inference described herein effectively illustrates a type of transcriptional relationship, with many methods being complementary to others. While a truly holistic approach for inferring and displaying GRNs remains one of the greatest challenges in the field of systems biology, we believe that the integration of multiple methods described herein provides an effective means with which experimental and computational biologists alike may obtain the most complete pictures of transcriptional relationships. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Federico Manuel Giorgi and Dr. Shaun Mahony.
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Affiliation(s)
- Daniele Mercatelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Laura Scalambra
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Luca Triboli
- Centre for Integrative Biology (CIBIO), University of Trento, Italy
| | - Forest Ray
- Department of Systems Biology, Columbia University Medical Center, New York, NY, United States
| | - Federico M Giorgi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
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50
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Determinants of enhancer and promoter activities of regulatory elements. Nat Rev Genet 2019; 21:71-87. [DOI: 10.1038/s41576-019-0173-8] [Citation(s) in RCA: 284] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2019] [Indexed: 12/13/2022]
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