1
|
Garrido-Godino AI, Gupta I, Pelechano V, Navarro F. RNA Pol II Assembly Affects ncRNA Expression. Int J Mol Sci 2023; 25:507. [PMID: 38203678 PMCID: PMC10778713 DOI: 10.3390/ijms25010507] [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: 11/30/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
RNA pol II assembly occurs in the cytoplasm before translocation of the enzyme to the nucleus. Affecting this assembly influences mRNA transcription in the nucleus and mRNA decay in the cytoplasm. However, very little is known about the consequences on ncRNA synthesis. In this work, we show that impairment of RNA pol II assembly leads to a decrease in cryptic non-coding RNAs (preferentially CUTs and SUTs). This alteration is partially restored upon overcoming the assembly defect. Notably, this drop in ncRNAs is only partially dependent on the nuclear exosome, which suggests a major specific effect of enzyme assembly. Our data also point out a defect in transcription termination, which leads us to propose that CTD phosphatase Rtr1 could be involved in this process.
Collapse
Affiliation(s)
- Ana I. Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain;
| | - Ishaan Gupta
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany;
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain;
- Instituto Universitario de Investigación en Olivar y Aceites de Oliva (INUO), Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
| |
Collapse
|
2
|
Gao X, Yi Y, Lv J, Li Y, Arulsamy K, Babu S, Bruno I, Zhang L, Cao Q, Chen K. Low RNA stability signifies strong expression regulatability of tumor suppressors. Nucleic Acids Res 2023; 51:11534-11548. [PMID: 37831104 PMCID: PMC10681714 DOI: 10.1093/nar/gkad838] [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: 04/25/2023] [Revised: 09/12/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023] Open
Abstract
RNA expression of a gene is determined by not only transcriptional regulation, but also post-transcriptional regulation of RNA decay. The precise regulation of RNA stability in the cell plays an important role in normal development. Dysregulation of RNA stability can lead to diseases such as cancer. Here we found tumor suppressor RNAs tended to decay fast in normal cell types when compared with other RNAs. Consistent with a negative effect of m6A modification on RNA stability, we observed preferential deposition of m6A on tumor suppressor RNAs. Moreover, abundant m6A and fast decay of tumor suppressor RNAs both tended to be further enhanced in prostate cancer cells relative to normal prostate epithelial cells. Further, knockdown of m6A methyltransferase METTL3 and reader YTHDF2 in prostate cancer cells both posed stronger effect on tumor suppressor RNAs than on other RNAs. These results indicated a strong post transcriptional expression regulatability mediated by abundant m6A modification on tumor suppressor RNAs.
Collapse
Affiliation(s)
- Xinlei Gao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Yang Yi
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jie Lv
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Yanqiang Li
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Kulandaisamy Arulsamy
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Sahana Suresh Babu
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Ivone Bruno
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Qi Cao
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
- Prostate Cancer Program, Dana-Farber Harvard cancer Center, Boston, MA 02115, USA
| |
Collapse
|
3
|
Bryll AR, Peterson CL. The circular logic of mRNA homeostasis. Transcription 2023; 14:18-26. [PMID: 36843061 PMCID: PMC10353332 DOI: 10.1080/21541264.2023.2183684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/28/2023] Open
Abstract
Eukaryotic cells rely upon dynamic, multifaceted regulation at each step of RNA biogenesis to maintain mRNA pools and ensure normal protein synthesis. Studies in budding yeast indicate a buffering phenomenon that preserves global mRNA levels through the reciprocal balancing of RNA synthesis rates and mRNA decay. In short, changes in transcription impact the efficiency of mRNA degradation and defects in either nuclear or cytoplasmic mRNA degradation are somehow sensed and relayed to control a compensatory change in mRNA transcription rates. Here, we review current views on molecular mechanisms that might explain this apparent bidirectional sensing process that ensures homeostasis of the stable mRNA pool.
Collapse
Affiliation(s)
- Alysia R. Bryll
- Program of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester
- Medical Scientist Training Program, University of Massachusetts Chan Medical School, Worcester
| | - Craig L. Peterson
- Program of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester
| |
Collapse
|
4
|
García-Martínez J, Singh A, Medina D, Chávez S, Pérez-Ortín JE. Enhanced gene regulation by cooperation between mRNA decay and gene transcription. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194910. [PMID: 36731791 PMCID: PMC10663100 DOI: 10.1016/j.bbagrm.2023.194910] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/31/2023]
Abstract
It has become increasingly clear in the last few years that gene expression in eukaryotes is not a linear process from mRNA synthesis in the nucleus to translation and degradation in the cytoplasm, but works as a circular one where the mRNA level is controlled by crosstalk between nuclear transcription and cytoplasmic decay pathways. One of the consequences of this crosstalk is the approximately constant level of mRNA. This is called mRNA buffering and happens when transcription and mRNA degradation act at compensatory rates. However, if transcription and mRNA degradation act additively, enhanced gene expression regulation occurs. In this work, we analyzed new and previously published genomic datasets obtained for several yeast mutants related to either transcription or mRNA decay that are not known to play any role in the other process. We show that some, which were presumed only transcription factors (Sfp1) or only decay factors (Puf3, Upf2/3), may represent examples of RNA-binding proteins (RBPs) that make specific crosstalk to enhance the control of the mRNA levels of their target genes by combining additive effects on transcription and mRNA stability. These results were mathematically modeled to see the effects of RBPs when they have positive or negative effects on mRNA synthesis and decay rates. We found that RBPs can be an efficient way to buffer or enhance gene expression responses depending on their respective effects on transcription and mRNA stability.
Collapse
Affiliation(s)
- José García-Martínez
- Instituto de Biotecnología y Biomedicina (Biotecmed), Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
| | - Daniel Medina
- Instituto de Biotecnología y Biomedicina (Biotecmed), Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain
| | - Sebastián Chávez
- Departamento de Genética, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, 41013 Seville, Spain; Dirección de Evaluación y Acreditación, Agencia Andaluza del Conocimiento, Doña Berenguela s/n, planta 3ª C.P. 14006, Córdoba, Spain
| | - José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (Biotecmed), Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain.
| |
Collapse
|
5
|
Li Y, Huang J, Bao L, Zhu J, Duan W, Zheng H, Wang H, Jiang Y, Liu W, Zhang M, Yu Y, Yi C, Ji X. RNA Pol II preferentially regulates ribosomal protein expression by trapping disassociated subunits. Mol Cell 2023; 83:1280-1297.e11. [PMID: 36924766 DOI: 10.1016/j.molcel.2023.02.028] [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: 03/30/2022] [Revised: 12/12/2022] [Accepted: 02/23/2023] [Indexed: 03/17/2023]
Abstract
RNA polymerase II (RNA Pol II) has been recognized as a passively regulated multi-subunit holoenzyme. However, the extent to which RNA Pol II subunits might be important beyond the RNA Pol II complex remains unclear. Here, fractions containing disassociated RPB3 (dRPB3) were identified by size exclusion chromatography in various cells. Through a unique strategy, i.e., "specific degradation of disassociated subunits (SDDS)," we demonstrated that dRPB3 functions as a regulatory component of RNA Pol II to enable the preferential control of 3' end processing of ribosomal protein genes directly through its N-terminal domain. Machine learning analysis of large-scale genomic features revealed that the little elongation complex (LEC) helps to specialize the functions of dRPB3. Mechanistically, dRPB3 facilitates CBC-PCF11 axis activity to increase the efficiency of 3' end processing. Furthermore, RPB3 is dynamically regulated during development and diseases. These findings suggest that RNA Pol II gains specific regulatory functions by trapping disassociated subunits in mammalian cells.
Collapse
Affiliation(s)
- Yuanjun Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jie Huang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Lijun Bao
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Junyi Zhu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Wenjia Duan
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Haonan Zheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yongpeng Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Weiwei Liu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Meiling Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yang Yu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
| |
Collapse
|
6
|
RNA-controlled nucleocytoplasmic shuttling of mRNA decay factors regulates mRNA synthesis and a novel mRNA decay pathway. Nat Commun 2022; 13:7184. [PMID: 36418294 PMCID: PMC9684461 DOI: 10.1038/s41467-022-34417-z] [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: 01/25/2021] [Accepted: 10/25/2022] [Indexed: 11/27/2022] Open
Abstract
mRNA level is controlled by factors that mediate both mRNA synthesis and decay, including the 5' to 3' exonuclease Xrn1. Here we show that nucleocytoplasmic shuttling of several yeast mRNA decay factors plays a key role in determining both mRNA synthesis and decay. Shuttling is regulated by RNA-controlled binding of the karyopherin Kap120 to two nuclear localization sequences (NLSs) in Xrn1, location of one of which is conserved from yeast to human. The decaying RNA binds and masks NLS1, establishing a link between mRNA decay and Xrn1 shuttling. Preventing Xrn1 import, either by deleting KAP120 or mutating the two Xrn1 NLSs, compromises transcription and, unexpectedly, also cytoplasmic decay, uncovering a cytoplasmic decay pathway that initiates in the nucleus. Most mRNAs are degraded by both pathways - the ratio between them represents a full spectrum. Importantly, Xrn1 shuttling is required for proper responses to environmental changes, e.g., fluctuating temperatures, involving proper changes in mRNA abundance and in cell proliferation rate.
Collapse
|
7
|
Garrido-Godino AI, Martín-Expósito M, Gutiérrez-Santiago F, Perez-Fernandez J, Navarro F. Rpb4/7, a key element of RNA pol II to coordinate mRNA synthesis in the nucleus with cytoplasmic functions in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194846. [PMID: 35905859 DOI: 10.1016/j.bbagrm.2022.194846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/11/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Affiliation(s)
- A I Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
| | - M Martín-Expósito
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
| | - F Gutiérrez-Santiago
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
| | - J Perez-Fernandez
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain.
| | - F Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain; Instituto Universitario de Investigación en Olivar y Aceites de Oliva, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain.
| |
Collapse
|
8
|
Pérez-Ortín JE, Chávez S. Nucleo-cytoplasmic shuttling of RNA-binding factors: mRNA buffering and beyond. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194849. [PMID: 35907432 DOI: 10.1016/j.bbagrm.2022.194849] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/18/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
Gene expression is a highly regulated process that adapts RNAs and proteins content to the cellular context. Under steady-state conditions, mRNA homeostasis is robustly maintained by tight controls that act on both nuclear transcription and cytoplasmic mRNA stability. In recent years, it has been revealed that several RNA-binding proteins (RBPs) that perform functions in mRNA decay can move to the nucleus and regulate transcription. The RBPs involved in transcription can also travel to the cytoplasm and regulate mRNA degradation and/or translation. The multifaceted functions of these shuttling nucleo-cytoplasm RBPs have raised the possibility that they can act as mRNA metabolism coordinators. In addition, this indicates the existence of crosstalk mechanisms between the enzymatic machineries that drive the different mRNA life-cycle phases. The buffering of the mRNA concentration is the best known consequence of a transcription-degradation crosstalk counteraction, but alternative ways of RBP action can also imply enhanced gene regulation.
Collapse
Affiliation(s)
- José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (Biotecmed), Facultad de Biológicas, Universitat de València. C/Dr. Moliner 50, E46100 Burjassot, Spain.
| | - Sebastián Chávez
- Departamento de Genética, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, 41013 Seville, Spain; Dirección de Evaluación y Acreditación, Agencia Andaluza del Conocimiento, Doña Berenguela s/n, planta 3ª C.P., 14006 Córdoba, Spain
| |
Collapse
|
9
|
Chappleboim A, Joseph-Strauss D, Gershon O, Friedman N. Transcription feedback dynamics in the wake of cytoplasmic mRNA degradation shutdown. Nucleic Acids Res 2022; 50:5864-5880. [PMID: 35640599 PMCID: PMC9177992 DOI: 10.1093/nar/gkac411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/02/2022] [Accepted: 05/09/2022] [Indexed: 01/02/2023] Open
Abstract
In the last decade, multiple studies demonstrated that cells maintain a balance of mRNA production and degradation, but the mechanisms by which cells implement this balance remain unknown. Here, we monitored cells' total and recently-transcribed mRNA profiles immediately following an acute depletion of Xrn1-the main 5'-3' mRNA exonuclease-which was previously implicated in balancing mRNA levels. We captured the detailed dynamics of the adaptation to rapid degradation of Xrn1 and observed a significant accumulation of mRNA, followed by a delayed global reduction in transcription and a gradual return to baseline mRNA levels. We found that this transcriptional response is not unique to Xrn1 depletion; rather, it is induced earlier when upstream factors in the 5'-3' degradation pathway are perturbed. Our data suggest that the mRNA feedback mechanism monitors the accumulation of inputs to the 5'-3' exonucleolytic pathway rather than its outputs.
Collapse
Affiliation(s)
- Alon Chappleboim
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Daphna Joseph-Strauss
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Omer Gershon
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nir Friedman
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| |
Collapse
|
10
|
Du J, Babik S, Li Y, Deol KK, Eyles SJ, Fejzo J, Tonelli M, Strieter E. A cryptic K48 ubiquitin chain binding site on UCH37 is required for its role in proteasomal degradation. eLife 2022; 11:e76100. [PMID: 35451368 PMCID: PMC9033301 DOI: 10.7554/elife.76100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/07/2022] [Indexed: 11/16/2022] Open
Abstract
Degradation by the 26 S proteasome is an intricately regulated process fine tuned by the precise nature of ubiquitin modifications attached to a protein substrate. By debranching ubiquitin chains composed of K48 linkages, the proteasome-associated ubiquitin C-terminal hydrolase UCHL5/UCH37 serves as a positive regulator of protein degradation. How UCH37 achieves specificity for K48 chains is unclear. Here, we use a combination of hydrogen-deuterium mass spectrometry, chemical crosslinking, small-angle X-ray scattering, nuclear magnetic resonance (NMR), molecular docking, and targeted mutagenesis to uncover a cryptic K48 ubiquitin (Ub) chain-specific binding site on the opposite face of UCH37 relative to the canonical S1 (cS1) ubiquitin-binding site. Biochemical assays demonstrate the K48 chain-specific binding site is required for chain debranching and proteasome-mediated degradation of proteins modified with branched chains. Using quantitative proteomics, translation shutoff experiments, and linkage-specific affinity tools, we then identify specific proteins whose degradation depends on the debranching activity of UCH37. Our findings suggest that UCH37 and potentially other DUBs could use more than one S1 site to perform different biochemical functions.
Collapse
Affiliation(s)
- Jiale Du
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Sandor Babik
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Yanfeng Li
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Kirandeep K Deol
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Stephen J Eyles
- Mass Spectrometry Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts AmherstAmherstUnited States
| | - Jasna Fejzo
- Biomolecular NMR Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts AmherstAmherstUnited States
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-MadisonMadisonUnited States
| | - Eric Strieter
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
- Molecular & Cellular Biology Graduate Program, University of Massachusetts AmherstAmherstUnited States
| |
Collapse
|
11
|
Garrido-Godino AI, Cuevas-Bermúdez A, Gutiérrez-Santiago F, Mota-Trujillo MDC, Navarro F. The Association of Rpb4 with RNA Polymerase II Depends on CTD Ser5P Phosphatase Rtr1 and Influences mRNA Decay in Saccharomyces cerevisiae. Int J Mol Sci 2022; 23:ijms23042002. [PMID: 35216121 PMCID: PMC8875030 DOI: 10.3390/ijms23042002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 02/04/2023] Open
Abstract
Rtr1 is an RNA polymerase II (RNA pol II) CTD-phosphatase that influences gene expression during the transition from transcription initiation to elongation and during transcription termination. Rtr1 interacts with the RNA pol II and this interaction depends on the phosphorylation state of the CTD of Rpb1, which may influence dissociation of the heterodimer Rpb4/7 during transcription. In addition, Rtr1 was proposed as an RNA pol II import factor in RNA pol II biogenesis and participates in mRNA decay by autoregulating the turnover of its own mRNA. Our work shows that Rtr1 acts in RNA pol II assembly by mediating the Rpb4/7 association with the rest of the enzyme. RTR1 deletion alters RNA pol II assembly and increases the amount of RNA pol II associated with the chromatin that lacks Rpb4, decreasing Rpb4-mRNA imprinting and, consequently, increasing mRNA stability. Thus, Rtr1 interplays RNA pol II biogenesis and mRNA decay regulation. Our data also indicate that Rtr1 mediates mRNA decay regulation more broadly than previously proposed by cooperating with Rpb4. Interestingly, our data include new layers in the mechanisms of gene regulation and in the crosstalk between mRNA synthesis and decay by demonstrating how the association of Rpb4/7 to the RNA pol II influences mRNA decay.
Collapse
Affiliation(s)
- Ana I. Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain; (A.I.G.-G.); (A.C.-B.); (F.G.-S.); (M.d.C.M.-T.)
| | - Abel Cuevas-Bermúdez
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain; (A.I.G.-G.); (A.C.-B.); (F.G.-S.); (M.d.C.M.-T.)
| | - Francisco Gutiérrez-Santiago
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain; (A.I.G.-G.); (A.C.-B.); (F.G.-S.); (M.d.C.M.-T.)
| | - Maria del Carmen Mota-Trujillo
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain; (A.I.G.-G.); (A.C.-B.); (F.G.-S.); (M.d.C.M.-T.)
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain; (A.I.G.-G.); (A.C.-B.); (F.G.-S.); (M.d.C.M.-T.)
- Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
- Correspondence: ; Tel.: +34-953-212-771; Fax: +34-953-211-875
| |
Collapse
|
12
|
Okuda M, Suwa T, Suzuki H, Yamaguchi Y, Nishimura Y. Three human RNA polymerases interact with TFIIH via a common RPB6 subunit. Nucleic Acids Res 2021; 50:1-16. [PMID: 34268577 PMCID: PMC8754651 DOI: 10.1093/nar/gkab612] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/29/2021] [Accepted: 07/08/2021] [Indexed: 11/17/2022] Open
Abstract
In eukaryotes, three RNA polymerases (RNAPs) play essential roles in the synthesis of various types of RNA: namely, RNAPI for rRNA; RNAPII for mRNA and most snRNAs; and RNAPIII for tRNA and other small RNAs. All three RNAPs possess a short flexible tail derived from their common subunit RPB6. However, the function of this shared N-terminal tail (NTT) is not clear. Here we show that NTT interacts with the PH domain (PH-D) of the p62 subunit of the general transcription/repair factor TFIIH, and present the structures of RPB6 unbound and bound to PH-D by nuclear magnetic resonance (NMR). Using available cryo-EM structures, we modelled the activated elongation complex of RNAPII bound to TFIIH. We also provide evidence that the recruitment of TFIIH to transcription sites through the p62–RPB6 interaction is a common mechanism for transcription-coupled nucleotide excision repair (TC-NER) of RNAPI- and RNAPII-transcribed genes. Moreover, point mutations in the RPB6 NTT cause a significant reduction in transcription of RNAPI-, RNAPII- and RNAPIII-transcribed genes. These and other results show that the p62–RPB6 interaction plays multiple roles in transcription, TC-NER, and cell proliferation, suggesting that TFIIH is engaged in all RNAP systems.
Collapse
Affiliation(s)
- Masahiko Okuda
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tetsufumi Suwa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Hidefumi Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Yuki Yamaguchi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8258, Japan
| |
Collapse
|
13
|
Herold I, Zolti A, Garduño-Rosales M, Wang Z, López-Giráldez F, Mouriño-Pérez RR, Townsend JP, Ulitsky I, Yarden O. The GUL-1 Protein Binds Multiple RNAs Involved in Cell Wall Remodeling and Affects the MAK-1 Pathway in Neurospora crassa. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:672696. [PMID: 37744127 PMCID: PMC10512220 DOI: 10.3389/ffunb.2021.672696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/19/2021] [Indexed: 09/26/2023]
Abstract
The Neurospora crassa GUL-1 is part of the COT-1 pathway, which plays key roles in regulating polar hyphal growth and cell wall remodeling. We show that GUL-1 is a bona fide RNA-binding protein (RBP) that can associate with 828 "core" mRNA species. When cell wall integrity (CWI) is challenged, expression of over 25% of genomic RNA species are modulated (2,628 mRNAs, including the GUL-1 mRNA). GUL-1 binds mRNAs of genes related to translation, cell wall remodeling, circadian clock, endoplasmic reticulum (ER), as well as CWI and MAPK pathway components. GUL-1 interacts with over 100 different proteins, including stress-granule and P-body proteins, ER components and components of the MAPK, COT-1, and STRIPAK complexes. Several additional RBPs were also shown to physically interact with GUL-1. Under stress conditions, GUL-1 can localize to the ER and affect the CWI pathway-evident via altered phosphorylation levels of MAK-1, interaction with mak-1 transcript, and involvement in the expression level of the transcription factor adv-1. We conclude that GUL-1 functions in multiple cellular processes, including the regulation of cell wall remodeling, via a mechanism associated with the MAK-1 pathway and stress-response.
Collapse
Affiliation(s)
- Inbal Herold
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Avihai Zolti
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Marisela Garduño-Rosales
- Departamento de Microbiología, CICESE (Centro de Investigación Científica y Educación Superior de Ensenada), Ensenada, Mexico
| | - Zheng Wang
- Department of Biostatistics, Yale University, New Haven, CT, United States
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Francesc López-Giráldez
- Yale Center for Genome Analysis, Department of Genetics, Yale University, New Haven, CT, United States
| | - Rosa R. Mouriño-Pérez
- Departamento de Microbiología, CICESE (Centro de Investigación Científica y Educación Superior de Ensenada), Ensenada, Mexico
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale University, New Haven, CT, United States
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| |
Collapse
|
14
|
Blumberg A, Zhao Y, Huang YF, Dukler N, Rice EJ, Chivu AG, Krumholz K, Danko CG, Siepel A. Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data. BMC Biol 2021; 19:30. [PMID: 33588838 PMCID: PMC7885420 DOI: 10.1186/s12915-021-00949-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/05/2021] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The concentrations of distinct types of RNA in cells result from a dynamic equilibrium between RNA synthesis and decay. Despite the critical importance of RNA decay rates, current approaches for measuring them are generally labor-intensive, limited in sensitivity, and/or disruptive to normal cellular processes. Here, we introduce a simple method for estimating relative RNA half-lives that is based on two standard and widely available high-throughput assays: Precision Run-On sequencing (PRO-seq) and RNA sequencing (RNA-seq). RESULTS Our method treats PRO-seq as a measure of transcription rate and RNA-seq as a measure of RNA concentration, and estimates the rate of RNA decay required for a steady-state equilibrium. We show that this approach can be used to assay relative RNA half-lives genome-wide, with good accuracy and sensitivity for both coding and noncoding transcription units. Using a structural equation model (SEM), we test several features of transcription units, nearby DNA sequences, and nearby epigenomic marks for associations with RNA stability after controlling for their effects on transcription. We find that RNA splicing-related features are positively correlated with RNA stability, whereas features related to miRNA binding and DNA methylation are negatively correlated with RNA stability. Furthermore, we find that a measure based on U1 binding and polyadenylation sites distinguishes between unstable noncoding and stable coding transcripts but is not predictive of relative stability within the mRNA or lincRNA classes. We also identify several histone modifications that are associated with RNA stability. CONCLUSION We introduce an approach for estimating the relative half-lives of individual RNAs. Together, our estimation method and systematic analysis shed light on the pervasive impacts of RNA stability on cellular RNA concentrations.
Collapse
Affiliation(s)
- Amit Blumberg
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yixin Zhao
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yi-Fei Huang
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Present Address: Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Noah Dukler
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Alexandra G Chivu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Katie Krumholz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| |
Collapse
|
15
|
Gilloteaux J, Bouchat J, Brion JP, Nicaise C. The osmotic demyelination syndrome: the resilience of thalamic neurons is verified with transmission electron microscopy. Ultrastruct Pathol 2021; 44:450-480. [DOI: 10.1080/01913123.2020.1853865] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Jacques Gilloteaux
- Unit of Research in Molecular Physiology (Urphym- NARILIS), Department of Medicine, Université de Namur, Namur, Belgium
- Department of Anatomical Sciences, St George’s University School of Medicine, KB Taylor Global Scholar’s Program at UNN, School of Health and Life Sciences, Newcastle upon Tyne, UK
| | - Joanna Bouchat
- Unit of Research in Molecular Physiology (Urphym- NARILIS), Department of Medicine, Université de Namur, Namur, Belgium
| | - Jean-Pierre Brion
- Laboratory of Histology, Neuroanatomy and Neuropathology, Faculté de Médecine Université Libre de Bruxelles, Brussels, Belgium
| | - Charles Nicaise
- Unit of Research in Molecular Physiology (Urphym- NARILIS), Department of Medicine, Université de Namur, Namur, Belgium
| |
Collapse
|
16
|
Richard S, Gross L, Fischer J, Bendalak K, Ziv T, Urim S, Choder M. Numerous Post-translational Modifications of RNA Polymerase II Subunit Rpb4/7 Link Transcription to Post-transcriptional Mechanisms. Cell Rep 2021; 34:108578. [PMID: 33440147 DOI: 10.1016/j.celrep.2020.108578] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 07/24/2020] [Accepted: 12/09/2020] [Indexed: 01/25/2023] Open
Abstract
Rpb4/7 binds RNA polymerase II (RNA Pol II) transcripts co-transcriptionally and accompanies them throughout their lives. By virtue of its capacity to interact with key regulators (e.g., RNA Pol II, eIF3, and Pat1) temporally and spatially, Rpb4/7 regulates the major stages of the mRNA life cycle. Here we show that Rpb4/7 can undergo more than 100 combinations of post-translational modifications (PTMs). Remarkably, the Rpb4/7 PTM repertoire changes as the mRNA/Rpb4/7 complex progresses from one stage to the next. These temporal PTMs regulate Rpb4 interactions with key regulators of gene expression that control transcriptional and post-transcriptional stages. Moreover, one mutant type specifically affects mRNA synthesis, whereas the other affects mRNA synthesis and decay; both types disrupt the balance between mRNA synthesis and decay ("mRNA buffering") and the cell's capacity to respond to the environment. We propose that temporal Rpb4/7 PTMs mediate the cross-talk among the various stages of the mRNA life cycle.
Collapse
Affiliation(s)
- Stephen Richard
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Lital Gross
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Jonathan Fischer
- Computer Science Division, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Keren Bendalak
- Smoler Proteomics Center, Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Tamar Ziv
- Smoler Proteomics Center, Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Shira Urim
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Mordechai Choder
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel.
| |
Collapse
|
17
|
Garrido-Godino AI, Gupta I, Gutiérrez-Santiago F, Martínez-Padilla AB, Alekseenko A, Steinmetz LM, Pérez-Ortín JE, Pelechano V, Navarro F. Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast. RNA Biol 2020; 18:1206-1220. [PMID: 33094674 DOI: 10.1080/15476286.2020.1839229] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, crosstalk in which mRNA decay machinery and transcription machinery respectively impact transcription and mRNA stability. Rpb4, and likely dimer Rpb4/7, seem the central components of the RNA pol II governing these processes. In this work we unravel the molecular mechanisms participated by Rpb4 that mediate the posttranscriptional events regulating mRNA imprinting and stability. By RIP-Seq, we analysed genome-wide the association of Rpb4 with mRNAs and demonstrated that it targeted a large population of more than 1400 transcripts. A group of these mRNAs was also the target of the RNA binding protein, Puf3. We demonstrated that Rpb4 and Puf3 physically, genetically, and functionally interact and also affect mRNA stability, and likely the imprinting, of a common group of mRNAs. Furthermore, the Rpb4 and Puf3 association with mRNAs depends on one another. We also demonstrated, for the first time, that Puf3 associates with chromatin in an Rpb4-dependent manner. Our data also suggest that Rpb4 could be a key element of the RNA pol II that coordinates mRNA synthesis, imprinting and stability in cooperation with RBPs.
Collapse
Affiliation(s)
- A I Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Jaén, Spain
| | - I Gupta
- Department of Biochemical Engineering and Biotechnology, IIT Delhi, Hauz Khas, India
| | - F Gutiérrez-Santiago
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Jaén, Spain
| | - A B Martínez-Padilla
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Jaén, Spain
| | - A Alekseenko
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - L M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.,Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - J E Pérez-Ortín
- E.R.I. Biotecmed, Facultad de Biológicas, Universitat de València, Burjassot, Spain
| | - V Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - F Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Jaén, Spain.,Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Jaén, Spain
| |
Collapse
|
18
|
Slobodin B, Dikstein R. So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes. EMBO Rep 2020; 21:e50799. [PMID: 32803873 PMCID: PMC7507372 DOI: 10.15252/embr.202050799] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/22/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Transcription of DNA into mRNA and translation of mRNA into proteins are two major processes underlying gene expression. Due to the distinct molecular mechanisms, timings, and locales of action, these processes are mainly considered to be independent. During the last two decades, however, multiple factors and elements were shown to coordinate transcription and translation, suggesting an intricate level of synchronization. This review discusses the molecular mechanisms that impact both processes in eukaryotic cells of different origins. The emerging global picture suggests evolutionarily conserved regulation and coordination between transcription and mRNA translation, indicating the importance of this phenomenon for the fine-tuning of gene expression and the adjustment to constantly changing conditions.
Collapse
Affiliation(s)
- Boris Slobodin
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
| | - Rivka Dikstein
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
| |
Collapse
|
19
|
Fischer J, Song YS, Yosef N, di Iulio J, Churchman LS, Choder M. The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5' and 3' gene regions. J Biol Chem 2020; 295:11435-11454. [PMID: 32518159 DOI: 10.1074/jbc.ra120.013426] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/05/2020] [Indexed: 11/06/2022] Open
Abstract
mRNA levels are determined by the balance between mRNA synthesis and decay. Protein factors that mediate both processes, including the 5'-3' exonuclease Xrn1, are responsible for a cross-talk between the two processes that buffers steady-state mRNA levels. However, the roles of these proteins in transcription remain elusive and controversial. Applying native elongating transcript sequencing (NET-seq) to yeast cells, we show that Xrn1 functions mainly as a transcriptional activator and that its disruption manifests as a reduction of RNA polymerase II (Pol II) occupancy downstream of transcription start sites. By combining our sequencing data and mathematical modeling of transcription, we found that Xrn1 modulates transcription initiation and elongation of its target genes. Furthermore, Pol II occupancy markedly increased near cleavage and polyadenylation sites in xrn1Δ cells, whereas its activity decreased, a characteristic feature of backtracked Pol II. We also provide indirect evidence that Xrn1 is involved in transcription termination downstream of polyadenylation sites. We noted that two additional decay factors, Dhh1 and Lsm1, seem to function similarly to Xrn1 in transcription, perhaps as a complex, and that the decay factors Ccr4 and Rpb4 also perturb transcription in other ways. Interestingly, the decay factors could differentiate between SAGA- and TFIID-dominated promoters. These two classes of genes responded differently to XRN1 deletion in mRNA synthesis and were differentially regulated by mRNA decay pathways, raising the possibility that one distinction between these two gene classes lies in the mechanisms that balance mRNA synthesis with mRNA decay.
Collapse
Affiliation(s)
- Jonathan Fischer
- Computer Science Division, University of California, Berkeley, California, USA.,Department of Statistics, University of California, Berkeley, California, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, California, USA.,Department of Statistics, University of California, Berkeley, California, USA.,Chan Zuckerberg BioHub, San Francisco, California, USA
| | - Nir Yosef
- Chan Zuckerberg BioHub, San Francisco, California, USA.,Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, USA.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Julia di Iulio
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Mordechai Choder
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| |
Collapse
|
20
|
Calvo O. RNA polymerase II phosphorylation and gene looping: new roles for the Rpb4/7 heterodimer in regulating gene expression. Curr Genet 2020; 66:927-937. [PMID: 32508001 DOI: 10.1007/s00294-020-01084-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 12/22/2022]
Abstract
In eukaryotes, cellular RNAs are produced by three nuclear RNA polymerases (RNAPI, II, and III), which are multisubunit complexes. They share structural and functional features, although they are specialized in the synthesis of specific RNAs. RNAPII transcribes the vast majority of cellular RNAs, including mRNAs and a large number of noncoding RNAs. The structure of RNAPII is highly conserved in all eukaryotes, consisting of 12 subunits (Rpb1-12) organized into five structural modules, among which the Rpb4 and Rpb7 subunits form the stalk. Early studies suggested an accessory role for Rpb4, because is required for specific gene transcription pathways. Far from this initial hypothesis, it is now well established that the Rpb4/7 heterodimer plays much wider roles in gene expression regulation. It participates in nuclear and cytosolic processes ranging from transcription to translation and mRNA degradation in a cyclical process. For this reason, Rpb4/7 is considered a coordinator of gene expression. New functions have been added to the list of stalk functions during transcription, which will be reviewed herein: first, a role in the maintenance of proper RNAPII phosphorylation levels, and second, a role in the establishment of a looped gene architecture in actively transcribed genes.
Collapse
Affiliation(s)
- Olga Calvo
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, C/ Zacarías González 2, Salamanca, 37007, España.
| |
Collapse
|
21
|
Slobodin B, Bahat A, Sehrawat U, Becker-Herman S, Zuckerman B, Weiss AN, Han R, Elkon R, Agami R, Ulitsky I, Shachar I, Dikstein R. Transcription Dynamics Regulate Poly(A) Tails and Expression of the RNA Degradation Machinery to Balance mRNA Levels. Mol Cell 2020; 78:434-444.e5. [PMID: 32294471 DOI: 10.1016/j.molcel.2020.03.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/25/2020] [Accepted: 03/14/2020] [Indexed: 02/02/2023]
Abstract
Gene expression is regulated by the rates of synthesis and degradation of mRNAs, but how these processes are coordinated is poorly understood. Here, we show that reduced transcription dynamics of specific genes leads to enhanced m6A deposition, preferential activity of the CCR4-Not complex, shortened poly(A) tails, and reduced stability of the respective mRNAs. These effects are also exerted by internal ribosome entry site (IRES) elements, which we found to be transcriptional pause sites. However, when transcription dynamics, and subsequently poly(A) tails, are globally altered, cells buffer mRNA levels by adjusting the expression of mRNA degradation machinery. Stress-provoked global impediment of transcription elongation leads to a dramatic inhibition of the mRNA degradation machinery and massive mRNA stabilization. Accordingly, globally enhanced transcription, such as following B cell activation or glucose stimulation, has the opposite effects. This study uncovers two molecular pathways that maintain balanced gene expression in mammalian cells by linking transcription to mRNA stability.
Collapse
Affiliation(s)
- Boris Slobodin
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Anat Bahat
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Urmila Sehrawat
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shirly Becker-Herman
- Department of Immunology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Binyamin Zuckerman
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Amanda N Weiss
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ruiqi Han
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Igor Ulitsky
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Idit Shachar
- Department of Immunology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rivka Dikstein
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel.
| |
Collapse
|
22
|
Hartenian E, Glaunsinger BA. Feedback to the central dogma: cytoplasmic mRNA decay and transcription are interdependent processes. Crit Rev Biochem Mol Biol 2019; 54:385-398. [PMID: 31656086 PMCID: PMC6871655 DOI: 10.1080/10409238.2019.1679083] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/13/2019] [Accepted: 10/08/2019] [Indexed: 02/06/2023]
Abstract
Transcription and RNA decay are key determinants of gene expression; these processes are typically considered as the uncoupled beginning and end of the messenger RNA (mRNA) lifecycle. Here we describe the growing number of studies demonstrating interplay between these spatially disparate processes in eukaryotes. Specifically, cells can maintain mRNA levels by buffering against changes in mRNA stability or transcription, and can also respond to virally induced accelerated decay by reducing RNA polymerase II gene expression. In addition to these global responses, there is also evidence that mRNAs containing a premature stop codon can cause transcriptional upregulation of homologous genes in a targeted fashion. In each of these systems, RNA binding proteins (RBPs), particularly those involved in mRNA degradation, are critical for cytoplasmic to nuclear communication. Although their specific mechanistic contributions are yet to be fully elucidated, differential trafficking of RBPs between subcellular compartments are likely to play a central role in regulating this gene expression feedback pathway.
Collapse
Affiliation(s)
- Ella Hartenian
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Britt A. Glaunsinger
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, Berkeley, CA 94720
| |
Collapse
|
23
|
Singh P, James RS, Mee CJ, Morozov IY. mRNA levels are buffered upon knockdown of RNA decay and translation factors via adjustment of transcription rates in human HepG2 cells. RNA Biol 2019; 16:1147-1155. [PMID: 31116665 DOI: 10.1080/15476286.2019.1621121] [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] [Indexed: 12/12/2022] Open
Abstract
Evidence from yeast and mammals argues the existence of cross-talk between transcription and mRNA decay. Stabilization of transcripts upon depletion of mRNA decay factors generally leads to no changes in mRNA abundance, attributing this to decreased transcription rates. We show that knockdown of human XRN1, CNOT6 and ETF1 genes in HepG2 cells led to significant alteration in stability of specific mRNAs, alterations in half-life were inversely associated with transcription rates, mostly not resulting in changes in abundance. We demonstrate the existence of the gene expression buffering mechanism in human cells that responds to both transcript stabilization and destabilization to maintain mRNA abundance via altered transcription rates and may involve translation. We propose that this buffering may hold novel cancer therapeutic targets.
Collapse
Affiliation(s)
- Pavneet Singh
- a Centre for Sport, Exercise and Life Sciences, Coventry University , Coventry , UK
| | - Rob S James
- a Centre for Sport, Exercise and Life Sciences, Coventry University , Coventry , UK
| | - Christopher J Mee
- a Centre for Sport, Exercise and Life Sciences, Coventry University , Coventry , UK
| | - Igor Y Morozov
- a Centre for Sport, Exercise and Life Sciences, Coventry University , Coventry , UK
| |
Collapse
|
24
|
Dronamraju R, Hepperla AJ, Shibata Y, Adams AT, Magnuson T, Davis IJ, Strahl BD. Spt6 Association with RNA Polymerase II Directs mRNA Turnover During Transcription. Mol Cell 2019; 70:1054-1066.e4. [PMID: 29932900 DOI: 10.1016/j.molcel.2018.05.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 03/23/2018] [Accepted: 05/17/2018] [Indexed: 10/28/2022]
Abstract
Spt6 is an essential histone chaperone that mediates nucleosome reassembly during gene transcription. Spt6 also associates with RNA polymerase II (RNAPII) via a tandem Src2 homology domain. However, the significance of Spt6-RNAPII interaction is not well understood. Here, we show that Spt6 recruitment to genes and the nucleosome reassembly functions of Spt6 can still occur in the absence of its association with RNAPII. Surprisingly, we found that Spt6-RNAPII association is required for efficient recruitment of the Ccr4-Not de-adenylation complex to transcribed genes for essential degradation of a range of mRNAs, including mRNAs required for cell-cycle progression. These findings reveal an unexpected control mechanism for mRNA turnover during transcription facilitated by a histone chaperone.
Collapse
Affiliation(s)
- Raghuvar Dronamraju
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Austin J Hepperla
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yoichiro Shibata
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexander T Adams
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Terry Magnuson
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, The Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ian J Davis
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, The Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA; Departments of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brian D Strahl
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| |
Collapse
|
25
|
Duek L, Barkai O, Elran R, Adawi I, Choder M. Dissociation of Rpb4 from RNA polymerase II is important for yeast functionality. PLoS One 2018; 13:e0206161. [PMID: 30359412 PMCID: PMC6201915 DOI: 10.1371/journal.pone.0206161] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/07/2018] [Indexed: 12/19/2022] Open
Abstract
Rpb4 is an RNA polymerase II (Pol II) subunit that binds Pol II transcripts co-transcriptionally, accompanies them to the cytoplasm and modulates mRNA export, translation and decay by interacting with cytoplasmic RNA modulators. The importance of the cytoplasmic roles of Rpb4 was challenged by a study reporting that the phenotype of rpb2Δ rpb4Δ cells can be rescued by an Rpb2-Rpb4 fusion protein, assuming that its Rpb4 moiety cannot dissociate from Pol II and functions in the cytoplasm. Here we demonstrate that although the fusion protein supports normal transcription, it adversely affects mRNA decay, cell proliferation and adaptability-e.g., response to stress. These defects are similar, albeit milder, than the defects that characterize rpb4Δ cells. At least two mechanisms alleviate the deleterious effect of the fusion protein. First, a portion of this fusion protein is cleaved into free Rpb2 and Rpb4. The free Rpb4 is functional, as it binds mRNAs and polysomes, like WT Rpb4. Second, the fusion protein is also capable of binding poly(A)+ mRNAs in the cytoplasm, in an Rpb7-mediated manner, probably complementing the functions of the diminished Rpb4. Collectively, normal coupling between mRNA synthesis and decay requires wild-type configuration of Rpb4, and fusing Rpb4 to Rpb2 compromises this coupling.
Collapse
Affiliation(s)
- Lea Duek
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa, Israel
| | - Oren Barkai
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa, Israel
| | - Ron Elran
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa, Israel
| | - Isra Adawi
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa, Israel
| | - Mordechai Choder
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa, Israel
- * E-mail:
| |
Collapse
|
26
|
Yamada T, Akimitsu N. Contributions of regulated transcription and mRNA decay to the dynamics of gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1508. [PMID: 30276972 DOI: 10.1002/wrna.1508] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 08/06/2018] [Accepted: 08/27/2018] [Indexed: 12/21/2022]
Abstract
Organisms have acquired sophisticated regulatory networks that control gene expression in response to cellular perturbations. Understanding of the mechanisms underlying the coordinated changes in gene expression in response to external and internal stimuli is a fundamental issue in biology. Recent advances in high-throughput technologies have enabled the measurement of diverse biological information, including gene expression levels, kinetics of gene expression, and interactions among gene expression regulatory molecules. By coupling these technologies with quantitative modeling, we can now uncover the biological roles and mechanisms of gene regulation at the system level. This review consists of two parts. First, we focus on the methods using uridine analogs that measure synthesis and decay rates of RNAs, which demonstrate how cells dynamically change the regulation of gene expression in response to both internal and external cues. Second, we discuss the underlying mechanisms of these changes in kinetics, including the functions of transcription factors and RNA-binding proteins. Overall, this review will help to clarify a system-level view of gene expression programs in cells. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Turnover and Surveillance > Regulation of RNA Stability RNA Methods > RNA Analyses in vitro and In Silico.
Collapse
Affiliation(s)
- Toshimichi Yamada
- Department of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Tokyo, Japan
| | | |
Collapse
|
27
|
Mullany LE, Herrick JS, Sakoda LC, Samowitz W, Stevens JR, Wolff RK, Slattery ML. MicroRNA-messenger RNA interactions involving JAK-STAT signaling genes in colorectal cancer. Genes Cancer 2018; 9:232-246. [PMID: 30603058 PMCID: PMC6305104 DOI: 10.18632/genesandcancer.177] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
JAK-STAT signaling influences many downstream processes that, unchecked, contribute to carcinogenesis and metastasis. MicroRNAs (miRNAs) are hypothesized as a mechanism to prevent uncontrolled growth from continuous JAK-STAT activation. We investigated differential expression between paired carcinoma and normal colorectal mucosa of messenger RNAs (mRNAs) and miRNAs using RNA-Seq and Agilent Human miRNA Microarray V19.0 data, respectively, using a negative binomial mixed effects model to test 122 JAK-STAT-signaling genes in 217 colorectal cancer (CRC) cases. Overall, 42 mRNAs were differentially expressed with a fold change of >1.50 or <0.67, remaining significant with a false discovery rate of < 0.05; four were dysregulated in microsatellite stable (MSS) tumors, eight were for microsatellite unstable (MSI)-specific tumors. Of these 54 mRNAs, 17 were associated with differential expression of 46 miRNAs, comprising 116 interactions: 16 were significant overall, one for MSS tumors only. Twenty of the 29 interactions with negative beta coefficients involved miRNA seed sequence matches with mRNAs, supporting miRNA-mediated mRNA repression; 17 of these mRNAs encode for receptor molecules. Receptor molecule degradation is an established JAK-STAT signaling control mechanism; our results suggest that miRNAs facilitate this process. Interactions involving positive beta coefficients may illustrate downstream effects of disrupted STAT activity, and subsequent miRNA upregulation.
Collapse
Affiliation(s)
- Lila E Mullany
- Department of Medicine, University of Utah, 383 Colorow, Salt Lake City, Utah
| | - Jennifer S Herrick
- Department of Medicine, University of Utah, 383 Colorow, Salt Lake City, Utah
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Wade Samowitz
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - John R Stevens
- Department of Mathematics and Statistics, Utah State University, Logan, Utah
| | - Roger K Wolff
- Department of Medicine, University of Utah, 383 Colorow, Salt Lake City, Utah
| | - Martha L Slattery
- Department of Medicine, University of Utah, 383 Colorow, Salt Lake City, Utah
| |
Collapse
|
28
|
Ma F, Lin P, Chen Q, Lu X, Zhang YE, Wu CI. Direct measurement of pervasive weak repression by microRNAs and their role at the network level. BMC Genomics 2018; 19:362. [PMID: 29764374 PMCID: PMC5952853 DOI: 10.1186/s12864-018-4757-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/02/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND A gene regulatory network (GRN) comprises many weak links that are often regulated by microRNAs. Since miRNAs rarely repress their target genes by more than 30%, doubts have been expressed about the biological relevance of such weak effects. These doubts raise the possibility of under-estimation as miRNA repression is usually estimated indirectly from equilibrium expression levels. RESULTS To measure miRNA repression directly, we inhibited transcript synthesis in Drosophila larvae and collected time-course data on mRNA abundance, the decline of which reflects transcript degradation. The rate of target degradation in the absence of miR310s, a moderately expressed miRNA family, was found to decrease by 5 to 15%. A conventional analysis that does not remove transcript synthesis yields an estimate of 6.5%, within the range of the new estimates. These data permit further examinations of the repression mechanisms by miRNAs including seed matching types, APA (alternative polyadenylation) sites, effects of other highly-expressed miRNAs and the length of 3'UTR. Our direct measurements suggest the latter two factors have a measurable effect on decay rate. CONCLUSION The direct measurement confirms pervasive weak repression by miRNAs, supporting the conclusions based on indirect assays. The confirmation suggests that this weak repression may indeed be miRNAs' main function. In this context, we discuss the recent proposal that weak repression is "cumulatively powerful" in stabilizing GRNs.
Collapse
Affiliation(s)
- Fuqiang Ma
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pei Lin
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Qingjian Chen
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Xuemei Lu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yong E Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Chung-I Wu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China.
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA.
| |
Collapse
|
29
|
Das S, Sarkar D, Das B. The interplay between transcription and mRNA degradation in Saccharomyces cerevisiae. MICROBIAL CELL 2017; 4:212-228. [PMID: 28706937 PMCID: PMC5507684 DOI: 10.15698/mic2017.07.580] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The cellular transcriptome is shaped by both the rates of mRNA synthesis in the nucleus and mRNA degradation in the cytoplasm under a specified condition. The last decade witnessed an exciting development in the field of post-transcriptional regulation of gene expression which underscored a strong functional coupling between the transcription and mRNA degradation. The functional integration is principally mediated by a group of specialized promoters and transcription factors that govern the stability of their cognate transcripts by “marking” them with a specific factor termed “coordinator.” The “mark” carried by the message is later decoded in the cytoplasm which involves the stimulation of one or more mRNA-decay factors, either directly by the “coordinator” itself or in an indirect manner. Activation of the decay factor(s), in turn, leads to the alteration of the stability of the marked message in a selective fashion. Thus, the integration between mRNA synthesis and decay plays a potentially significant role to shape appropriate gene expression profiles during cell cycle progression, cell division, cellular differentiation and proliferation, stress, immune and inflammatory responses, and may enhance the rate of biological evolution.
Collapse
Affiliation(s)
- Subhadeep Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Debasish Sarkar
- Present Address: Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201-2002, USA
| | - Biswadip Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| |
Collapse
|
30
|
Bloom ALM, Leipheimer J, Panepinto JC. mRNA decay: an adaptation tool for the environmental fungal pathogen Cryptococcus neoformans. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28524625 DOI: 10.1002/wrna.1424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 12/22/2022]
Abstract
Fungi are ubiquitous in the environment and humans constantly encounter them in the soil, air, water, and food. The vast majority of these interactions are inconsequential. However, in the context of immunodeficiency precipitated by HIV infection, hematologic malignancy, or transplantation, a small subset of fungi can cause devastating, systemic infection. The most deadly of the opportunistic environmental fungi, Cryptococcus neoformans, is estimated to cause hundreds of thousands of deaths per year, mostly in the context of HIV co-infection. The cellular processes that mediate adaptation to the host environment are of great interest as potential novel therapeutic targets. One such cellular process important for host adaptation is mRNA decay, which mediates the specific degradation of subsets of functionally related mRNAs in response to stressors relevant to pathogenesis, including human core body temperature, carbon limitation, and reactive oxygen stress. Thus, for C. neoformans, host adaptation requires mRNA decay to mediate rapid transcriptome remodeling in the face of stressors encountered in the host. Several nodes of stress-responsive signaling that govern the stress-responsive transcriptome also control the decay rate of mRNAs cleared from the ribosome during stress, suggesting an additional layer of coupling between mRNA synthesis and decay that allows C. neoformans to be a successful pathogen of humans. WIREs RNA 2017, 8:e1424. doi: 10.1002/wrna.1424 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Amanda L M Bloom
- Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Jay Leipheimer
- Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - John C Panepinto
- Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
| |
Collapse
|
31
|
Yang CY, Ramamoorthy S, Boller S, Rosenbaum M, Rodriguez Gil A, Mittler G, Imai Y, Kuba K, Grosschedl R. Interaction of CCR4-NOT with EBF1 regulates gene-specific transcription and mRNA stability in B lymphopoiesis. Genes Dev 2016; 30:2310-2324. [PMID: 27807034 PMCID: PMC5110997 DOI: 10.1101/gad.285452.116] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 10/04/2016] [Indexed: 02/07/2023]
Abstract
Yang et al. used SILAC-based mass spectrometry of proteins associated with endogenous EBF1 in pro-B cells and identified most components of the multifunctional CCR4–NOT complex, which regulates transcription and mRNA degradation. The interaction of the CCR4–NOT complex with EBF1 diversifies the function of EBF1 in a context-dependent manner and may coordinate transcriptional and post-transcriptional gene regulation. Transcription factor EBF1 (early B-cell factor 1) regulates early B-cell differentiation by poising or activating lineage-specific genes and repressing genes associated with alternative cell fates. To identify proteins that regulate the diverse functions of EBF1, we used SILAC (stable isotope labeling by amino acids in cell culture)-based mass spectrometry of proteins associated with endogenous EBF1 in pro-B cells. This analysis identified most components of the multifunctional CCR4–NOT complex, which regulates transcription and mRNA degradation. CNOT3 interacts with EBF1, and we identified histidine 240 in EBF1 as a critical residue for this interaction. Complementation of Ebf1−/− progenitors with EBF1H240A revealed a partial block of pro-B-cell differentiation and altered expression of specific EBF1 target genes that show either reduced transcription or increased mRNA stability. Most deregulated EBF1 target genes show normal occupancy by EBF1H240A, but we also detected genes with altered occupancy, suggesting that the CCR4–NOT complex affects multiple activities of EBF1. Mice with conditional Cnot3 inactivation recapitulate the block of early B-cell differentiation, which we found to be associated with an impaired autoregulation of Ebf1 and reduced expression of pre-B-cell receptor components. Thus, the interaction of the CCR4–NOT complex with EBF1 diversifies the function of EBF1 in a context-dependent manner and may coordinate transcriptional and post-transcriptional gene regulation.
Collapse
Affiliation(s)
- Cheng-Yuan Yang
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Senthilkumar Ramamoorthy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Sören Boller
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Marc Rosenbaum
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Alfonso Rodriguez Gil
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Gerhard Mittler
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Yumiko Imai
- Department of Biochemistry and Metabolic Sciences, Akita University Graduate School of Medicine, Akita 010-8543, Japan
| | - Keiji Kuba
- Department of Biochemistry and Metabolic Sciences, Akita University Graduate School of Medicine, Akita 010-8543, Japan
| | - Rudolf Grosschedl
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| |
Collapse
|
32
|
Rambout X, Detiffe C, Bruyr J, Mariavelle E, Cherkaoui M, Brohée S, Demoitié P, Lebrun M, Soin R, Lesage B, Guedri K, Beullens M, Bollen M, Farazi TA, Kettmann R, Struman I, Hill DE, Vidal M, Kruys V, Simonis N, Twizere JC, Dequiedt F. The transcription factor ERG recruits CCR4-NOT to control mRNA decay and mitotic progression. Nat Struct Mol Biol 2016; 23:663-72. [PMID: 27273514 DOI: 10.1038/nsmb.3243] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/13/2016] [Indexed: 01/08/2023]
Abstract
Control of mRNA levels, a fundamental aspect in the regulation of gene expression, is achieved through a balance between mRNA synthesis and decay. E26-related gene (Erg) proteins are canonical transcription factors whose previously described functions are confined to the control of mRNA synthesis. Here, we report that ERG also regulates gene expression by affecting mRNA stability and identify the molecular mechanisms underlying this function in human cells. ERG is recruited to mRNAs via interaction with the RNA-binding protein RBPMS, and it promotes mRNA decay by binding CNOT2, a component of the CCR4-NOT deadenylation complex. Transcriptome-wide mRNA stability analysis revealed that ERG controls the degradation of a subset of mRNAs highly connected to Aurora signaling, whose decay during S phase is necessary for mitotic progression. Our data indicate that control of gene expression by mammalian transcription factors may follow a more complex scheme than previously anticipated, integrating mRNA synthesis and degradation.
Collapse
Affiliation(s)
- Xavier Rambout
- Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège (ULg), Liège, Belgium.,GIGA-Molecular Biology in Diseases, ULg, Liège, Belgium
| | - Cécile Detiffe
- Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège (ULg), Liège, Belgium.,GIGA-Molecular Biology in Diseases, ULg, Liège, Belgium
| | - Jonathan Bruyr
- Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège (ULg), Liège, Belgium.,GIGA-Molecular Biology in Diseases, ULg, Liège, Belgium
| | - Emeline Mariavelle
- Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège (ULg), Liège, Belgium.,GIGA-Molecular Biology in Diseases, ULg, Liège, Belgium
| | - Majid Cherkaoui
- Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège (ULg), Liège, Belgium.,GIGA-Molecular Biology in Diseases, ULg, Liège, Belgium
| | - Sylvain Brohée
- BiGRe, Université Libre de Bruxelles (ULB), Bruxelles, Belgium.,Computer Science Department, ULB, Bruxelles, Belgium
| | - Pauline Demoitié
- Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège (ULg), Liège, Belgium.,GIGA-Molecular Biology in Diseases, ULg, Liège, Belgium
| | - Marielle Lebrun
- Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège (ULg), Liège, Belgium.,GIGA-Inflammation, Infection &Immunity, ULg, Liège, Belgium
| | | | - Bart Lesage
- Department of Cellular and Molecular Medicine, University of Leuven (KUL), Leuven, Belgium
| | - Katia Guedri
- Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège (ULg), Liège, Belgium.,GIGA-Molecular Biology in Diseases, ULg, Liège, Belgium
| | - Monique Beullens
- Department of Cellular and Molecular Medicine, University of Leuven (KUL), Leuven, Belgium
| | - Mathieu Bollen
- Department of Cellular and Molecular Medicine, University of Leuven (KUL), Leuven, Belgium
| | - Thalia A Farazi
- Howard Hughes Medical Institute, Rockefeller University, New York, New York, USA
| | - Richard Kettmann
- Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège (ULg), Liège, Belgium.,GIGA-Molecular Biology in Diseases, ULg, Liège, Belgium
| | - Ingrid Struman
- Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège (ULg), Liège, Belgium.,GIGA-Cancer, ULg, Liège, Belgium
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Department of Cancer Biology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Department of Cancer Biology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Nicolas Simonis
- BiGRe, Université Libre de Bruxelles (ULB), Bruxelles, Belgium
| | - Jean-Claude Twizere
- Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège (ULg), Liège, Belgium.,GIGA-Molecular Biology in Diseases, ULg, Liège, Belgium
| | - Franck Dequiedt
- Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège (ULg), Liège, Belgium.,GIGA-Molecular Biology in Diseases, ULg, Liège, Belgium
| |
Collapse
|
33
|
Chávez S, García-Martínez J, Delgado-Ramos L, Pérez-Ortín JE. The importance of controlling mRNA turnover during cell proliferation. Curr Genet 2016; 62:701-710. [PMID: 27007479 DOI: 10.1007/s00294-016-0594-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 12/13/2022]
Abstract
Microbial gene expression depends not only on specific regulatory mechanisms, but also on cellular growth because important global parameters, such as abundance of mRNAs and ribosomes, could be growth rate dependent. Understanding these global effects is necessary to quantitatively judge gene regulation. In the last few years, transcriptomic works in budding yeast have shown that a large fraction of its genes is coordinately regulated with growth rate. As mRNA levels depend simultaneously on synthesis and degradation rates, those studies were unable to discriminate the respective roles of both arms of the equilibrium process. We recently analyzed 80 different genomic experiments and found a positive and parallel correlation between both RNA polymerase II transcription and mRNA degradation with growth rates. Thus, the total mRNA concentration remains roughly constant. Some gene groups, however, regulate their mRNA concentration by uncoupling mRNA stability from the transcription rate. Ribosome-related genes modulate their transcription rates to increase mRNA levels under fast growth. In contrast, mitochondria-related and stress-induced genes lower mRNA levels by reducing mRNA stability or the transcription rate, respectively. We critically review here these results and analyze them in relation to their possible extrapolation to other organisms and in relation to the new questions they open.
Collapse
Affiliation(s)
- Sebastián Chávez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, Seville, Spain. .,Departamento de Genética, Universidad de Sevilla, Seville, Spain.
| | - José García-Martínez
- Departamento de Genética, Universitat de València, Burjassot, Spain.,ERI Biotecmed, Universitat de València, Burjassot, Spain
| | - Lidia Delgado-Ramos
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - José E Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Spain. .,ERI Biotecmed, Universitat de València, Burjassot, Spain.
| |
Collapse
|
34
|
Garrido-Godino AI, García-López MC, García-Martínez J, Pelechano V, Medina DA, Pérez-Ortín JE, Navarro F. Rpb1 foot mutations demonstrate a major role of Rpb4 in mRNA stability during stress situations in yeast. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:731-43. [PMID: 27001033 DOI: 10.1016/j.bbagrm.2016.03.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 01/22/2023]
Abstract
The RPB1 mutants in the foot region of RNA polymerase II affect the assembly of the complex by altering the correct association of both the Rpb6 and the Rpb4/7 dimer. Assembly defects alter both transcriptional activity as well as the amount of enzyme associated with genes. Here, we show that the global transcriptional analysis of foot mutants reveals the activation of an environmental stress response (ESR), which occurs at a permissive temperature under optimal growth conditions. Our data indicate that the ESR that occurs in foot mutants depends mostly on a global post-transcriptional regulation mechanism which, in turn, depends on Rpb4-mRNA imprinting. Under optimal growth conditions, we propose that Rpb4 serves as a key to globally modulate mRNA stability as well as to coordinate transcription and decay. Overall, our results imply that post-transcriptional regulation plays a major role in controlling the ESR at both the transcription and mRNA decay levels.
Collapse
Affiliation(s)
- A I Garrido-Godino
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Paraje de las Lagunillas, s/n, 23071 Jaén, Spain
| | - M C García-López
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Paraje de las Lagunillas, s/n, 23071 Jaén, Spain
| | - J García-Martínez
- Departamento de Genética, Facultad de Biológicas, Universitat de València, Dr Moliner 50, E-46100 Burjassot, Valencia, Spain; ERI Biotecmed, Universitat de València, Dr Moliner 50, E-46100 Burjassot, Valencia, Spain
| | - V Pelechano
- European Molecular Biology Laboratories (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - D A Medina
- ERI Biotecmed, Universitat de València, Dr Moliner 50, E-46100 Burjassot, Valencia, Spain; Departamento de Bioquímica y Biología Molecular, Facultad de Biológicas, Universitat de València, Dr Moliner 50, E-46100 Burjassot, Valencia, Spain
| | - J E Pérez-Ortín
- ERI Biotecmed, Universitat de València, Dr Moliner 50, E-46100 Burjassot, Valencia, Spain; Departamento de Bioquímica y Biología Molecular, Facultad de Biológicas, Universitat de València, Dr Moliner 50, E-46100 Burjassot, Valencia, Spain.
| | - F Navarro
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Paraje de las Lagunillas, s/n, 23071 Jaén, Spain.
| |
Collapse
|
35
|
Snf1-Dependent Transcription Confers Glucose-Induced Decay upon the mRNA Product. Mol Cell Biol 2015; 36:628-44. [PMID: 26667037 DOI: 10.1128/mcb.00436-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 11/30/2015] [Indexed: 01/11/2023] Open
Abstract
In the yeast Saccharomyces cerevisiae, the switch from respiratory metabolism to fermentation causes rapid decay of transcripts encoding proteins uniquely required for aerobic metabolism. Snf1, the yeast ortholog of AMP-activated protein kinase, has been implicated in this process because inhibiting Snf1 mimics the addition of glucose. In this study, we show that the SNF1-dependent ADH2 promoter, or just the major transcription factor binding site, is sufficient to confer glucose-induced mRNA decay upon heterologous transcripts. SNF1-independent expression from the ADH2 promoter prevented glucose-induced mRNA decay without altering the start site of transcription. SNF1-dependent transcripts are enriched for the binding motif of the RNA binding protein Vts1, an important mediator of mRNA decay and mRNA repression whose expression is correlated with decreased abundance of SNF1-dependent transcripts during the yeast metabolic cycle. However, deletion of VTS1 did not slow the rate of glucose-induced mRNA decay. ADH2 mRNA rapidly dissociated from polysomes after glucose repletion, and sequences bound by RNA binding proteins were enriched in the transcripts from repressed cells. Inhibiting the protein kinase A pathway did not affect glucose-induced decay of ADH2 mRNA. Our results suggest that Snf1 may influence mRNA stability by altering the recruitment activity of the transcription factor Adr1.
Collapse
|
36
|
Abstract
In this mini-review, we summarize our current knowledge about the cross-talk between the different levels of gene expression. We introduce the Ccr4 (carbon catabolite repressed 4)–Not (negative on TATA-less) complex as a candidate to be a master regulator that orchestrates between the different levels of gene expression. An integrated view of the findings about the Ccr4–Not complex suggests that it is involved in gene expression co-ordination. Since the discovery of the Not proteins in a selection for transcription regulators in yeast [Collart and Struhl (1994) Genes Dev. 8, 525–537], the Ccr4–Not complex has been connected to every step of the mRNA lifecycle. Moreover, it has been found to be relevant for appropriate protein folding and quaternary protein structure by being involved in co-translational protein complex assembly.
Collapse
|
37
|
Montenegro-Montero A, Larrondo LF. In the Driver's Seat: The Case for Transcriptional Regulation and Coupling as Relevant Determinants of the Circadian Transcriptome and Proteome in Eukaryotes. J Biol Rhythms 2015; 31:37-47. [PMID: 26446874 DOI: 10.1177/0748730415607321] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Circadian clocks drive daily oscillations in a variety of biological processes through the coordinate orchestration of precise gene expression programs. Global expression profiling experiments have suggested that a significant fraction of the transcriptome and proteome is under circadian control, and such output rhythms have historically been assumed to rely on the rhythmic transcription of these genes. Recent genome-wide studies, however, have challenged this long-held view and pointed to a major contribution of posttranscriptional regulation in driving oscillations at the messenger RNA (mRNA) level, while others have highlighted extensive clock translational regulation, regardless of mRNA rhythms. There are various examples of genes that are uniformly transcribed throughout the day but that exhibit rhythmic mRNA levels, and of flat mRNAs, with oscillating protein levels, and such observations have largely been considered to result from independent regulation at each step. These studies have thereby obviated any connections, or coupling, that might exist between the different steps of gene expression and the impact that any of them could have on subsequent ones. Here, we argue that due to both biological and technical reasons, the jury is still out on the determination of the relative contributions of each of the different stages of gene expression in regulating output molecular rhythms. In addition, we propose that through a variety of coupling mechanisms, gene transcription (even when apparently arrhythmic) might play a much relevant role in determining oscillations in gene expression than currently estimated, regulating rhythms at downstream steps. Furthermore, we posit that eukaryotic genomes regulate daily RNA polymerase II (RNAPII) recruitment and histone modifications genome-wide, setting the stage for global nascent transcription, but that tissue-specific mechanisms locally specify the different processes under clock control.
Collapse
Affiliation(s)
- Alejandro Montenegro-Montero
- Millennium Nucleus for Fungal Integrative and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luis F Larrondo
- Millennium Nucleus for Fungal Integrative and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
38
|
Kim HH, Lee SJ, Gardiner AS, Perrone-Bizzozero NI, Yoo S. Different motif requirements for the localization zipcode element of β-actin mRNA binding by HuD and ZBP1. Nucleic Acids Res 2015; 43:7432-46. [PMID: 26152301 PMCID: PMC4551932 DOI: 10.1093/nar/gkv699] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 06/29/2015] [Indexed: 11/13/2022] Open
Abstract
Interactions of RNA-binding proteins (RBPs) with their target transcripts are essential for regulating gene expression at the posttranscriptional level including mRNA export/localization, stability, and translation. ZBP1 and HuD are RBPs that play pivotal roles in mRNA transport and local translational control in neuronal processes. While HuD possesses three RNA recognition motifs (RRMs), ZBP1 contains two RRMs and four K homology (KH) domains that either increase target specificity or provide a multi-target binding capability. Here we used isolated cis-element sequences of the target mRNA to examine directly protein-RNA interactions in cell-free systems. We found that both ZBP1 and HuD bind the zipcode element in rat β-actin mRNA's 3' UTR. Differences between HuD and ZBP1 were observed in their binding preference to the element. HuD showed a binding preference for U-rich sequence. In contrast, ZBP1 binding to the zipcode RNA depended more on the structural level, as it required the proper spatial organization of a stem-loop that is mainly determined by the U-rich element juxtaposed to the 3' end of a 5'-ACACCC-3' motif. On the basis of this work, we propose that ZBP1 and HuD bind to overlapping sites in the β-actin zipcode, but they recognize different features of this target sequence.
Collapse
Affiliation(s)
- Hak Hee Kim
- Nemours Biomedical Research, Alfred I. duPont Hosp. for Children, Wilmington, DE 19803, USA
| | - Seung Joon Lee
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Amy S Gardiner
- Department of Neuroscience, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
| | - Nora I Perrone-Bizzozero
- Department of Neuroscience, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
| | - Soonmoon Yoo
- Nemours Biomedical Research, Alfred I. duPont Hosp. for Children, Wilmington, DE 19803, USA
| |
Collapse
|
39
|
Transcriptomic variation between different Chinese hamster ovary cell lines. Biotechnol Lett 2015; 37:1737-45. [PMID: 25967036 DOI: 10.1007/s10529-015-1850-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 05/01/2015] [Indexed: 10/23/2022]
Abstract
OBJECTIVES To identify transcription markers that uniquely determine specific Chinese hamster ovary (CHO) cell lines and can be used for the identification of cell lines in the process of biopharmaceutical cell-line development. RESULTS Five CHO cell lines with different origins were extensively characterised at the transcriptomic level and the results were compared to their karyotype characterisation. The analysed cell lines differ in their karyotype but, due to the genome instability observed during parental and recombinant cell-line establishment, karyotyping is not the preferred method for accurate identification of the various CHO cell lines. Marker genes unique to a specific cell line were identified by microarrays, and their expression was validated by reverse-transcription quantitative real-time PCR. The analysed cell lines can be differentiated by the presence/absence of detectable marker gene expression. Additionally, the similarity of the transcriptional profiles is dependent on cell-line history but independent of the manipulation steps involved in the recombinant cell-line development process. CONCLUSIONS Certain transcripts can be used as markers for the identification of a CHO cell line undergoing recombinant development and thus represent a powerful tool for ensuring the maintenance of high quality standards.
Collapse
|
40
|
Posttranscriptional adaptations of the vascular endothelium to hypoxia. Curr Opin Hematol 2015; 22:243-51. [PMID: 25767954 DOI: 10.1097/moh.0000000000000139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PURPOSE OF REVIEW Remarkable new advances have been made in the field of posttranscriptional gene regulation over recent years. These include the revelation of noncoding RNAs, such as microRNAs, antisense transcripts and their interactions with RNA-binding proteins (RBPs) in the context of both health and disease settings, such as hypoxia. In particular, these discoveries bear much relevance to the field of vascular biology, which historically has focused upon transcriptional processes. Thus, the contributions of these posttranscriptional gene regulatory mechanisms to vascular and endothelial biology represent a newer concept that warrants discussion. RECENT FINDINGS Recent studies have revealed two emerging themes that are critical to endothelial/vascular biology and function. First is the functional integration between the microRNA pathway and the cellular hypoxic response, which, in addition to specific microRNAs, involves key components of the microRNA biogenesis machinery. A key concept here is the regulation of a master transcriptional programme through posttranscriptional mechanisms. The second major theme involves the dynamic interactions between RBPs, microRNAs and antisense RNAs. The condition-dependent collaborations and competitions between these different classes of posttranscriptional regulators reveal a critical layer of control for gene expression. SUMMARY Taken together, these findings bear significant diagnostic and therapeutic implications for vascular disease.
Collapse
|
41
|
Palumbo MC, Farina L, Paci P. Kinetics effects and modeling of mRNA turnover. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:327-36. [PMID: 25727049 DOI: 10.1002/wrna.1277] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 12/12/2014] [Accepted: 01/09/2015] [Indexed: 01/08/2023]
Abstract
Broader comprehension of gene expression regulatory mechanisms can be gained from a global analysis of how transcription and degradation are coordinated to orchestrate complex cell responses. The role of messenger RNA (mRNA) turnover modulation in gene expression levels has become increasingly recognized. From such perspective, in this review we briefly illustrate how a simple but effective mathematical model of mRNA turnover and some experimental findings, may together shed light on the molecular mechanisms underpinning the major role of mRNA decay rates in shaping the kinetics of gene activation and repression.
Collapse
Affiliation(s)
- Maria Concetta Palumbo
- Institute for Computing Applications "Mauro Picone", National Research Council, Rome, Italy
| | | | | |
Collapse
|
42
|
Choder M. mRNA imprinting: Additional level in the regulation of gene expression. CELLULAR LOGISTICS 2014; 1:37-40. [PMID: 21686103 DOI: 10.4161/cl.1.1.14465] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 12/15/2010] [Indexed: 12/12/2022]
Abstract
Following its synthesis in the nucleus, mRNA undergoes various stages that are critical for the proper synthesis, localization and possibly functionality of its encoded protein. Recently, we have shown that two RNA polymerase II (Pol II) subunits, Rpb4p and Rpb7p, associate with the nascent transcript co-transcriptionally. This "mRNA imprinting" lasts throughout the mRNA lifetime and is required for proper regulation of all major stages that the mRNA undergoes. Other possible cases of co-transcriptional imprinting are discussed. Since mRNAs can be transported from the synthesizing cell to other cells, we propose that mRNA imprinting can also affect the phenotype of the recipient cells. This can be viewed as "mRNA-based epigenetics."
Collapse
Affiliation(s)
- Mordechai Choder
- Department of Molecular Microbiology; Rappaport Faculty of Medicine; Technion-Israel Institute of Technology; Haifa, Israel
| |
Collapse
|
43
|
The Not5 subunit of the ccr4-not complex connects transcription and translation. PLoS Genet 2014; 10:e1004569. [PMID: 25340856 PMCID: PMC4207488 DOI: 10.1371/journal.pgen.1004569] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 07/01/2014] [Indexed: 11/19/2022] Open
Abstract
Recent studies have suggested that a sub-complex of RNA polymerase II composed of Rpb4 and Rpb7 couples the nuclear and cytoplasmic stages of gene expression by associating with newly made mRNAs in the nucleus, and contributing to their translation and degradation in the cytoplasm. Here we show by yeast two hybrid and co-immunoprecipitation experiments, followed by ribosome fractionation and fluorescent microscopy, that a subunit of the Ccr4-Not complex, Not5, is essential in the nucleus for the cytoplasmic functions of Rpb4. Not5 interacts with Rpb4; it is required for the presence of Rpb4 in polysomes, for interaction of Rpb4 with the translation initiation factor eIF3 and for association of Rpb4 with mRNAs. We find that Rpb7 presence in the cytoplasm and polysomes is much less significant than that of Rpb4, and that it does not depend upon Not5. Hence Not5-dependence unlinks the cytoplasmic functions of Rpb4 and Rpb7. We additionally determine with RNA immunoprecipitation and native gel analysis that Not5 is needed in the cytoplasm for the co-translational assembly of RNA polymerase II. This stems from the importance of Not5 for the association of the R2TP Hsp90 co-chaperone with polysomes translating RPB1 mRNA to protect newly synthesized Rpb1 from aggregation. Hence taken together our results show that Not5 interconnects translation and transcription.
Collapse
|
44
|
Forget A, Chartrand P. Cotranscriptional assembly of mRNP complexes that determine the cytoplasmic fate of mRNA. Transcription 2014; 2:86-90. [PMID: 21468235 DOI: 10.4161/trns.2.2.14857] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Revised: 01/17/2011] [Accepted: 01/18/2011] [Indexed: 12/22/2022] Open
Abstract
Unlike prokaryotes, in which transcription and translation are coupled, eukaryotes physically separate transcription in the nucleus from mRNA translation and degradation in the cytoplasm. However, recent evidence has revealed that the full picture is more complex and that the nuclear transcription machinery plays specific roles in regulating the cytoplasmic fate of mRNA.
Collapse
Affiliation(s)
- Amélie Forget
- Département de Biochimie; Université de Montréal; Montréal QC Canada
| | | |
Collapse
|
45
|
Marguerat S, Lawler K, Brazma A, Bähler J. Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress. RNA Biol 2014; 11:702-14. [PMID: 25007214 PMCID: PMC4156502 DOI: 10.4161/rna.29196] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The cooperation of transcriptional and post-transcriptional levels of control to shape gene regulation is only partially understood. Here we show that a combination of two simple and non-invasive genomic techniques, coupled with kinetic mathematical modeling, afford insight into the intricate dynamics of RNA regulation in response to oxidative stress in the fission yeast Schizosaccharomyces pombe. This study reveals a dominant role of transcriptional regulation in response to stress, but also points to the first minutes after stress induction as a critical time when the coordinated control of mRNA turnover can support the control of transcription for rapid gene regulation. In addition, we uncover specialized gene expression strategies associated with distinct functional gene groups, such as simultaneous transcriptional repression and mRNA destabilization for genes encoding ribosomal proteins, delayed mRNA destabilization with varying contribution of transcription for ribosome biogenesis genes, dominant roles of mRNA stabilization for genes functioning in protein degradation, and adjustment of both transcription and mRNA turnover during the adaptation to stress. We also show that genes regulated independently of the bZIP transcription factor Atf1p are predominantly controlled by mRNA turnover, and identify putative cis-regulatory sequences that are associated with different gene expression strategies during the stress response. This study highlights the intricate and multi-faceted interplay between transcription and RNA turnover during the dynamic regulatory response to stress.
Collapse
Affiliation(s)
- Samuel Marguerat
- Department of Genetics, Evolution & Environment and UCL Cancer Institute; University College London; London, UK
| | - Katherine Lawler
- European Molecular Biology Laboratory; EMBL-EBI; Wellcome Trust Genome Campus; Hinxton, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory; EMBL-EBI; Wellcome Trust Genome Campus; Hinxton, UK
| | - Jürg Bähler
- Department of Genetics, Evolution & Environment and UCL Cancer Institute; University College London; London, UK
| |
Collapse
|
46
|
Chapat C, Corbo L. Novel roles of the CCR4-NOT complex. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:883-901. [PMID: 25044499 DOI: 10.1002/wrna.1254] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 06/02/2014] [Accepted: 06/04/2014] [Indexed: 12/21/2022]
Abstract
The CCR4-NOT complex is a multi-subunit protein complex evolutionarily conserved across eukaryotes which regulates several aspects of gene expression. A fascinating model is emerging in which this complex acts as a regulation platform, controlling gene products 'from birth to death' through the coordination of different cellular machineries involved in diverse cellular functions. Recently the CCR4-NOT functions have been extended to the control of the innate immune response through the regulation of interferon signaling. Thus, a more comprehensive picture of how CCR4-NOT allows the rapid adaptation of cells to external stress, from transcription to mRNA and protein decay, is presented and discussed here. Overall, CCR4-NOT permits the efficient and rapid adaptation of cellular gene expression in response to changes in environmental conditions and stimuli.
Collapse
Affiliation(s)
- Clément Chapat
- Université Lyon 1, Lyon, France; CNRS UMR 5286, Lyon, France; Inserm U1052, Lyon, France; Cancer Research Center of Lyon, Centre Léon Bérard, Lyon, France
| | | |
Collapse
|
47
|
Deshpande SM, Sadhale PP, Vijayraghavan U. Involvement of S. cerevisiae Rpb4 in subset of pathways related to transcription elongation. Gene 2014; 545:126-31. [DOI: 10.1016/j.gene.2014.04.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 04/10/2014] [Accepted: 04/25/2014] [Indexed: 11/28/2022]
|
48
|
Schulz D, Pirkl N, Lehmann E, Cramer P. Rpb4 subunit functions mainly in mRNA synthesis by RNA polymerase II. J Biol Chem 2014; 289:17446-52. [PMID: 24802753 DOI: 10.1074/jbc.m114.568014] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
RNA polymerase II (Pol II) is the central enzyme that carries out eukaryotic mRNA transcription and consists of a 10-subunit catalytic core and a subcomplex of subunits Rpb4 and Rpb7 (Rpb4/7). Rpb4/7 has been proposed to dissociate from Pol II, enter the cytoplasm, and function there in mRNA translation and degradation. Here we provide evidence that Rpb4 mainly functions in nuclear mRNA synthesis by Pol II, as well as evidence arguing against an important cytoplasmic role in mRNA degradation. We used metabolic RNA labeling and comparative Dynamic Transcriptome Analysis to show that Rpb4 deletion in Saccharomyces cerevisiae causes a drastic defect in mRNA synthesis that is compensated by down-regulation of mRNA degradation, resulting in mRNA level buffering. Deletion of Rpb4 can be rescued by covalent fusion of Rpb4 to the Pol II core subunit Rpb2, which largely restores mRNA synthesis and degradation defects caused by Rpb4 deletion. Thus, Rpb4 is a bona fide Pol II core subunit that functions mainly in mRNA synthesis.
Collapse
Affiliation(s)
- Daniel Schulz
- From the Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich and
| | - Nicole Pirkl
- From the Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich and
| | - Elisabeth Lehmann
- From the Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich and
| | - Patrick Cramer
- From the Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich and the Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| |
Collapse
|
49
|
Depletion of the Trypanosome Pumilio domain protein PUF2 or of some other essential proteins causes transcriptome changes related to coding region length. EUKARYOTIC CELL 2014; 13:664-74. [PMID: 24681684 DOI: 10.1128/ec.00018-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Pumilio domain RNA-binding proteins are known mainly as posttranscriptional repressors of gene expression that reduce mRNA translation and stability. Trypanosoma brucei has 11 PUF proteins. We show here that PUF2 is in the cytosol, with roughly the same number of molecules per cell as there are mRNAs. Although PUF2 exhibits a low level of in vivo RNA binding, it is not associated with polysomes. PUF2 also decreased reporter mRNA levels in a tethering assay, consistent with a repressive role. Depletion of PUF2 inhibited growth of bloodstream-form trypanosomes, causing selective loss of mRNAs with long open reading frames and increases in mRNAs with shorter open reading frames. Reexamination of published RNASeq data revealed the same trend in cells depleted of some other proteins. We speculate that these length effects could be caused by inhibition of the elongation phase of transcription or by an influence of translation status or polysomal conformation on mRNA decay.
Collapse
|
50
|
Bloom ALM, Panepinto JC. RNA biology and the adaptation of Cryptococcus neoformans to host temperature and stress. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:393-406. [PMID: 24497369 DOI: 10.1002/wrna.1219] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 12/06/2013] [Accepted: 12/20/2013] [Indexed: 01/26/2023]
Abstract
Cryptococcus neoformans is an environmental fungus that can cause severe disease in humans. C. neoformans encounters a multitude of stresses within the human host to which it must adapt in order to survive and proliferate. Upon stressful changes in the external milieu, C. neoformans must reprogram its gene expression to properly respond to and combat stress in order to maintain homeostasis. Several studies have investigated the changes that occur in response to these stresses to begin to unravel the mechanisms of adaptation in this organism. Here, we review studies that have explored stress-induced changes in gene expression with a focus on host temperature adaptation. We compare global messenger RNA (mRNA) expression data compiled from several studies and identify patterns that suggest that orchestrated, transient responses occur. We also utilize the available expression data to explore the possibility of a common stress response that may contribute to cellular protection against a variety of stresses in C. neoformans. In addition, we review studies that have revealed the significance of post-transcriptional mechanisms of mRNA regulation in response to stress, and discuss how these processes may contribute to adaptation and virulence.
Collapse
Affiliation(s)
- Amanda L M Bloom
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, University at Buffalo, the State University of New York, Buffalo, NY, USA
| | | |
Collapse
|