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Davidenko A, Bogomazova A, Illarioshkin S, Lagarkova M. Molecular Mechanisms of Spinocerebellar Ataxia Type 17. Mol Neurobiol 2025; 62:5720-5729. [PMID: 39614971 DOI: 10.1007/s12035-024-04645-z] [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: 07/29/2024] [Accepted: 11/25/2024] [Indexed: 03/29/2025]
Abstract
Spinocerebellar ataxia type 17 (SCA17) is a hereditary neurodegenerative disorder characterized by progressive motor and cognitive decline, leading to severe disability and death. SCA17 is caused by a CAG repeat expansion mutation in the TBP gene, resulting in the production of an abnormally long polyglutamine tract, which classifies it as a polyglutamine disorder. At present, there is no effective treatment for SCA17, and existing therapies provide only symptomatic relief. While the exact pathogenic mechanisms of SCA17 remain unclear, the TBP mutation affects a well-characterized transcription factor, making it an ideal model for studying polyglutamine-related neurodegeneration. Here, we review the clinical features of SCA17 and explore proposed mechanisms of its pathogenesis.
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Affiliation(s)
- Alina Davidenko
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia.
- Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Alexandra Bogomazova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, 119435, Russia
| | | | - Maria Lagarkova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
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2
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So CL, Lee YJ, Vokshi BH, Chen W, Huang B, De Sousa E, Gao Y, Portuallo ME, Begum S, Jagirdar K, Linehan WM, Rebecca VW, Ji H, Toska E, Cai D. TFE3 fusion oncoprotein condensates drive transcriptional reprogramming and cancer progression in translocation renal cell carcinoma. Cell Rep 2025; 44:115539. [PMID: 40222010 PMCID: PMC12077596 DOI: 10.1016/j.celrep.2025.115539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Revised: 01/28/2025] [Accepted: 03/18/2025] [Indexed: 04/15/2025] Open
Abstract
Translocation renal cell carcinoma (tRCC) presents a significant clinical challenge due to its aggressiveness and limited treatment options. It is primarily driven by fusion oncoproteins (FOs), yet their role in oncogenesis is not fully understood. Here, we investigate TFE3 fusions in tRCC, focusing on NONO::TFE3 and SFPQ::TFE3. We demonstrate that TFE3 FOs form liquid-like condensates with increased transcriptional activity, localizing to TFE3 target genes and promoting cell proliferation and migration. The coiled-coil domains (CCDs) of NONO and SFPQ are essential for condensate formation, prolonging TFE3 FOs' chromatin binding time and enhancing transcription. Compared with wild-type TFE3, TFE3 FOs bind to new chromatin regions, alter chromatin accessibility, and form new enhancers and super-enhancers at pro-growth gene loci. Disruption of condensate formation via CCD modification abolishes these genome-wide changes. Altogether, our integrated analyses underscore the critical functions of TFE3 FO condensates in driving tumor cell growth, providing key insights for future therapeutic strategies.
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Affiliation(s)
- Choon Leng So
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Ye Jin Lee
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Bujamin H Vokshi
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Wanlu Chen
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Binglin Huang
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Emily De Sousa
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Yangzhenyu Gao
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Marie Elena Portuallo
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Sumaiya Begum
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Kasturee Jagirdar
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - W Marston Linehan
- Urologic Oncology Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Vito W Rebecca
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Eneda Toska
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
| | - Danfeng Cai
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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3
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Marian AJ. Causes and consequences of DNA double-stranded breaks in cardiovascular disease. Mol Cell Biochem 2025; 480:2043-2064. [PMID: 39404936 DOI: 10.1007/s11010-024-05131-9] [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: 08/13/2024] [Accepted: 09/29/2024] [Indexed: 04/02/2025]
Abstract
The genome, whose stability is essential for survival, is incessantly exposed to internal and external stressors, which introduce an estimated 104 to 105 lesions, such as oxidation, in the nuclear genome of each mammalian cell each day. A delicate homeostatic balance between the generation and repair of DNA lesions maintains genomic stability. To initiate transcription, DNA strands unwind to form a transcription bubble and provide a template for the RNA polymerase II (RNAPII) complex to synthesize nascent RNA. The process generates DNA supercoils and introduces torsional stress. To enable RNAPII processing, the supercoils are released by topoisomerases by introducing strand breaks, including double-stranded breaks (DSBs). Thus, DSBs are intrinsic genomic features of gene expression. The breaks are quickly repaired upon processing of the transcription. DNA lesions and damaged proteins involved in transcription could impede the integrity and efficiency of RNAPII processing. The impediment, which is referred to as transcription stress, not only could lead to the generation of aberrant RNA species but also the accumulation of DSBs. The latter is particularly the case when topoisomerase processing and/or the repair mechanisms are compromised. The DSBs activate the DNA damage response (DDR) pathways to repair the damaged DNA and/or impose cell cycle arrest and cell death. In addition, the release of DSBs into the cytosol activates the cytosolic DNA-sensing proteins (CDSPs), which along with the nuclear DDR pathways induce the expression of senescence-associated secretory phenotype (SASP), cell cycle arrest, senescence, cell death, inflammation, and aging. The primary stimulus in hereditary cardiomyopathies is a mutation(s) in genes encoding the protein constituents of cardiac myocytes; however, the phenotype is the consequence of intertwined complex interactions among numerous stressors and the causal mutation(s). Increased internal DNA stressors, such as oxidation, alkylation, and cross-linking, are expected to be common in pathological conditions, including in hereditary cardiomyopathies. In addition, dysregulation of gene expression also imposes transcriptional stress and collectively with other stressors provokes the generation of DSBs. In addition, the depletion of nicotinamide adenine dinucleotide (NAD), which occurs in pathological conditions, impairs the repair mechanism and further facilitates the accumulation of DSBs. Because DSBs activate the DDR pathways, they are expected to contribute to the pathogenesis of cardiomyopathies. Thus, interventions to reduce the generation of DSBs, enhance their repair, and block the deleterious DDR pathways would be expected to impart salubrious effects not only in pathological states, as in hereditary cardiomyopathies but also aging.
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Affiliation(s)
- A J Marian
- Center for Cardiovascular Genetic Studies, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX, 77030, USA.
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4
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Lin S. A decade of dinoflagellate genomics illuminating an enigmatic eukaryote cell. BMC Genomics 2024; 25:932. [PMID: 39367346 PMCID: PMC11453091 DOI: 10.1186/s12864-024-10847-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Accepted: 09/27/2024] [Indexed: 10/06/2024] Open
Abstract
Dinoflagellates are a remarkable group of protists, not only for their association with harmful algal blooms and coral reefs but also for their numerous characteristics deviating from the rules of eukaryotic biology. Genome research on dinoflagellates has lagged due to their immense genome sizes in most species (~ 1-250 Gbp). Nevertheless, the last decade marked a fruitful era of dinoflagellate genomics, with 27 genomes sequenced and many insights attained. This review aims to synthesize information from these genomes, along with other omic data, to reflect on where we are now in understanding dinoflagellates and where we are heading in the future. The most notable insights from the decade-long genomics work include: (1) dinoflagellate genomes have been expanded in multiple times independently, probably by a combination of rampant retroposition, accumulation of repetitive DNA, and genome duplication; (2) Symbiodiniacean genomes are highly divergent, but share about 3,445 core unigenes concentrated in 219 KEGG pathways; (3) Most dinoflagellate genes are encoded unidirectionally and are not intron-poor; (4) The dinoflagellate nucleus has undergone extreme evolutionary changes, including complete or nearly complete loss of nucleosome and histone H1, and acquisition of dinoflagellate viral nuclear protein (DVNP); (5) Major basic nuclear protein (MBNP), histone-like protein (HLP), and bacterial HU-like protein (HCc) belong to the same protein family, and MBNP can be the unifying name; (6) Dinoflagellate gene expression is regulated by poorly understood mechanisms, but microRNA and other epigenetic mechanisms are likely important; (7) Over 50% of dinoflagellate genes are "dark" and their functions remain to be deciphered using functional genetics; (8) Initial insights into the genomic basis of parasitism and mutualism have emerged. The review then highlights functionally unique and interesting genes. Future research needs to obtain a finished genome, tackle large genomes, characterize the unknown genes, and develop a quantitative molecular ecological model for addressing ecological questions.
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Affiliation(s)
- Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT, 06340, USA.
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Yang S, Wang Y, Yang J, Tian Z, Wu M, Sun H, Zhang X, Zhao Y, Luo J, Guan G, Yin H, Hao R, Niu Q. African swine fever virus RNA polymerase subunits C315R and H359L inhibition host translation by activating the PKR-eIF2a pathway and suppression inflammatory responses. Front Microbiol 2024; 15:1469166. [PMID: 39380677 PMCID: PMC11458487 DOI: 10.3389/fmicb.2024.1469166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Accepted: 09/05/2024] [Indexed: 10/10/2024] Open
Abstract
ASFV C315R is homologous to the transcription factor TFIIB of large unclassified DNA viruses, and H359L is identical to the subunit 3 (RPB3) of eukaryotic RNA polymerase II. The C315R and H359L may play an important role in ASFV replication and transcription. Here, we evaluated the biological function of the C315R and H359L genes during virus replication in vitro and during infection in pigs. Results showed that C315R and H359L are highly conserved among ASFV genotype II strains; quantitative PCR (qPCR) and western blotting analyses revealed that C315R and H359L are early transcribed genes prior to viral DNA replication, but their protein expression is delayed. The immunofluorescence and western blotting analysis revealed that both proteins localized in the cell cytoplasm and nucleus at 24 h post infection, however, pH359L was mainly detected in the cell cytoplasm. Furthermore, overexpression of pH359L in MA104 cells significantly increased viral titer, RNA transcription levels, and viral protein expression levels, while overexpression of pC315R slightly enhanced ASFV replication. In contrast, siRNA targeting ASFV-H359L or C315R reduced replication efficiency in porcine macrophage culture compared to the parent ASFV-CN/SC/2019, demonstrating that C315R and H359L genes are necessary for ASFV replication. Finally, the functional role of C315R or H359L on PKR and eIF2α phosphorylation status and SG formation, as well as cytokine production were evaluated. These studies demonstrated that C315R and H359L are involved in virus replication processes in swine and play important roles in ASFV replication.
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Affiliation(s)
- Saixia Yang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- African Swine Fever Regional Laboratory of China (Lanzhou), Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, Gansu, China
| | - Yiwang Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- African Swine Fever Regional Laboratory of China (Lanzhou), Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, Gansu, China
| | - Jifei Yang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- African Swine Fever Regional Laboratory of China (Lanzhou), Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, Gansu, China
| | - Zhancheng Tian
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- African Swine Fever Regional Laboratory of China (Lanzhou), Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, Gansu, China
| | - Mengli Wu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- African Swine Fever Regional Laboratory of China (Lanzhou), Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, Gansu, China
| | - Hualin Sun
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- African Swine Fever Regional Laboratory of China (Lanzhou), Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, Gansu, China
| | - Xiaoqiang Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- African Swine Fever Regional Laboratory of China (Lanzhou), Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, Gansu, China
| | - Yaru Zhao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- African Swine Fever Regional Laboratory of China (Lanzhou), Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, Gansu, China
| | - Jianxun Luo
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- African Swine Fever Regional Laboratory of China (Lanzhou), Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, Gansu, China
| | - Guiquan Guan
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- African Swine Fever Regional Laboratory of China (Lanzhou), Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, Gansu, China
| | - Hong Yin
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- African Swine Fever Regional Laboratory of China (Lanzhou), Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, Gansu, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
| | - Rongzeng Hao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- African Swine Fever Regional Laboratory of China (Lanzhou), Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, Gansu, China
| | - Qingli Niu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- African Swine Fever Regional Laboratory of China (Lanzhou), Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, Gansu, China
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Kawaguchi K, Satoh S, Obokata J. Transcription of damage-induced RNA in Arabidopsis was frequently initiated from DSB loci within the genic regions. Genes Cells 2024; 29:681-689. [PMID: 38845450 DOI: 10.1111/gtc.13133] [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: 03/28/2024] [Revised: 05/08/2024] [Accepted: 05/23/2024] [Indexed: 08/07/2024]
Abstract
DNA double-strand breaks (DSBs) are the most severe DNA lesions and need to be removed immediately to prevent loss of genomic information. Recently, it has been revealed that DSBs induce novel transcription from the cleavage sites in various species, resulting in RNAs being referred to as damage-induced RNAs (diRNAs). While diRNA synthesis is an early event in the DNA damage response and plays an essential role in DSB repair activation, the location where diRNAs are newly generated in plants remains unclear, as does their transcriptional mechanism. Here, we performed the sequencing of polyadenylated (polyA) diRNAs that emerged around all DSB loci in Arabidopsis thaliana under the expression of the exogenous restriction enzyme Sbf I and observed 88 diRNAs transcribed via RNA polymerase II in 360 DSB loci. Most of the detected diRNAs originated within active genes and were transcribed from DSBs in a bidirectional manner. Furthermore, we found that diRNA elongation tends to terminate at the boundary of an endogenous gene located near DSB loci. Our results provide reliable evidence for understanding the importance of new transcription at DSBs and show that diRNA is a crucial factor for successful DSB repair.
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Affiliation(s)
- Kohei Kawaguchi
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Kyoto, Japan
| | - Soichirou Satoh
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Kyoto, Japan
| | - Junichi Obokata
- Faculty of Agriculture, Setsunan University, Hirakata, Osaka, Japan
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Li Q, Wang Y, Sun Z, Li H, Liu H. The Biosynthesis Process of Small RNA and Its Pivotal Roles in Plant Development. Int J Mol Sci 2024; 25:7680. [PMID: 39062923 PMCID: PMC11276867 DOI: 10.3390/ijms25147680] [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: 05/26/2024] [Revised: 07/01/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
In the realm of plant biology, small RNAs (sRNAs) are imperative in the orchestration of gene expression, playing pivotal roles across a spectrum of developmental sequences and responses to environmental stressors. The biosynthetic cascade of sRNAs is characterized by an elaborate network of enzymatic pathways that meticulously process double-stranded RNA (dsRNA) precursors into sRNA molecules, typically 20 to 30 nucleotides in length. These sRNAs, chiefly microRNAs (miRNAs) and small interfering RNAs (siRNAs), are integral in guiding the RNA-induced silencing complex (RISC) to selectively target messenger RNAs (mRNAs) for post-transcriptional modulation. This regulation is achieved either through the targeted cleavage or the suppression of translational efficiency of the mRNAs. In plant development, sRNAs are integral to the modulation of key pathways that govern growth patterns, organ differentiation, and developmental timing. The biogenesis of sRNA itself is a fine-tuned process, beginning with transcription and proceeding through a series of processing steps involving Dicer-like enzymes and RNA-binding proteins. Recent advances in the field have illuminated the complex processes underlying the generation and function of small RNAs (sRNAs), including the identification of new sRNA categories and the clarification of their involvement in the intercommunication among diverse regulatory pathways. This review endeavors to evaluate the contemporary comprehension of sRNA biosynthesis and to underscore the pivotal role these molecules play in directing the intricate performance of plant developmental processes.
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Affiliation(s)
| | | | | | - Haiyang Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China; (Q.L.); (Y.W.); (Z.S.)
| | - Huan Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China; (Q.L.); (Y.W.); (Z.S.)
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8
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Kieft R, Zhang Y, Yan H, Schmitz RJ, Sabatini R. Protein phosphatase PP1 regulation of RNA polymerase II transcription termination and allelic exclusion of VSG genes in trypanosomes. Nucleic Acids Res 2024; 52:6866-6885. [PMID: 38783162 PMCID: PMC11229358 DOI: 10.1093/nar/gkae392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 04/19/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024] Open
Abstract
The genomes of Leishmania and trypanosomes are organized into polycistronic transcription units flanked by a modified DNA base J involved in promoting RNA polymerase II (Pol II) termination. We recently characterized a Leishmania complex containing a J-binding protein, PP1 protein phosphatase 1, and PP1 regulatory protein (PNUTS) that controls transcription termination potentially via dephosphorylation of Pol II by PP1. While T. brucei contains eight PP1 isoforms, none purified with the PNUTS complex, complicating the analysis of PP1 function in termination. We now demonstrate that the PP1-binding motif of TbPNUTS is required for function in termination in vivo and that TbPP1-1 modulates Pol II termination in T. brucei and dephosphorylation of the large subunit of Pol II. PP1-1 knock-down results in increased cellular levels of phosphorylated RPB1 accompanied by readthrough transcription and aberrant transcription of the chromosome by Pol II, including Pol I transcribed loci that are typically silent, such as telomeric VSG expression sites involved in antigenic variation. These results provide important insights into the mechanism underlying Pol II transcription termination in primitive eukaryotes that rely on polycistronic transcription and maintain allelic exclusion of VSG genes.
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Affiliation(s)
- Rudo Kieft
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Yang Zhang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Haidong Yan
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Robert Sabatini
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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9
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Nordin A, Pagella P, Zambanini G, Cantù C. Exhaustive identification of genome-wide binding events of transcriptional regulators. Nucleic Acids Res 2024; 52:e40. [PMID: 38499482 PMCID: PMC11040144 DOI: 10.1093/nar/gkae180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/20/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Genome-wide binding assays aspire to map the complete binding pattern of gene regulators. Common practice relies on replication-duplicates or triplicates-and high stringency statistics to favor false negatives over false positives. Here we show that duplicates and triplicates of CUT&RUN are not sufficient to discover the entire activity of transcriptional regulators. We introduce ICEBERG (Increased Capture of Enrichment By Exhaustive Replicate aGgregation), a pipeline that harnesses large numbers of CUT&RUN replicates to discover the full set of binding events and chart the line between false positives and false negatives. We employed ICEBERG to map the full set of H3K4me3-marked regions, the targets of the co-factor β-catenin, and those of the transcription factor TBX3, in human colorectal cancer cells. The ICEBERG datasets allow benchmarking of individual replicates, comparing the performance of peak calling and replication approaches, and expose the arbitrary nature of strategies to identify reproducible peaks. Instead of a static view of genomic targets, ICEBERG establishes a spectrum of detection probabilities across the genome for a given factor, underlying the intrinsic dynamicity of its mechanism of action, and permitting to distinguish frequent from rare regulation events. Finally, ICEBERG discovered instances, undetectable with other approaches, that underlie novel mechanisms of colorectal cancer progression.
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Affiliation(s)
- Anna Nordin
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Pierfrancesco Pagella
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Gianluca Zambanini
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
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10
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Bose D, Singh RK, Robertson ES. KSHV-encoded LANA bypasses transcriptional block through the stabilization of RNA Pol II in hypoxia. mBio 2024; 15:e0277423. [PMID: 38095447 PMCID: PMC10790784 DOI: 10.1128/mbio.02774-23] [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: 10/13/2023] [Accepted: 11/07/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Hypoxia can induce the reactivation of Kaposi sarcoma-associated virus (KSHV), which necessitates the synthesis of critical structural proteins. Despite the unfavorable energetic conditions of hypoxia, KSHV utilizes mechanisms to prevent the degradation of essential cellular machinery required for successful reactivation. Our study provides new insights on strategies employed by KSHV-infected cells to maintain steady-state transcription by overcoming hypoxia-mediated metabolic stress to enable successful reactivation. Our discovery that the interaction of latency-associated nuclear antigen with HIF1α and NEDD4 inhibits its polyubiquitination activity, which blocks the degradation of RNA Pol II during hypoxia, is a significant contribution to our understanding of KSHV biology. This newfound knowledge provides new leads in the development of novel therapies for KSHV-associated diseases.
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Affiliation(s)
- Dipayan Bose
- Tumor Virology Program, Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rajnish Kumar Singh
- Tumor Virology Program, Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Erle S. Robertson
- Tumor Virology Program, Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Qi L, Bennett E, Isalan M. A Directed Evolution Protocol for Engineering Minimal Transcription Factors, Based on CIS Display. Methods Mol Biol 2024; 2774:1-13. [PMID: 38441754 DOI: 10.1007/978-1-0716-3718-0_1] [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: 03/07/2024]
Abstract
Directed evolution is an efficient strategy for obtaining desired biomolecules. Since the 1990s, the emergence of display techniques has enabled high-throughput screening of functional proteins. However, classical methods require library construction by plasmid cloning and are limited by transformation efficiencies, typically limiting library sizes to ~106-107 variants. More recently, in vitro techniques have emerged that avoid cloning, allowing library sizes of >1012 members. One of these, CIS display, is a DNA-based display technique which allows high-throughput selection of biomolecules in vitro. CIS display creates the genotype-phenotype link required for selection by a DNA replication initiator protein, RepA, that binds exclusively to the template from which it has been expressed. This method has been successfully used to evolve new protein-protein interactions but has not been used before to select DNA-binding proteins, which are major components in mammalian synthetic biology. In this chapter, we describe a directed evolution method using CIS display to efficiently select functional DNA-binding proteins from pools of nonbinding proteins. The method is illustrated by enriching the minimal transcription factor Cro from a low starting frequency (1 in 109). This protocol is also applicable to engineering other DNA-binding proteins or transcription factors from combinatorial libraries.
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Affiliation(s)
- Lin Qi
- Department of Life Sciences, Imperial College London, London, UK
| | - Emily Bennett
- Department of Life Sciences, Imperial College London, London, UK
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London, UK.
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12
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Kieft R, Zhang Y, Yan H, Schmitz RJ, Sabatini R. Protein Phosphatase PP1 Regulation of Pol II Phosphorylation is Linked to Transcription Termination and Allelic Exclusion of VSG Genes and TERRA in Trypanosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.21.563358. [PMID: 37905150 PMCID: PMC10614956 DOI: 10.1101/2023.10.21.563358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The genomes of Leishmania and trypanosomes are organized into polycistronic transcription units flanked by a modified DNA base J involved in promoting RNA polymerase II (Pol II) termination. We recently characterized a Leishmania complex containing a J-binding protein, PP1 protein phosphatase 1, and PP1 regulatory protein (PNUTS) that controls transcription termination potentially via dephosphorylation of Pol II by PP1. While T. brucei contains eight PP1 isoforms, none purified with the PNUTS complex, suggesting a unique PP1-independent mechanism of termination. We now demonstrate that the PP1-binding motif of TbPNUTS is required for function in termination in vivo and that TbPP1-1 modulates Pol II termination in T. brucei involving dephosphorylation of the C-terminal domain of the large subunit of Pol II. PP1-1 knock-down results in increased cellular levels of phosphorylated large subunit of Pol II accompanied by readthrough transcription and pervasive transcription of the entire genome by Pol II, including Pol I transcribed loci that are typically silent, such as telomeric VSG expression sites involved in antigenic variation and production of TERRA RNA. These results provide important insights into the mechanism underlying Pol II transcription termination in primitive eukaryotes that rely on polycistronic transcription and maintain allelic exclusion of VSG genes.
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13
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Zhu SY, Wang XY, Xie H, Liu LZ. Comprehensive analysis of circular RNAs in nasopharyngeal cancer. Genes Genomics 2023; 45:1339-1346. [PMID: 37651065 DOI: 10.1007/s13258-023-01438-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/07/2023] [Indexed: 09/01/2023]
Abstract
BACKGROUND Nasopharyngeal cancer (NPC) is a type of epithelial malignancy that is positive for Epstein-Barr virus (EBV) and affects several populations worldwide. Due to the high rates of relapse and metastasis following primary treatment, there is an urgent need to identify new candidates for NPC therapy. Recently, circular RNA (circRNA) has emerged as a promising target for cancer diagnosis and prevention. OBJECTIVE This study aimed to study the circRNAs enriched in NPC patients, and further analyze potential signaling pathways involved. METHODS A new bioinformatic tool named psirc was used to analyze RNA-sequencing datasets from NPC patients and normal specimens to study the NPC-enriched circRNAs. RESULTS We identified and quantified the full-length circRNA in these samples and found the top 10 enriched circRNAs in NPC patients compared to control samples. Furthermore, we selected the most enriched circRNA, circEEF1A1_E8B1, and studied its protein coding ability, microRNA and RNA-binding protein (RBP) binding capacity. We also constructed a protein-protein interaction (PPI) network for its binding proteins and extracted hub genes. Finally, we conducted survival analysis for these hub genes in head and neck cancer patients. CONCLUSIONS In summary, our study has revealed the presence of previously unidentified circRNAs that are enriched in NPC patients. Through an analysis of their molecular functions, we have advanced our understanding of the potential role of circRNAs in NPC development.
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Affiliation(s)
- Si-Yu Zhu
- Department of Radiology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, 510060, Guangzhou, Guangdong, People's Republic of China
| | - Xiao-Yi Wang
- Department of Radiology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, China
| | - Hui Xie
- Department of Radiology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, 510060, Guangzhou, Guangdong, People's Republic of China.
| | - Li-Zhi Liu
- Department of Radiology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, 510060, Guangzhou, Guangdong, People's Republic of China.
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14
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Zhang X, Yang L, Gan Q, Jiang S, Liang D, Gao J, Meng Y. BmTBP upregulates the transcription of BmSuc1 in silkworm (Bombyx mori) by binding to BmTfΙΙA-S. INSECT SCIENCE 2023; 30:1405-1419. [PMID: 36585848 DOI: 10.1111/1744-7917.13168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/06/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The BmSuc1 gene, which encodes a novel animal-type β-fructofuranosidase (EC 3.2.1.26), was first cloned and identified in silkworm (Bombyx mori). As an essential sucrase, the activity of BmSUC1 is unaffected by alkaloidal sugar mimics in mulberry leaves. This enzyme may also directly regulate the degree of sucrose hydrolysis in the silkworm midgut. In addition, BmSUC1 is involved in the synthesis of sericin 1 in the silk gland tissue. However, the mechanism underlying the regulation of BmSuc1 transcription remains unclear. In this study, we analyzed the BmSuc1 promoter activity using a dual-luciferase reporter assay and identified 4 regions that are critical for transcriptional activation. The gene encoding a predicted transcription factor (TATA-box-binding protein; BmTBP) capable of binding to the core promoter regions was cloned. A quantitative real-time polymerase chain reaction analysis indicated the gene was highly expressed in the midgut. Downregulating BmTBP expression via RNA interference decreased the expression of BmSuc1 at the transcript and protein levels. An electrophoretic mobility shift analysis and chromatin immunoprecipitation indicated that BmTBP can bind to the TATA-box cis-regulatory element in the BmSuc1 promoter. Furthermore, a bioinformatics-based analysis and a far-western blot revealed the interaction between BmTBP and another transcription factor (BmTfIIA-S). The luciferase reporter gene assay results confirmed that the BmTBP-BmTfIIA-S complex increases the BmSuc1 promoter activity. Considered together, these findings suggest that BmTBP regulates BmSuc1 expression through its interaction with BmTfIIA-S.
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Affiliation(s)
- Xinwei Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Department of Pathology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Liangli Yang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Anhui International Joint Research and Development Center of Sericulture Resources Utilization, Hefei, China
| | - Quan Gan
- Anhui Academy of Agricultural Sciences, Hefei, China
| | - Song Jiang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Anhui International Joint Research and Development Center of Sericulture Resources Utilization, Hefei, China
| | - Dan Liang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Anhui International Joint Research and Development Center of Sericulture Resources Utilization, Hefei, China
| | - Junshan Gao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yan Meng
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- Anhui International Joint Research and Development Center of Sericulture Resources Utilization, Hefei, China
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15
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Dou X, Xiao Y, Shen C, Wang K, Wu T, Liu C, Li Y, Yu X, Liu J, Dai Q, Pajdzik K, Ye C, Ge R, Gao B, Yu J, Sun S, Chen M, Chen J, He C. RBFOX2 recognizes N 6-methyladenosine to suppress transcription and block myeloid leukaemia differentiation. Nat Cell Biol 2023; 25:1359-1368. [PMID: 37640841 PMCID: PMC10495261 DOI: 10.1038/s41556-023-01213-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/21/2023] [Indexed: 08/31/2023]
Abstract
N6-methyladenosine (m6A) methylation can be deposited on chromatin-associated RNAs (caRNAs) by the RNA methyltransferase complex (MTC) to regulate chromatin state and transcription. However, the mechanism by which MTC is recruited to distinct genomic loci remains elusive. Here we identify RBFOX2, a well-studied RNA-binding protein, as a chromatin factor that preferentially recognizes m6A on caRNAs. RBFOX2 can recruit RBM15, an MTC component, to facilitate methylation of promoter-associated RNAs. RBM15 also physically interacts with YTHDC1 and recruits polycomb repressive complex 2 (PRC2) to the RBFOX2-bound loci for chromatin silencing and transcription suppression. Furthermore, we found that this RBFOX2/m6A/RBM15/YTHDC1/PRC2 axis plays a critical role in myeloid leukaemia. Downregulation of RBFOX2 notably inhibits survival/proliferation of acute myeloid leukaemia cells and promotes their myeloid differentiation. RBFOX2 is also required for self-renewal of leukaemia stem/initiation cells and acute myeloid leukaemia maintenance. Our study presents a pathway of m6A MTC recruitment and m6A deposition on caRNAs, resulting in locus-selective chromatin regulation, which has potential therapeutic implications in leukaemia.
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Affiliation(s)
- Xiaoyang Dou
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
| | - Yu Xiao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
| | - Chao Shen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA, USA
| | - Kitty Wang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA, USA
| | - Tong Wu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
| | - Chang Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
| | - Yini Li
- Department of Physiology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xianbin Yu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
| | - Jun Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Qing Dai
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
| | - Kinga Pajdzik
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
| | - Chang Ye
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
| | - Ruiqi Ge
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
| | - Boyang Gao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, Chicago, IL, USA
| | - Jianhua Yu
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA, USA
- Hematologic Malignancies Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Shuying Sun
- Department of Physiology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mengjie Chen
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA.
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA.
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA, USA.
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, Chicago, IL, USA.
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16
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Brickner JH. Inheritance of epigenetic transcriptional memory through read-write replication of a histone modification. Ann N Y Acad Sci 2023; 1526:50-58. [PMID: 37391188 PMCID: PMC11216120 DOI: 10.1111/nyas.15033] [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] [Indexed: 07/02/2023]
Abstract
Epigenetic transcriptional regulation frequently requires histone modifications. Some, but not all, of these modifications are able to template their own inheritance. Here, I discuss the molecular mechanisms by which histone modifications can be inherited and relate these ideas to new results about epigenetic transcriptional memory, a phenomenon that poises recently repressed genes for faster reactivation and has been observed in diverse organisms. Recently, we found that the histone H3 lysine 4 dimethylation that is associated with this phenomenon plays a critical role in sustaining memory and, when factors critical for the establishment of memory are inactivated, can be stably maintained through multiple mitoses. This chromatin-mediated inheritance mechanism may involve a physical interaction between an H3K4me2 reader, SET3C, and an H3K4me2 writer, Spp1- COMPASS. This is the first example of a chromatin-mediated inheritance of a mark that promotes transcription.
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Affiliation(s)
- Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
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17
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Fan K, Pfister E, Weng Z. Toward a comprehensive catalog of regulatory elements. Hum Genet 2023; 142:1091-1111. [PMID: 36935423 DOI: 10.1007/s00439-023-02519-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/03/2023] [Indexed: 03/21/2023]
Abstract
Regulatory elements are the genomic regions that interact with transcription factors to control cell-type-specific gene expression in different cellular environments. A precise and complete catalog of functional elements encoded by the human genome is key to understanding mammalian gene regulation. Here, we review the current state of regulatory element annotation. We first provide an overview of assays for characterizing functional elements, including genome, epigenome, transcriptome, three-dimensional chromatin interaction, and functional validation assays. We then discuss computational methods for defining regulatory elements, including peak-calling and other statistical modeling methods. Finally, we introduce several high-quality lists of regulatory element annotations and suggest potential future directions.
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Affiliation(s)
- Kaili Fan
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, 368 Plantation Street, ASC5-1069, Worcester, MA, 01605, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Edith Pfister
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, 368 Plantation Street, ASC5-1069, Worcester, MA, 01605, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, 368 Plantation Street, ASC5-1069, Worcester, MA, 01605, USA.
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18
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Savinkova LK, Sharypova EB, Kolchanov NA. On the Role of TATA Boxes and TATA-Binding Protein in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2023; 12:1000. [PMID: 36903861 PMCID: PMC10005294 DOI: 10.3390/plants12051000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/13/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
For transcription initiation by RNA polymerase II (Pol II), all eukaryotes require assembly of basal transcription machinery on the core promoter, a region located approximately in the locus spanning a transcription start site (-50; +50 bp). Although Pol II is a complex multi-subunit enzyme conserved among all eukaryotes, it cannot initiate transcription without the participation of many other proteins. Transcription initiation on TATA-containing promoters requires the assembly of the preinitiation complex; this process is triggered by an interaction of TATA-binding protein (TBP, a component of the general transcription factor TFIID (transcription factor II D)) with a TATA box. The interaction of TBP with various TATA boxes in plants, in particular Arabidopsis thaliana, has hardly been investigated, except for a few early studies that addressed the role of a TATA box and substitutions in it in plant transcription systems. This is despite the fact that the interaction of TBP with TATA boxes and their variants can be used to regulate transcription. In this review, we examine the roles of some general transcription factors in the assembly of the basal transcription complex, as well as functions of TATA boxes of the model plant A. thaliana. We review examples showing not only the involvement of TATA boxes in the initiation of transcription machinery assembly but also their indirect participation in plant adaptation to environmental conditions in responses to light and other phenomena. Examples of an influence of the expression levels of A. thaliana TBP1 and TBP2 on morphological traits of the plants are also examined. We summarize available functional data on these two early players that trigger the assembly of transcription machinery. This information will deepen the understanding of the mechanisms underlying transcription by Pol II in plants and will help to utilize the functions of the interaction of TBP with TATA boxes in practice.
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19
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Erenpreisa J, Giuliani A, Yoshikawa K, Falk M, Hildenbrand G, Salmina K, Freivalds T, Vainshelbaum N, Weidner J, Sievers A, Pilarczyk G, Hausmann M. Spatial-Temporal Genome Regulation in Stress-Response and Cell-Fate Change. Int J Mol Sci 2023; 24:2658. [PMID: 36769000 PMCID: PMC9917235 DOI: 10.3390/ijms24032658] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/17/2023] [Accepted: 01/22/2023] [Indexed: 02/04/2023] Open
Abstract
Complex functioning of the genome in the cell nucleus is controlled at different levels: (a) the DNA base sequence containing all relevant inherited information; (b) epigenetic pathways consisting of protein interactions and feedback loops; (c) the genome architecture and organization activating or suppressing genetic interactions between different parts of the genome. Most research so far has shed light on the puzzle pieces at these levels. This article, however, attempts an integrative approach to genome expression regulation incorporating these different layers. Under environmental stress or during cell development, differentiation towards specialized cell types, or to dysfunctional tumor, the cell nucleus seems to react as a whole through coordinated changes at all levels of control. This implies the need for a framework in which biological, chemical, and physical manifestations can serve as a basis for a coherent theory of gene self-organization. An international symposium held at the Biomedical Research and Study Center in Riga, Latvia, on 25 July 2022 addressed novel aspects of the abovementioned topic. The present article reviews the most recent results and conclusions of the state-of-the-art research in this multidisciplinary field of science, which were delivered and discussed by scholars at the Riga symposium.
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Affiliation(s)
| | - Alessandro Giuliani
- Istituto Superiore di Sanita Environment and Health Department, 00161 Roma, Italy
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Martin Falk
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Faculty of Engineering, University of Applied Science Aschaffenburg, 63743 Aschaffenburg, Germany
| | - Kristine Salmina
- Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
| | - Talivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV1004 Riga, Latvia
| | - Ninel Vainshelbaum
- Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
- Doctoral Study Program, University of Latvia, LV1004 Riga, Latvia
| | - Jonas Weidner
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Aaron Sievers
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Institute for Human Genetics, University Hospital Heidelberg, 69117 Heidelberg, Germany
| | - Götz Pilarczyk
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
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20
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Zheng P, Qi Y, Li X, Liu Y, Yao Y, Huang G. A capsule network-based method for identifying transcription factors. Front Microbiol 2022; 13:1048478. [PMID: 36560938 PMCID: PMC9763301 DOI: 10.3389/fmicb.2022.1048478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 10/26/2022] [Indexed: 12/12/2022] Open
Abstract
Transcription factors (TFs) are typical regulators for gene expression and play versatile roles in cellular processes. Since it is time-consuming, costly, and labor-intensive to detect it by using physical methods, it is desired to develop a computational method to detect TFs. Here, we presented a capsule network-based method for identifying TFs. This method is an end-to-end deep learning method, consisting mainly of an embedding layer, bidirectional long short-term memory (LSTM) layer, capsule network layer, and three fully connected layers. The presented method obtained an accuracy of 0.8820, being superior to the state-of-the-art methods. These empirical experiments showed that the inclusion of the capsule network promoted great performances and that the capsule network-based representation was superior to the property-based representation for distinguishing between TFs and non-TFs. We also implemented the presented method into a user-friendly web server, which is freely available at http://www.biolscience.cn/Capsule_TF/ for all scientific researchers.
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Affiliation(s)
- Peijie Zheng
- School of Electrical Engineering, Shaoyang University, Shaoyang, China
| | - Yue Qi
- School of Electrical Engineering, Shaoyang University, Shaoyang, China
| | - Xueyong Li
- School of Electrical Engineering, Shaoyang University, Shaoyang, China
| | - Yuewu Liu
- College of Information and Intelligence, Hunan Agricultural University, Changsha, China
| | - Yuhua Yao
- School of Mathematics and Statistics, Hainan Normal University, Haikou, China
| | - Guohua Huang
- School of Electrical Engineering, Shaoyang University, Shaoyang, China,*Correspondence: Guohua Huang,
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21
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Zambanini G, Nordin A, Jonasson M, Pagella P, Cantù C. A new CUT&RUN low volume-urea (LoV-U) protocol optimized for transcriptional co-factors uncovers Wnt/β-catenin tissue-specific genomic targets. Development 2022; 149:dev201124. [PMID: 36355069 PMCID: PMC10112916 DOI: 10.1242/dev.201124] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022]
Abstract
Upon WNT/β-catenin pathway activation, stabilized β-catenin travels to the nucleus where it associates with the TCF/LEF transcription factors, constitutively bound to genomic Wnt-responsive elements (WREs), to activate target gene transcription. Discovering the binding profile of β-catenin is therefore required to unambiguously assign direct targets of WNT signaling. Cleavage under targets and release using nuclease (CUT&RUN) has emerged as prime technique for mapping the binding profile of DNA-interacting proteins. Here, we present a modified version of CUT&RUN, named LoV-U (low volume and urea), that enables the robust and reproducible generation of β-catenin binding profiles, uncovering direct WNT/β-catenin target genes in human cells, as well as in cells isolated from developing mouse tissues. CUT&RUN-LoV-U outperforms original CUT&RUN when targeting co-factors that do not bind the DNA, can profile all classes of chromatin regulators and is well suited for simultaneous processing of several samples. We believe that the application of our protocol will allow the detection of the complex system of tissue-specific WNT/β-catenin target genes, together with other non-DNA-binding transcriptional regulators that act downstream of ontogenetically fundamental signaling cascades.
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Affiliation(s)
- Gianluca Zambanini
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping SE-58183, Sweden
- Department of Biomedical and Clinical Sciences (BKV), Division of Molecular Medicine and Virology (MMV), Faculty of Medicine and Health Sciences, Linköping University, Linköping SE-58183, Sweden
| | - Anna Nordin
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping SE-58183, Sweden
- Department of Biomedical and Clinical Sciences (BKV), Division of Molecular Medicine and Virology (MMV), Faculty of Medicine and Health Sciences, Linköping University, Linköping SE-58183, Sweden
| | - Mattias Jonasson
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping SE-58183, Sweden
- Department of Biomedical and Clinical Sciences (BKV), Division of Molecular Medicine and Virology (MMV), Faculty of Medicine and Health Sciences, Linköping University, Linköping SE-58183, Sweden
| | - Pierfrancesco Pagella
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping SE-58183, Sweden
- Department of Biomedical and Clinical Sciences (BKV), Division of Molecular Medicine and Virology (MMV), Faculty of Medicine and Health Sciences, Linköping University, Linköping SE-58183, Sweden
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping SE-58183, Sweden
- Department of Biomedical and Clinical Sciences (BKV), Division of Molecular Medicine and Virology (MMV), Faculty of Medicine and Health Sciences, Linköping University, Linköping SE-58183, Sweden
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22
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Forgham H, Kakinen A, Qiao R, Davis TP. Keeping up with the COVID's-Could siRNA-based antivirals be a part of the answer? EXPLORATION (BEIJING, CHINA) 2022; 2:20220012. [PMID: 35941991 PMCID: PMC9349879 DOI: 10.1002/exp.20220012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/11/2022] [Indexed: 01/08/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a highly contagious viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This deadly infection has resulted in more than 5.2 million deaths worldwide. The global rollout of COVID-19 vaccines has without doubt saved countless lives by reducing the severity of symptoms for patients. However, as the virus continues to evolve, there is a risk that the vaccines and antiviral designed to target the infection will no longer be therapeutically viable. Furthermore, there remain fears over both the short and long-term side effects of repeat exposure to currently available vaccines. In this review, we discuss the pros and cons of the vaccine rollout and promote the idea of a COVID medicinal toolbox made up of different antiviral treatment modalities, and present some of the latest therapeutic strategies that are being explored in this respect to try to combat the COVID-19 virus and other COVID viruses that are predicted to follow. Lastly, we review current literature on the use of siRNA therapeutics as a way to remain adaptable and in tune with the ever-evolving mutation rate of the COVID-19 virus.
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Affiliation(s)
- Helen Forgham
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandBrisbaneQueenslandAustralia
| | - Aleksandr Kakinen
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandBrisbaneQueenslandAustralia
- Institute of Biotechnology, HiLIFEUniversity of HelsinkiHelsinkiFinland
| | - Ruirui Qiao
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandBrisbaneQueenslandAustralia
| | - Thomas P. Davis
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandBrisbaneQueenslandAustralia
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23
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Cardoso TF, Bruscadin JJ, Afonso J, Petrini J, Andrade BGN, de Oliveira PSN, Malheiros JM, Rocha MIP, Zerlotini A, Ferraz JBS, Mourão GB, Coutinho LL, Regitano LCA. EEF1A1 transcription cofactor gene polymorphism is associated with muscle gene expression and residual feed intake in Nelore cattle. Mamm Genome 2022; 33:619-628. [PMID: 35816191 DOI: 10.1007/s00335-022-09959-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 06/22/2022] [Indexed: 12/01/2022]
Abstract
Cis-acting effects of noncoding variants on gene expression and regulatory molecules constitute a significant factor for phenotypic variation in complex traits. To provide new insights into the impacts of single-nucleotide polymorphisms (SNPs) on transcription factors (TFs) and transcription cofactors (TcoF) coding genes, we carried out a multi-omic analysis to identify cis-regulatory effects of SNPs on these genes' expression in muscle and describe their association with feed efficiency-related traits in Nelore cattle. As a result, we identified one SNP, the rs137256008C > T, predicted to impact the EEF1A1 gene expression (β = 3.02; P-value = 3.51E-03) and the residual feed intake trait (β = - 3.47; P-value = 0.02). This SNP was predicted to modify transcription factor sites and overlaps with several QTL for feed efficiency traits. In addition, co-expression network analyses showed that animals containing the T allele of the rs137256008 SNP may be triggering changes in the gene network. Therefore, our analyses reinforce and contribute to a better understanding of the biological mechanisms underlying gene expression control of feed efficiency traits in bovines. The cis-regulatory SNP can be used as biomarker for feed efficiency in Nelore cattle.
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Affiliation(s)
- T F Cardoso
- Embrapa Southeast Livestock, São Carlos, SP, Brazil
| | - J J Bruscadin
- Program on Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - J Afonso
- Embrapa Southeast Livestock, São Carlos, SP, Brazil
| | - J Petrini
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo/ESALQ, Piracicaba, SP, Brazil
| | - B G N Andrade
- Computer Science Department, Munster Technological University, MTU/ADAPT, Cork, Ireland
| | - P S N de Oliveira
- Program on Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - J M Malheiros
- Federal University of Latin American Integration, Foz do Iguaçu, Paraná, Brazil
| | - M I P Rocha
- Program on Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - A Zerlotini
- Embrapa Agricultural Informatics, Campinas, SP, Brazil
| | - J B S Ferraz
- Department of Veterinary Medicine, University of São Paulo/FZEA, Pirassununga, Brazil
| | - G B Mourão
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo/ESALQ, Piracicaba, SP, Brazil
| | - L L Coutinho
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo/ESALQ, Piracicaba, SP, Brazil
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24
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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: 14] [Impact Index Per Article: 4.7] [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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25
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Liu Z, Wu A, Wu Z, Wang T, Pan Y, Li B, Zhang X, Yu M. TOX4 facilitates promoter-proximal pausing and C-terminal domain dephosphorylation of RNA polymerase II in human cells. Commun Biol 2022; 5:300. [PMID: 35365735 PMCID: PMC8975821 DOI: 10.1038/s42003-022-03214-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/02/2022] [Indexed: 11/24/2022] Open
Abstract
TOX4 is one of the regulatory factors of PP1 phosphatases with poorly understood functions. Here we show that chromatin occupancy pattern of TOX4 resembles that of RNA polymerase II (Pol II), and its loss increases cellular level of C-terminal domain (CTD) phosphorylated Pol II but mainly decreases Pol II occupancy on promoters. In addition, elongation rate analyses by 4sUDRB-seq suggest that TOX4 restricts pause release and early elongation but promotes late elongation. Moreover, TT-seq analyses indicate that TOX4 loss mainly decreases transcriptional output. Mechanistically, TOX4 may restrict pause release through facilitating CTD serine 2 and DSIF dephosphorylation, and promote Pol II recycling and reinitiation through facilitating CTD serines 2 and 5 dephosphorylation. Furthermore, among the PP1 phosphatases, TOX4 preferentially binds PP1α and is capable of facilitating Pol II CTD dephosphorylation in vitro. These results lay the foundation for a better understanding of the role of TOX4 in transcriptional regulation. As a role of TOX4, one of the regulatory proteins of PP1 phosphatases, in transcriptional regulation, authors here show that TOX4 restricts pause release and early productive elongation, and promotes Pol II recycling and transcriptional reinitiation.
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Affiliation(s)
- Ziling Liu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Aiwei Wu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Zhen Wu
- State key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Talang Wang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Yixuan Pan
- Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Bing Li
- Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Xumin Zhang
- State key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Ming Yu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China. .,Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, 200240, Shanghai, China.
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26
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Xu Z, Zhang N, Fu H, Wang F, Wen M, Chang H, Wu J, Abdelaala WB, Luo Q, Li Y, Li C, Wang Q, Wang ZY. Salt Stress Modulates the Landscape of Transcriptome and Alternative Splicing in Date Palm ( Phoenix dactylifera L.). FRONTIERS IN PLANT SCIENCE 2022; 12:807739. [PMID: 35126432 PMCID: PMC8810534 DOI: 10.3389/fpls.2021.807739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/20/2021] [Indexed: 05/14/2023]
Abstract
Date palm regards as a valuable genomic resource for exploring the tolerance genes due to its ability to survive under the sever condition. Although a large number of differentiated genes were identified in date palm responding to salt stress, the genome-wide study of alternative splicing (AS) landscape under salt stress conditions remains unknown. In the current study, we identified the stress-related genes through transcriptomic analysis to characterize their function under salt. A total of 17,169 genes were differentially expressed under salt stress conditions. Gene expression analysis confirmed that the salt overly sensitive (SOS) pathway genes, such as PdSOS2;1, PdSOS2;2, PdSOS4, PdSOS5, and PdCIPK11 were involved in the regulation of salt response in date palm, which is consistent with the physiological analysis that high salinity affected the Na+/K+ homeostasis and amino acid profile of date palm resulted in the inhibition of plant growth. Interestingly, the pathway of "spliceosome" was enriched in the category of upregulation, indicating their potential role of AS in date palm response to salt stress. Expectedly, many differentially alternative splicing (DAS) events were found under salt stress conditions, and some splicing factors, such as PdRS40, PdRSZ21, PdSR45a, and PdU2Af genes were abnormally spliced under salt, suggesting that AS-related proteins might participated in regulating the salt stress pathway. Moreover, the number of differentially DAS-specific genes was gradually decreased, while the number of differentially expressed gene (DEG)-specific genes was increased with prolonged salt stress treatment, suggesting that AS and gene expression could be distinctively regulated in response to salt stress. Therefore, our study highlighted the pivotal role of AS in the regulation of salt stress and provided novel insights for enhancing the resistance to salt in date palm.
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Affiliation(s)
- Zhongliang Xu
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Ning Zhang
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Haiquan Fu
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Fuyou Wang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Mingfu Wen
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Zhanjiang, China
- Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Hailong Chang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Zhanjiang, China
| | - Jiantao Wu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Zhanjiang, China
| | - Walid Badawy Abdelaala
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
- Central Laboratory for Date Palm Research and Development of Agriculture Research Center, Giza, Egypt
| | - Qingwen Luo
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Zhanjiang, China
- Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Yang Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Zhanjiang, China
- Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Cong Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Zhanjiang, China
- Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Qinnan Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Zhanjiang, China
| | - Zhen-Yu Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Zhanjiang, China
- Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
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27
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Bernstein C. DNA Methylation and Establishing Memory. Epigenet Insights 2022; 15:25168657211072499. [PMID: 35098021 PMCID: PMC8793415 DOI: 10.1177/25168657211072499] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/17/2021] [Indexed: 11/30/2022] Open
Abstract
A single event can cause a life-long memory. Memories physically reside in neurons, and changes in neuronal gene expression are considered to be central to memory. Early models proposed that specific DNA methylations of cytosines in neuronal DNA encode memories in a stable biochemical form. This review describes recent research that elucidates the molecular mechanisms used by the mammalian brain to form DNA methylcytosine encoded memories. For example, neuron activation initiates cytosine demethylation by stimulating DNA topoisomerase II beta (TOP2B) protein to make a temporary DNA double-strand break (repaired within about 2 hours) at a promoter of an immediate early gene, EGR1, allowing expression of this gene. The EGR1 proteins then recruit methylcytosine dioxygenase TET1 proteins to initiate demethylation at several hundred genes, facilitating expression of those genes. Initiation of demethylation of cytosine also occurs when OGG1 localizes at oxidized guanine in a methylated CpG site and recruits TET1 for initiation of demethylation at that site. DNMT3A2 is another immediate early gene upregulated by synaptic activity. DNMT3A2 protein catalyzes de novo DNA methylations. These several mechanisms convert external experiences into DNA methylations and initiated demethylations of neuronal DNA cytosines, causing changes in gene expression that are the basis of long-term memories.
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Affiliation(s)
- Carol Bernstein
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
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28
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Dahale S, Ruiz-Orera J, Silhavy J, Hübner N, van Heesch S, Pravenec M, Atanur SS. Cap analysis of gene expression reveals alternative promoter usage in a rat model of hypertension. Life Sci Alliance 2022; 5:5/4/e202101234. [PMID: 34996843 PMCID: PMC8742872 DOI: 10.26508/lsa.202101234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/26/2021] [Accepted: 12/28/2021] [Indexed: 11/24/2022] Open
Abstract
The role of alternative promoter usage in tissue-specific gene expression has been well established; however, its role in complex diseases is poorly understood. We performed cap analysis of gene expression (CAGE) sequencing from the left ventricle of a rat model of hypertension, the spontaneously hypertensive rat (SHR), and a normotensive strain, Brown Norway to understand the role of alternative promoter usage in complex disease. We identified 26,560 CAGE-defined transcription start sites in the rat left ventricle, including 1,970 novel cardiac transcription start sites. We identified 28 genes with alternative promoter usage between SHR and Brown Norway, which could lead to protein isoforms differing at the amino terminus between two strains and 475 promoter switching events altering the length of the 5' UTR. We found that the shift in Insr promoter usage was significantly associated with insulin levels and blood pressure within a panel of HXB/BXH recombinant inbred rat strains, suggesting that hyperinsulinemia due to insulin resistance might lead to hypertension in SHR. Our study provides a preliminary evidence of alternative promoter usage in complex diseases.
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Affiliation(s)
- Sonal Dahale
- Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, UK.,Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Jan Silhavy
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.,Charité -Universitätsmedizin, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | | | - Michal Pravenec
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Santosh S Atanur
- Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, UK .,The National Institute for Health Research, Imperial Biomedical Research Centre, ITMAT Data Science Group, Imperial College London, London, UK
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29
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Khandelwal R, Jain D, Jaishankar J, Barman A, Srivastava P, Bisaria VS. Characterization of Zymomonas mobilis promoters that are functional in Escherichia coli. J Biosci Bioeng 2022; 133:301-308. [DOI: 10.1016/j.jbiosc.2021.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/19/2021] [Accepted: 12/26/2021] [Indexed: 02/08/2023]
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30
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He Q, Wu Y, Wang M, Chen S, Jia R, Yang Q, Zhu D, Liu M, Zhao X, Zhang S, Huang J, Ou X, Mao S, Gao Q, Sun D, Tian B, Cheng A. ICP22/IE63 Mediated Transcriptional Regulation and Immune Evasion: Two Important Survival Strategies for Alphaherpesviruses. Front Immunol 2021; 12:743466. [PMID: 34925320 PMCID: PMC8674840 DOI: 10.3389/fimmu.2021.743466] [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: 07/19/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
In the process of infecting the host, alphaherpesviruses have derived a series of adaptation and survival strategies, such as latent infection, autophagy and immune evasion, to survive in the host environment. Infected cell protein 22 (ICP22) or its homologue immediate early protein 63 (IE63) is a posttranslationally modified multifunctional viral regulatory protein encoded by all alphaherpesviruses. In addition to playing an important role in the efficient use of host cell RNA polymerase II, it also plays an important role in the defense process of the virus overcoming the host immune system. These two effects of ICP22/IE63 are important survival strategies for alphaherpesviruses. In this review, we summarize the complex mechanism by which the ICP22 protein regulates the transcription of alphaherpesviruses and their host genes and the mechanism by which ICP22/IE63 participates in immune escape. Reviewing these mechanisms will also help us understand the pathogenesis of alphaherpesvirus infections and provide new strategies to combat these viral infections.
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Affiliation(s)
- Qing He
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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31
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Beyond the canonical role of TFIIB in eukaryotic transcription. Curr Genet 2021; 68:61-67. [PMID: 34797379 PMCID: PMC8602988 DOI: 10.1007/s00294-021-01223-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 02/06/2023]
Abstract
The role of general transcription factor TFIIB in transcription extends well beyond its evolutionarily conserved function in initiation. Chromatin localization studies demonstrating binding of TFIIB to both the 5’ and 3’ ends of genes in a diverse set of eukaryotes strongly suggested a rather unexpected role of the factor in termination. TFIIB indeed plays a role in termination of transcription. TFIIB occupancy of the 3’ end is possibly due to its interaction with the termination factors residing there. Interaction of the promoter-bound TFIIB with factors occupying the 3’ end of a gene may be the basis of transcription-dependent gene looping. The proximity of the terminator-bound factors with the promoter in a gene loop has the potential to terminate promoter-initiated upstream anti-sense transcription thereby conferring promoter directionality. TFIIB, therefore, is emerging as a factor with pleiotropic roles in the transcription cycle. This could be the reason for preferential targeting of TFIIB by viruses. Further studies are needed to understand the critical role of TFIIB in viral pathogenesis in the context of its newly identified roles in termination, gene looping and promoter directionality.
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32
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Parrello D, Vlasenok M, Kranz L, Nechaev S. Targeting the Transcriptome Through Globally Acting Components. Front Genet 2021; 12:749850. [PMID: 34603400 PMCID: PMC8481634 DOI: 10.3389/fgene.2021.749850] [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: 07/30/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
Transcription is a step in gene expression that defines the identity of cells and its dysregulation is associated with diseases. With advancing technologies revealing molecular underpinnings of the cell with ever-higher precision, our ability to view the transcriptomes may have surpassed our knowledge of the principles behind their organization. The human RNA polymerase II (Pol II) machinery comprises thousands of components that, in conjunction with epigenetic and other mechanisms, drive specialized programs of development, differentiation, and responses to the environment. Parts of these programs are repurposed in oncogenic transformation. Targeting of cancers is commonly done by inhibiting general or broadly acting components of the cellular machinery. The critical unanswered question is how globally acting or general factors exert cell type specific effects on transcription. One solution, which is discussed here, may be among the events that take place at genes during early Pol II transcription elongation. This essay turns the spotlight on the well-known phenomenon of promoter-proximal Pol II pausing as a step that separates signals that establish pausing genome-wide from those that release the paused Pol II into the gene. Concepts generated in this rapidly developing field will enhance our understanding of basic principles behind transcriptome organization and hopefully translate into better therapies at the bedside.
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Affiliation(s)
- Damien Parrello
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
| | - Maria Vlasenok
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Lincoln Kranz
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
| | - Sergei Nechaev
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
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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: 38] [Impact Index Per Article: 9.5] [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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O'Brien MJ, Ansari A. Critical Involvement of TFIIB in Viral Pathogenesis. Front Mol Biosci 2021; 8:669044. [PMID: 33996913 PMCID: PMC8119876 DOI: 10.3389/fmolb.2021.669044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/08/2021] [Indexed: 11/23/2022] Open
Abstract
Viral infections and the harm they cause to their host are a perpetual threat to living organisms. Pathogenesis and subsequent spread of infection requires replication of the viral genome and expression of structural and non-structural proteins of the virus. Generally, viruses use transcription and translation machinery of the host cell to achieve this objective. The viral genome encodes transcriptional regulators that alter the expression of viral and host genes by manipulating initiation and termination steps of transcription. The regulation of the initiation step is often through interactions of viral factors with gene specific factors as well as general transcription factors (GTFs). Among the GTFs, TFIIB (Transcription Factor IIB) is a frequent target during viral pathogenesis. TFIIB is utilized by a plethora of viruses including human immunodeficiency virus, herpes simplex virus, vaccinia virus, Thogoto virus, hepatitis virus, Epstein-Barr virus and gammaherpesviruses to alter gene expression. A number of viral transcriptional regulators exhibit a direct interaction with host TFIIB in order to accomplish expression of their genes and to repress host transcription. Some viruses have evolved proteins with a three-dimensional structure very similar to TFIIB, demonstrating the importance of TFIIB for viral persistence. Upon viral infection, host transcription is selectively altered with viral transcription benefitting. The nature of viral utilization of TFIIB for expression of its own genes, along with selective repression of host antiviral genes and downregulation of general host transcription, makes TFIIB a potential candidate for antiviral therapies.
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Affiliation(s)
- Michael J O'Brien
- Department of Biological Science, Wayne State University, Detroit, MI, United States
| | - Athar Ansari
- Department of Biological Science, Wayne State University, Detroit, MI, United States
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Ayelign B, Negash M, Andualem H, Wondemagegn T, Kassa E, Shibabaw T, Akalu Y, Molla MD. Association of IL-10 (- 1082 A/G) and IL-6 (- 174 G/C) gene polymorphism with type 2 diabetes mellitus in Ethiopia population. BMC Endocr Disord 2021; 21:70. [PMID: 33858419 PMCID: PMC8051082 DOI: 10.1186/s12902-021-00738-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Interleukin (IL)-6 and IL-10 are the most important cytokine with pro and anti-inflammatory activities, respectively. Dysregulation of IL-6 and IL-10 are associated with increased risk of developing Type 2 Diabetes Mellitus (T2DM). Despite this, a fundamental understanding of both cytokine gene polymorphisms with its expression is critical in understanding of cellular mechanism of insulin resistance as well as T2DM intervention. Therefore, this study aimed to assess IL-6 (- 174 G/C) and IL-10 (- 1082 A/G) gene polymorphism, and its association with T2DM, North West Ethiopia. METHODS A comparative cross-sectional study from January to May 2018 was conducted on study participants with T2DM and apparently healthy controls. Deoxyribonucleic acid (DNA) extraction and genotyping was carried out by using amplification refractory mutation system polymerase chain reaction to detect polymorphism of IL-6 and IL-10 gene at the position - 174 and - 1082, respectively. The logistic regression model was fitted to assess the association of between cytokine gene polymorphisms and T2DM. Odds ratio with 95% CI was determined to assess the presence and strength of association between the explanatory variables and outcome variable. A P-value < 0.05 was considered as statistically significant. RESULT Participants carrying the GG genotype of IL-6 (- 174) (OR (95% CI) = 4.61 (2.07-10.54) was a high likelihood of having T2DM compared to those carrying the CC and AA genotypes. AA and AG genotypes of IL-10 (- 1082) were at lower odd of developing T2DM compared to those carrying the GG genotype. In addition, individuals carrying the G allele of IL-6 (- 174) have 2.82-fold odds of developing T2DM compared to individuals carrying the C allele (OR (95% CI) =2.81 (1.78-4.50)). CONCLUSION Our study revealed that genetic polymorphisms of IL-6 (- 174) GG genotype is the potential host genetic risk factors to T2DM. While, IL-10 (- 1082) AA genotype is negatively associated with T2DM. Therefore, IL-6 (- 174) and IL-10 (- 1082) genetic variation may be considered as a biomarker for early screening and diagnosis of T2DM.
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Affiliation(s)
- Birhanu Ayelign
- Department of Immunology and Molecular Biology, School of Biomedical and Laboratory Science, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia.
| | - Markos Negash
- Department of Immunology and Molecular Biology, School of Biomedical and Laboratory Science, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Henok Andualem
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Debretabor University, Debretabor, Ethiopia
| | - Tadelo Wondemagegn
- Department of Immunology and Molecular Biology, School of Biomedical and Laboratory Science, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Eyuel Kassa
- University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Tewodros Shibabaw
- Department of Biochemistry, School of Medicine, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Yonas Akalu
- Department of Physiology, School of Medicine, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Meseret Derbew Molla
- Department of Biochemistry, School of Medicine, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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Basova L, Lindsey A, McGovern AM, Ellis RJ, Marcondes MCG. Detection of H3K4me3 Identifies NeuroHIV Signatures, Genomic Effects of Methamphetamine and Addiction Pathways in Postmortem HIV+ Brain Specimens that Are Not Amenable to Transcriptome Analysis. Viruses 2021; 13:544. [PMID: 33805201 PMCID: PMC8064323 DOI: 10.3390/v13040544] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/30/2022] Open
Abstract
Human postmortem specimens are extremely valuable resources for investigating translational hypotheses. Tissue repositories collect clinically assessed specimens from people with and without HIV, including age, viral load, treatments, substance use patterns and cognitive functions. One challenge is the limited number of specimens suitable for transcriptional studies, mainly due to poor RNA quality resulting from long postmortem intervals. We hypothesized that epigenomic signatures would be more stable than RNA for assessing global changes associated with outcomes of interest. We found that H3K27Ac or RNA Polymerase (Pol) were not consistently detected by Chromatin Immunoprecipitation (ChIP), while the enhancer H3K4me3 histone modification was abundant and stable up to the 72 h postmortem. We tested our ability to use HeK4me3 in human prefrontal cortex from HIV+ individuals meeting criteria for methamphetamine use disorder or not (Meth +/-) which exhibited poor RNA quality and were not suitable for transcriptional profiling. Systems strategies that are typically used in transcriptional metadata were applied to H3K4me3 peaks revealing consistent genomic activity differences in regions where addiction and neuronal synapses pathway genes are represented, including genes of the dopaminergic system, as well as inflammatory pathways. The resulting comparisons mirrored previously observed effects of Meth on suppressing gene expression and provided insights on neurological processes affected by Meth. The results suggested that H3K4me3 detection in chromatin may reflect transcriptional patterns, thus providing opportunities for analysis of larger numbers of specimens from cases with substance use and neurological deficits. In conclusion, the detection of H3K4me3 in isolated chromatin can be an alternative to transcriptome strategies to increase the power of association using specimens with long postmortem intervals and low RNA quality.
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Affiliation(s)
- Liana Basova
- San Diego Biomedical Research Institute, San Diego, CA 92121, USA; (L.B.); (A.L.); (A.M.M.)
| | - Alexander Lindsey
- San Diego Biomedical Research Institute, San Diego, CA 92121, USA; (L.B.); (A.L.); (A.M.M.)
| | - Anne Marie McGovern
- San Diego Biomedical Research Institute, San Diego, CA 92121, USA; (L.B.); (A.L.); (A.M.M.)
| | - Ronald J. Ellis
- Departments of Neurosciences and Psychiatry, University of California San Diego, San Diego, CA 92103, USA;
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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: 1.5] [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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38
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An emerging role of chromatin-interacting RNA-binding proteins in transcription regulation. Essays Biochem 2020; 64:907-918. [PMID: 33034346 DOI: 10.1042/ebc20200004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/08/2020] [Accepted: 09/15/2020] [Indexed: 01/01/2023]
Abstract
Transcription factors (TFs) are well-established key factors orchestrating gene transcription, and RNA-binding proteins (RBPs) are mainly thought to participate in post-transcriptional control of gene. In fact, these two steps are functionally coupled, offering a possibility for reciprocal communications between transcription and regulatory RNAs and RBPs. Recently, a series of exploratory studies, utilizing functional genomic strategies, have revealed that RBPs are prevalently involved in transcription control genome-wide through their interactions with chromatin. Here, we present a refined census of RBPs to grope for such an emerging role and discuss the global view of RBP-chromatin interactions and their functional diversities in transcription regulation.
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Schüller A, Wolansky L, Berger H, Studt L, Gacek-Matthews A, Sulyok M, Strauss J. A novel fungal gene regulation system based on inducible VPR-dCas9 and nucleosome map-guided sgRNA positioning. Appl Microbiol Biotechnol 2020; 104:9801-9822. [PMID: 33006690 PMCID: PMC7595996 DOI: 10.1007/s00253-020-10900-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/31/2020] [Accepted: 09/08/2020] [Indexed: 12/16/2022]
Abstract
Programmable transcriptional regulation is a powerful tool to study gene functions. Current methods to selectively regulate target genes are mainly based on promoter exchange or on overexpressing transcriptional activators. To expand the discovery toolbox, we designed a dCas9-based RNA-guided synthetic transcription activation system for Aspergillus nidulans that uses enzymatically disabled "dead" Cas9 fused to three consecutive activation domains (VPR-dCas9). The dCas9-encoding gene is under the control of an estrogen-responsive promoter to allow induction timing and to avoid possible negative effects by strong constitutive expression of the highly active VPR domains. Especially in silent genomic regions, facultative heterochromatin and strictly positioned nucleosomes can constitute a relevant obstacle to the transcriptional machinery. To avoid this negative impact and to facilitate optimal positioning of RNA-guided VPR-dCas9 to targeted promoters, we have created a genome-wide nucleosome map from actively growing cells and stationary cultures to identify the cognate nucleosome-free regions (NFRs). Based on these maps, different single-guide RNAs (sgRNAs) were designed and tested for their targeting and activation potential. Our results demonstrate that the system can be used to regulate several genes in parallel and, depending on the VPR-dCas9 positioning, expression can be pushed to very high levels. We have used the system to turn on individual genes within two different biosynthetic gene clusters (BGCs) which are silent under normal growth conditions. This method also opens opportunities to stepwise activate individual genes in a cluster to decipher the correlated biosynthetic pathway. Graphical abstract KEYPOINTS: • An inducible RNA-guided transcriptional regulator based on VPR-dCas9 was established in Aspergillus nidulans. • Genome-wide nucleosome positioning maps were created that facilitate sgRNA positioning. • The system was successfully applied to activate genes within two silent biosynthetic gene clusters.
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Affiliation(s)
- Andreas Schüller
- Fungal Genetics Lab, Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences Vienna, BOKU-Campus Tulln, Konrad Lorenz Strasse 24, A-3430, Tulln an der Donau, Austria
| | - Lisa Wolansky
- Institute Krems Bioanalytics , IMC FH Krems University of Applied Sciences , Krems, Austria
| | - Harald Berger
- Fungal Genetics Lab, Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences Vienna, BOKU-Campus Tulln, Konrad Lorenz Strasse 24, A-3430, Tulln an der Donau, Austria
| | - Lena Studt
- Fungal Genetics Lab, Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences Vienna, BOKU-Campus Tulln, Konrad Lorenz Strasse 24, A-3430, Tulln an der Donau, Austria
| | - Agnieszka Gacek-Matthews
- Fungal Genetics Lab, Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences Vienna, BOKU-Campus Tulln, Konrad Lorenz Strasse 24, A-3430, Tulln an der Donau, Austria
- Institute of Microbiology, Functional Microbiology Division, University of Veterinary Sciences Vienna, Wien, Austria
| | - Michael Sulyok
- Institute of Bioanalytics and Agrometabolomics, Department of Agrobiotechnology, BOKU-University of Natural Resources and Life Sciences Vienna, BOKU-Campus Tulln, Konrad-Lorenz-Straße 20, A-3430 Tulln an der Donau, Austria
| | - Joseph Strauss
- Fungal Genetics Lab, Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences Vienna, BOKU-Campus Tulln, Konrad Lorenz Strasse 24, A-3430, Tulln an der Donau, Austria.
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Dasgupta T, Ferdous S, Tse-Dinh YC. Mechanism of Type IA Topoisomerases. Molecules 2020; 25:E4769. [PMID: 33080770 PMCID: PMC7587558 DOI: 10.3390/molecules25204769] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022] Open
Abstract
Topoisomerases in the type IA subfamily can catalyze change in topology for both DNA and RNA substrates. A type IA topoisomerase may have been present in a last universal common ancestor (LUCA) with an RNA genome. Type IA topoisomerases have since evolved to catalyze the resolution of topological barriers encountered by genomes that require the passing of nucleic acid strand(s) through a break on a single DNA or RNA strand. Here, based on available structural and biochemical data, we discuss how a type IA topoisomerase may recognize and bind single-stranded DNA or RNA to initiate its required catalytic function. Active site residues assist in the nucleophilic attack of a phosphodiester bond between two nucleotides to form a covalent intermediate with a 5'-phosphotyrosine linkage to the cleaved nucleic acid. A divalent ion interaction helps to position the 3'-hydroxyl group at the precise location required for the cleaved phosphodiester bond to be rejoined following the passage of another nucleic acid strand through the break. In addition to type IA topoisomerase structures observed by X-ray crystallography, we now have evidence from biophysical studies for the dynamic conformations that are required for type IA topoisomerases to catalyze the change in the topology of the nucleic acid substrates.
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Affiliation(s)
- Tumpa Dasgupta
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (T.D.); (S.F.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
- Biochemistry PhD Program, Florida International University, Miami, FL 33199, USA
| | - Shomita Ferdous
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (T.D.); (S.F.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
- Biochemistry PhD Program, Florida International University, Miami, FL 33199, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (T.D.); (S.F.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
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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: 1.0] [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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Mohanta TK, Yadav D, Khan A, Hashem A, Tabassum B, Khan AL, Abd_Allah EF, Al-Harrasi A. Genomics, molecular and evolutionary perspective of NAC transcription factors. PLoS One 2020; 15:e0231425. [PMID: 32275733 PMCID: PMC7147800 DOI: 10.1371/journal.pone.0231425] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/23/2020] [Indexed: 01/05/2023] Open
Abstract
NAC (NAM, ATAF1,2, and CUC2) transcription factors are one of the largest transcription factor families found in the plants and are involved in diverse developmental and signalling events. Despite the availability of comprehensive genomic information from diverse plant species, the basic genomic, biochemical, and evolutionary details of NAC TFs have not been established. Therefore, NAC TFs family proteins from 160 plant species were analyzed in the current study. Study revealed, Brassica napus (410) encodes highest number and Klebsormidium flaccidum (3) encodes the lowest number of TFs. The study further revealed the presence of NAC TF in the Charophyte algae K. flaccidum. On average, the monocot plants encode higher number (141.20) of NAC TFs compared to the eudicots (125.04), gymnosperm (75), and bryophytes (22.66). Furthermore, our analysis revealed that several NAC TFs are membrane bound and contain monopartite, bipartite, and multipartite nuclear localization signals. NAC TFs were also found to encode several novel chimeric proteins and regulate a complex interactome network. In addition to the presence of NAC domain, several NAC proteins were found to encode other functional signature motifs as well. Relative expression analysis of NAC TFs in A. thaliana revealed root tissue treated with urea and ammonia showed higher level of expression and leaf tissues treated with urea showed lower level of expression. The synonymous codon usage is absent in the NAC TFs and it appears that they have evolved from orthologous ancestors and undergone vivid duplications to give rise to paralogous NAC TFs. The presence of novel chimeric NAC TFs are of particular interest and the presence of chimeric NAC domain with other functional signature motifs in the NAC TF might encode novel functional properties in the plants.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medicinal Plant Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Dhananjay Yadav
- Dept. of Medical Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| | - Adil Khan
- Natural and Medicinal Plant Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, ARC, Giza, Egypt
| | - Baby Tabassum
- Department of Zoology, Toxicology laboratory, Raza P.G. College, Rampur, Uttar Pradesh, India
| | - Abdul Latif Khan
- Natural and Medicinal Plant Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Elsayed Fathi Abd_Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Al-Harrasi
- Natural and Medicinal Plant Sciences Research Center, University of Nizwa, Nizwa, Oman
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Roeder RG. 50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms. Nat Struct Mol Biol 2019; 26:783-791. [PMID: 31439941 DOI: 10.1038/s41594-019-0287-x] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 07/26/2019] [Indexed: 12/12/2022]
Abstract
The landmark 1969 discovery of nuclear RNA polymerases I, II and III in diverse eukaryotes represented a major turning point in the field that, with subsequent elucidation of the distinct structures and functions of these enzymes, catalyzed an avalanche of further studies. In this Review, written from a personal and historical perspective, I highlight foundational biochemical studies that led to the discovery of an expanding universe of the components of the transcriptional and regulatory machineries, and a parallel complexity in gene-specific mechanisms that continue to be explored to the present day.
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Affiliation(s)
- Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York, USA.
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Stages identifying and transcriptome profiling of the floral transition in Juglans regia. Sci Rep 2019; 9:7092. [PMID: 31068628 PMCID: PMC6506622 DOI: 10.1038/s41598-019-43582-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 04/27/2019] [Indexed: 11/30/2022] Open
Abstract
Using paraffin sections, the stages of walnut female flower bud differentiation were divided into the predifferentiation period (F_1), initial differentiation period (F_2) and flower primordium differentiation period (F_3). Leaf buds collected at the same stage as F_2 were designated JRL. Transcriptomic profiling was performed, and a total of 132,154 unigenes were obtained with lengths ranging from 201 bp to 16,831 bp. The analysis of differentially expressed genes (DEGs) showed that there were 597, 784 and 532 DEGs in the three combinations F_1vsF_2, F_1vsF_3, and F_2vsF_3, respectively. The comparison F_2vsJRL showed that 374 DEGs were differentially expressed between female buds and leaf buds. Thirty-one DEGs related to flowering time were further used to construct coexpression networks, and CRY2 and NF-YA were identified as core DEGs in flowering time regulation. Eighteen DEGs related to flowering time were subjected to real-time quantitative analysis. Our work provides a foundation for further research on the walnut floral transition and provides new resources for future research on walnut biology and biotechnology.
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Dannappel MV, Sooraj D, Loh JJ, Firestein R. Molecular and in vivo Functions of the CDK8 and CDK19 Kinase Modules. Front Cell Dev Biol 2019; 6:171. [PMID: 30693281 PMCID: PMC6340071 DOI: 10.3389/fcell.2018.00171] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/06/2018] [Indexed: 12/21/2022] Open
Abstract
CDK8 and its paralog, CDK19, collectively termed ‘Mediator Kinase,’ are cyclin-dependent kinases that have been implicated as key rheostats in cellular homeostasis and developmental programming. CDK8 and CDK19 are incorporated, in a mutually exclusive manner, as part of a 4-protein complex called the Mediator kinase module. This module reversibly associates with the Mediator, a 26 subunit protein complex that regulates RNA Polymerase II mediated gene expression. As part of this complex, the Mediator kinases have been implicated in diverse process such as developmental signaling, metabolic homeostasis and in innate immunity. In recent years, dysregulation of Mediator kinase module proteins, including CDK8/19, has been implicated in the development of different human diseases, and in particular cancer. This has led to intense efforts to understand how CDK8/19 regulate diverse biological outputs and develop Mediator kinase inhibitors that can be exploited therapeutically. Herein, we review both context and function of the Mediator kinases at a molecular, cellular and animal level. In so doing, we illuminate emerging concepts underpinning Mediator kinase biology and highlight certain aspects that remain unsolved.
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Affiliation(s)
- Marius Volker Dannappel
- Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Dhanya Sooraj
- Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Jia Jian Loh
- Hudson Institute of Medical Research, Clayton, VIC, Australia.,Faculty of Science, School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Ron Firestein
- Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
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46
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Jin W, Qazi TJ, Quan Z, Li N, Qing H. Dysregulation of Transcription Factors: A Key Culprit Behind Neurodegenerative Disorders. Neuroscientist 2018; 25:548-565. [PMID: 30484370 DOI: 10.1177/1073858418811787] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Neurodegenerative diseases (NDs) are considered heterogeneous disorders characterized by progressive pathological changes in neuronal systems. Transcription factors are protein molecules that are important in regulating the expression of genes. Although the clinical manifestations of NDs vary, the pathological processes appear similar with regard to neuroinflammation, oxidative stress, and proteostasis, to which, as numerous studies have discovered, transcription factors are closely linked. In this review, we summarized and reviewed the roles of transcription factors in NDs, and then we elucidated their functions during pathological processes, and finally we discussed their therapeutic values in NDs.
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Affiliation(s)
- Wei Jin
- Beijing Key Laboratory of Separation and Analysis in Biomedical and Pharmaceuticals, Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Haidian District, Beijing, China
| | - Talal Jamil Qazi
- Beijing Key Laboratory of Separation and Analysis in Biomedical and Pharmaceuticals, Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Haidian District, Beijing, China
| | - Zhenzhen Quan
- Beijing Key Laboratory of Separation and Analysis in Biomedical and Pharmaceuticals, Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Haidian District, Beijing, China
| | - Nuomin Li
- Beijing Key Laboratory of Separation and Analysis in Biomedical and Pharmaceuticals, Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Haidian District, Beijing, China
| | - Hong Qing
- Beijing Key Laboratory of Separation and Analysis in Biomedical and Pharmaceuticals, Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Haidian District, Beijing, China
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47
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Zarrabi N, Schluesche P, Meisterernst M, Börsch M, Lamb DC. Analyzing the Dynamics of Single TBP-DNA-NC2 Complexes Using Hidden Markov Models. Biophys J 2018; 115:2310-2326. [PMID: 30527334 DOI: 10.1016/j.bpj.2018.11.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 11/12/2018] [Accepted: 11/12/2018] [Indexed: 10/27/2022] Open
Abstract
Single-pair Förster resonance energy transfer (spFRET) has become an important tool for investigating conformational dynamics in biological systems. To extract dynamic information from the spFRET traces measured with total internal reflection fluorescence microscopy, we extended the hidden Markov model (HMM) approach. In our extended HMM analysis, we incorporated the photon-shot noise from camera-based systems into the HMM. Thus, the variance in Förster resonance energy transfer (FRET) efficiency of the various states, which is typically a fitted parameter, is explicitly included in the analysis estimated from the number of detected photons. It is also possible to include an additional broadening of the FRET state, which would then only reflect the inherent flexibility of the dynamic biological systems. This approach is useful when comparing the dynamics of individual molecules for which the total intensities vary significantly. We used spFRET with the extended HMM analysis to investigate the dynamics of TATA-box-binding protein (TBP) on promoter DNA in the presence of negative cofactor 2 (NC2). We compared the dynamics of two promoters as well as DNAs of different length and labeling location. For the adenovirus major late promoter, four FRET states were observed; three states correspond to different conformations of the DNA in the TBP-DNA-NC2 complex and a four-state model in which the complex has shifted along the DNA. The HMM analysis revealed that the states are connected via a linear, four-well model. For the H2B promoter, more complex dynamics were observed. By clustering the FRET states detected with the HMM analysis, we could compare the general dynamics observed for the two promoter sequences. We observed that the dynamics from a stretched DNA conformation to a bent conformation for the two promoters were similar, whereas the bent conformation of the TBP-DNA-NC2 complex for the H2B promoter is approximately three times more stable than for the adenovirus major late promoter.
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Affiliation(s)
- Nawid Zarrabi
- Physikalisches Institut, University of Stuttgart, Stuttgart, Baden-Württemberg, Germany; Single-Molecule Microscopy Group, Jena University Hospital, Jena, Thuringia, Germany
| | - Peter Schluesche
- Department Chemie, Center for Nano Science, Center for Integrated Protein Science, and Nanosystems Initiative München, Ludwig-Maximilians-Universität Munich, Munich, Bavaria, Germany
| | - Michael Meisterernst
- GSF-National Research Center for Environment and Health, Gene Expression, Munich, Bavaria, Germany; Institute of Molecular Tumor Biology, Faculty of Medicine, University of Muenster, Muenster, North Rhine-Westphalia, Germany
| | - Michael Börsch
- Physikalisches Institut, University of Stuttgart, Stuttgart, Baden-Württemberg, Germany; Single-Molecule Microscopy Group, Jena University Hospital, Jena, Thuringia, Germany
| | - Don C Lamb
- Department Chemie, Center for Nano Science, Center for Integrated Protein Science, and Nanosystems Initiative München, Ludwig-Maximilians-Universität Munich, Munich, Bavaria, Germany.
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48
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de Souza MM, Zerlotini A, Geistlinger L, Tizioto PC, Taylor JF, Rocha MIP, Diniz WJS, Coutinho LL, Regitano LCA. A comprehensive manually-curated compendium of bovine transcription factors. Sci Rep 2018; 8:13747. [PMID: 30213987 PMCID: PMC6137171 DOI: 10.1038/s41598-018-32146-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/29/2018] [Indexed: 01/28/2023] Open
Abstract
Transcription factors (TFs) are pivotal regulatory proteins that control gene expression in a context-dependent and tissue-specific manner. In contrast to human, where comprehensive curated TF collections exist, bovine TFs are only rudimentary recorded and characterized. In this article, we present a manually-curated compendium of 865 sequence-specific DNA-binding bovines TFs, which we analyzed for domain family distribution, evolutionary conservation, and tissue-specific expression. In addition, we provide a list of putative transcription cofactors derived from known interactions with the identified TFs. Since there is a general lack of knowledge concerning the regulation of gene expression in cattle, the curated list of TF should provide a basis for an improved comprehension of regulatory mechanisms that are specific to the species.
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Affiliation(s)
- Marcela M de Souza
- Post-graduation Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, São Paulo, 13560-970, Brazil.,Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, São Paulo, 13560-970, Brazil
| | - Adhemar Zerlotini
- Bioinformatic Multi-user Laboratory, Embrapa Informática Agropecuária, Campinas, São Paulo, 70770-901, Brazil
| | - Ludwig Geistlinger
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, São Paulo, 13560-970, Brazil
| | | | - Jeremy F Taylor
- Division of Animal Science, University of Missouri, Columbia, Missouri, 65211-5300, USA
| | - Marina I P Rocha
- Post-graduation Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, São Paulo, 13560-970, Brazil
| | - Wellison J S Diniz
- Post-graduation Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, São Paulo, 13560-970, Brazil
| | - Luiz L Coutinho
- Functional Genomic Center, University of São Paulo, Piracicaba, São Paulo, 13418-900, Brazil
| | - Luciana C A Regitano
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, São Paulo, 13560-970, Brazil.
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Deng X, Fang L. VGLL4 is a transcriptional cofactor acting as a novel tumor suppressor via interacting with TEADs. Am J Cancer Res 2018; 8:932-943. [PMID: 30034932 PMCID: PMC6048398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/18/2018] [Indexed: 06/08/2023] Open
Abstract
Vestigial Like Family Member 4 (VGLL4) is a transcriptional cofactor of VGLL family, which includes VGLL1-4. Unlike other members of VGLL family, VGLL4 was described as a novel tumor suppressor containing two TDU motifs. VGLL4 executes its biological function through two TDU domains via interacting with TEA domain (TEAD) transcription factors. Lower expression of VGLL4 usually indicates poor survival in many cancers, such as lung cancer, gastric cancer, breast cancer, colorectal cancer, bladder cancer, pancreatic adenocarcinoma and esophageal squamous cancer. In cancer cells, the expression of VGLL4 is lower than that of normal tissues, moreover, expression level of VGLL4 is positively related to survival rate. VGLL4 is found to play an important role in several signal pathways, mainly acts as a tumor suppressor interacting with TEADs. In Hippo signaling pathway, VGLL4 competes with YAP in binding to TEADs and inhibits the downstream of YAP. In Wnt/β-catenin signaling pathway, VGLL4 negatively regulates Wnt/β-catenin signaling pathway via inhibiting β-catenin and TCF (T-cell factor). VGLL4 can also suppress epithelial-mesenchymal transition (EMT) and contribute to apoptosis signaling pathway.
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Affiliation(s)
- Xiaochong Deng
- Department of Thyroid and Breast, Division of General Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University Shanghai 200072, People's Republic of China
| | - Lin Fang
- Department of Thyroid and Breast, Division of General Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University Shanghai 200072, People's Republic of China
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Moon S, Chandran AKN, Gho YS, Park SA, Kim SR, Yoo YH, Jung KH. Integrated omics analysis of root-preferred genes across diverse rice varieties including Japonica and indica cultivars. JOURNAL OF PLANT PHYSIOLOGY 2018; 220:11-23. [PMID: 29132026 DOI: 10.1016/j.jplph.2017.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 10/02/2017] [Accepted: 10/16/2017] [Indexed: 06/07/2023]
Abstract
Plant root systems play essential roles in developmental processes, such as the absorption of water and inorganic nutrients, and structural support. Gene expression is affected by growth conditions and the genetic background of plants. To identify highly conserved root-preferred genes in rice across diverse growth conditions and varieties, we used two independent meta-anatomical expression profiles based on a large collection of Affymetrix and Agilent 44K microarray data sets available for public use. We then identified 684 loci with root-preferred expression, which were validated with in silico analysis using both meta-expression profiles. The expression patterns of four candidate genes were confirmed in vivo by monitoring expression of β-glucuronidase under control of the candidate-gene promoters, providing new tools to manipulate agronomic traits associated with roots. We also utilized real-time PCR to examine the root-preferential expression of 14 genes across four rice varieties, including japonica and indica cultivars. Using a database of rice genes with known functions, we identified the reported functions of 39 out of the 684 candidate genes. Sixteen genes are directly involved in root development, while the remaining are involved in processes indirectly related to root development (i.e., soil-stress tolerance or growth retardation). This indicates the importance of our candidate genes for studies on root development and function. Gene ontology enrichment analysis in the 'biological processes' category revealed that root-preferred genes in rice are closely associated with nutrient transport-related genes, indicating that the primary role of roots is the uptake of nutrients from soil. In addition, predicted protein-protein interaction analysis suggested a molecular network for root development composed of 215 interactions associated with 44 root-preferred or root development-related genes. Taken together, our data provide an important foundation for future research on root development in rice.
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Affiliation(s)
- Sunok Moon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | | | - Yun-Shil Gho
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Sun-A Park
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Sung-Ryul Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Yo-Han Yoo
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
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