1
|
Lopez Martinez D, Svejstrup JQ. Mechanisms of RNA Polymerase II Termination at the 3'-End of Genes. J Mol Biol 2024:168735. [PMID: 39098594 DOI: 10.1016/j.jmb.2024.168735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/23/2024] [Accepted: 07/30/2024] [Indexed: 08/06/2024]
Abstract
RNA polymerase II (RNAPII) is responsible for the synthesis of a diverse set of RNA molecules, including protein-coding messenger RNAs (mRNAs) and many short non-coding RNAs (ncRNAs). For this purpose, RNAPII relies on a multitude of factors that regulate the transcription cycle, from initiation and promoter-proximal pausing, through elongation and finally termination. RNAPII transcription termination at the end of genes ensures the release of RNAPII from the DNA template and its efficient recycling for further rounds of transcription. Termination of RNAPII is tightly coupled to 3'-end mRNA processing, which constitutes an important trigger for the subsequent transcription termination event. In this review, we discuss the current understanding of RNAPII termination mechanisms, focusing on 'canonical' termination at the 3'-end of genes. We also integrate the allosteric and 'torpedo' models into a unified model of termination, and describe the different termination factors that have been identified to date, paying special attention to the human factors and their mechanism of action at the molecular level. Indeed, in recent years the development of novel approaches in structural biology, biochemistry and cell biology have together led to a more detailed comprehension of the different mechanisms of RNAPII termination, and a better understanding of their importance in regulating gene expression, especially under cellular stress and pathological situations.
Collapse
Affiliation(s)
- David Lopez Martinez
- Centre for Gene Expression, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
| | - Jesper Q Svejstrup
- Centre for Gene Expression, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
2
|
Ni Z, Ahmed N, Nabeel-Shah S, Guo X, Pu S, Song J, Marcon E, Burke G, Tong AH, Chan K, Ha KH, Blencowe B, Moffat J, Greenblatt J. Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter. Nucleic Acids Res 2024; 52:4483-4501. [PMID: 38587191 PMCID: PMC11077057 DOI: 10.1093/nar/gkae240] [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: 09/23/2023] [Revised: 01/29/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024] Open
Abstract
Messenger RNA precursors (pre-mRNA) generally undergo 3' end processing by cleavage and polyadenylation (CPA), which is specified by a polyadenylation site (PAS) and adjacent RNA sequences and regulated by a large variety of core and auxiliary CPA factors. To date, most of the human CPA factors have been discovered through biochemical and proteomic studies. However, genetic identification of the human CPA factors has been hampered by the lack of a reliable genome-wide screening method. We describe here a dual fluorescence readthrough reporter system with a PAS inserted between two fluorescent reporters. This system enables measurement of the efficiency of 3' end processing in living cells. Using this system in combination with a human genome-wide CRISPR/Cas9 library, we conducted a screen for CPA factors. The screens identified most components of the known core CPA complexes and other known CPA factors. The screens also identified CCNK/CDK12 as a potential core CPA factor, and RPRD1B as a CPA factor that binds RNA and regulates the release of RNA polymerase II at the 3' ends of genes. Thus, this dual fluorescence reporter coupled with CRISPR/Cas9 screens reliably identifies bona fide CPA factors and provides a platform for investigating the requirements for CPA in various contexts.
Collapse
Affiliation(s)
- Zuyao Ni
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Nujhat Ahmed
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Syed Nabeel-Shah
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Xinghua Guo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Shuye Pu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Jingwen Song
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Edyta Marcon
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Giovanni L Burke
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Amy Hin Yan Tong
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Katherine Chan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Kevin C H Ha
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Benjamin J Blencowe
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Jason Moffat
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON Canada
| | - Jack F Greenblatt
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| |
Collapse
|
3
|
Alemany M. The Metabolic Syndrome, a Human Disease. Int J Mol Sci 2024; 25:2251. [PMID: 38396928 PMCID: PMC10888680 DOI: 10.3390/ijms25042251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
This review focuses on the question of metabolic syndrome (MS) being a complex, but essentially monophyletic, galaxy of associated diseases/disorders, or just a syndrome of related but rather independent pathologies. The human nature of MS (its exceptionality in Nature and its close interdependence with human action and evolution) is presented and discussed. The text also describes the close interdependence of its components, with special emphasis on the description of their interrelations (including their syndromic development and recruitment), as well as their consequences upon energy handling and partition. The main theories on MS's origin and development are presented in relation to hepatic steatosis, type 2 diabetes, and obesity, but encompass most of the MS components described so far. The differential effects of sex and its biological consequences are considered under the light of human social needs and evolution, which are also directly related to MS epidemiology, severity, and relations with senescence. The triggering and maintenance factors of MS are discussed, with especial emphasis on inflammation, a complex process affecting different levels of organization and which is a critical element for MS development. Inflammation is also related to the operation of connective tissue (including the adipose organ) and the widely studied and acknowledged influence of diet. The role of diet composition, including the transcendence of the anaplerotic maintenance of the Krebs cycle from dietary amino acid supply (and its timing), is developed in the context of testosterone and β-estradiol control of the insulin-glycaemia hepatic core system of carbohydrate-triacylglycerol energy handling. The high probability of MS acting as a unique complex biological control system (essentially monophyletic) is presented, together with additional perspectives/considerations on the treatment of this 'very' human disease.
Collapse
Affiliation(s)
- Marià Alemany
- Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
| |
Collapse
|
4
|
Mehta P, Chattopadhyay P, Mohite R, D'Rozario R, Bandopadhyay P, Sarif J, Ray Y, Ganguly D, Pandey R. Suppressed transcript diversity and immune response in COVID-19 ICU patients: a longitudinal study. Life Sci Alliance 2024; 7:e202302305. [PMID: 37918965 PMCID: PMC10622646 DOI: 10.26508/lsa.202302305] [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: 08/03/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023] Open
Abstract
Understanding the dynamic changes in gene expression during Acute Respiratory Distress Syndrome (ARDS) progression in post-acute infection patients is crucial for unraveling the underlying mechanisms. Study investigates the longitudinal changes in gene/transcript expression patterns in hospital-admitted severe COVID-19 patients with ARDS post-acute SARS-CoV-2 infection. Blood samples were collected at three time points and patients were stratified into severe and mild ARDS, based on their oxygenation saturation (SpO2/FiO2) kinetics over 7 d. Decline in transcript diversity was observed over time, particularly in patients with higher severity, indicating dysregulated transcriptional landscape. Comparing gene/transcript-level analyses highlighted a rather limited overlap. With disease progression, a transition towards an inflammatory state was evident. Strong association was found between antibody response and disease severity, characterized by decreased antibody response and activated B cell population in severe cases. Bayesian network analysis identified various factors associated with disease progression and severity, viz. humoral response, TLR signaling, inflammatory response, interferon response, and effector T cell abundance. The findings highlight dynamic gene/transcript expression changes during ARDS progression, impact on tissue oxygenation and elucidate disease pathogenesis.
Collapse
Affiliation(s)
- Priyanka Mehta
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Partha Chattopadhyay
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ramakant Mohite
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Ranit D'Rozario
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- https://ror.org/01kh0x418 IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Purbita Bandopadhyay
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- https://ror.org/01kh0x418 IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Jafar Sarif
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- https://ror.org/01kh0x418 IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Yogiraj Ray
- Infectious Disease and Beleghata General Hospital, Kolkata, India
- Department of Infectious Diseases, Shambhunath Pandit Hospital, Institute of Postgraduate Medical Education and Research, Kolkata, India
| | - Dipyaman Ganguly
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- https://ror.org/01kh0x418 IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Rajesh Pandey
- https://ror.org/05ef28661 Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
5
|
Li W, Li X, Gao Y, Xiong C, Tang Z. Emerging roles of RNA binding proteins in intervertebral disc degeneration and osteoarthritis. Orthop Surg 2023; 15:3015-3025. [PMID: 37803912 PMCID: PMC10694020 DOI: 10.1111/os.13851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/06/2023] [Accepted: 07/19/2023] [Indexed: 10/08/2023] Open
Abstract
The etiology of intervertebral disc degeneration (IDD) and osteoarthritis (OA) is complex and multifactorial. Both predisposing genes and environmental factors are involved in the pathogenesis of IDD and OA. Moreover, epigenetic modifications affect the development of IDD and OA. Dysregulated phenotypes of nucleus pulposus (NP) cells and OA chondrocytes, including apoptosis, extracellular matrix disruption, inflammation, and angiogenesis, are involved at all developmental stages of IDD and OA. RNA binding proteins (RBPs) have recently been recognized as essential post-transcriptional regulators of gene expression. RBPs are implicated in many cellular processes, such as proliferation, differentiation, and apoptosis. Recently, several RBPs have been reported to be associated with the pathogenesis of IDD and OA. This review briefly summarizes the current knowledge on the RNA-regulatory networks controlled by RBPs and their potential roles in the pathogenesis of IDD and OA. These initial findings support the idea that specific modulation of RBPs represents a promising approach for managing IDD and OA.
Collapse
Affiliation(s)
- Wen Li
- Department of EmergencyGeneral Hospital of Central Theater Command of PLAWuhanChina
| | - Xing‐Hua Li
- Department of EmergencyGeneral Hospital of Central Theater Command of PLAWuhanChina
| | - Yang Gao
- Department of OrthopaedicGeneral Hospital of Central Theater Command of PLAWuhanChina
| | - Cheng‐Jie Xiong
- Department of OrthopaedicGeneral Hospital of Central Theater Command of PLAWuhanChina
| | - Zhong‐Zhi Tang
- Department of EmergencyGeneral Hospital of Central Theater Command of PLAWuhanChina
| |
Collapse
|