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Nemsick S, Hansen AS. Molecular models of bidirectional promoter regulation. Curr Opin Struct Biol 2024; 87:102865. [PMID: 38905929 DOI: 10.1016/j.sbi.2024.102865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/30/2024] [Accepted: 05/27/2024] [Indexed: 06/23/2024]
Abstract
Approximately 11% of human genes are transcribed by a bidirectional promoter (BDP), defined as two genes with <1 kb between their transcription start sites. Despite their evolutionary conservation and enrichment for housekeeping genes and oncogenes, the regulatory role of BDPs remains unclear. BDPs have been suggested to facilitate gene coregulation and/or decrease expression noise. This review discusses these potential regulatory functions through the context of six prospective underlying mechanistic models: a single nucleosome free region, shared transcription factor/regulator binding, cooperative negative supercoiling, bimodal histone marks, joint activation by enhancer(s), and RNA-mediated recruitment of regulators. These molecular mechanisms may act independently and/or cooperatively to facilitate the coregulation and/or decreased expression noise predicted of BDPs.
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Affiliation(s)
- Sarah Nemsick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA.
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Ventura I, Revert F, Revert-Ros F, Gómez-Tatay L, Prieto-Ruiz JA, Hernández-Andreu JM. SP1 and NFY Regulate the Expression of PNPT1, a Gene Encoding a Mitochondrial Protein Involved in Cancer. Int J Mol Sci 2022; 23:ijms231911399. [PMID: 36232701 PMCID: PMC9570217 DOI: 10.3390/ijms231911399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/13/2022] [Accepted: 09/23/2022] [Indexed: 11/26/2022] Open
Abstract
The Polyribonucleotide nucleotidyltransferase 1 gene (PNPT1) encodes polynucleotide phosphorylase (PNPase), a 3′-5′ exoribonuclease involved in mitochondrial RNA degradation and surveillance and RNA import into the mitochondrion. Here, we have characterized the PNPT1 promoter by in silico analysis, luciferase reporter assays, electrophoretic mobility shift assays (EMSA), chromatin immunoprecipitation (ChIP), siRNA-based mRNA silencing and RT-qPCR. We show that the Specificity protein 1 (SP1) transcription factor and Nuclear transcription factor Y (NFY) bind the PNPT1 promoter, and have a relevant role regulating the promoter activity, PNPT1 expression, and mitochondrial activity. We also found in Kaplan–Meier survival curves that a high expression of either PNPase, SP1 or NFY subunit A (NFYA) is associated with a poor prognosis in liver cancer. In summary, our results show the relevance of SP1 and NFY in PNPT1 expression, and point to SP1/NFY and PNPase as possible targets in anti-cancer therapy.
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Häkkinen A, Oliveira SMD, Neeli-Venkata R, Ribeiro AS. Transcription closed and open complex formation coordinate expression of genes with a shared promoter region. J R Soc Interface 2019; 16:20190507. [PMID: 31822223 DOI: 10.1098/rsif.2019.0507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many genes are spaced closely, allowing coordination without explicit control through shared regulatory elements and molecular interactions. We study the dynamics of a stochastic model of a gene-pair in a head-to-head configuration, sharing promoter elements, which accounts for the rate-limiting steps in transcription initiation. We find that only in specific regions of the parameter space of the rate-limiting steps is orderly coexpression exhibited, suggesting that successful cooperation between closely spaced genes requires the coevolution of compatible rate-limiting step configuration. The model predictions are validated using in vivo single-cell, single-RNA measurements of the dynamics of pairs of genes sharing promoter elements. Our results suggest that, in E. coli, the kinetics of the rate-limiting steps in active transcription can play a central role in shaping the dynamics of gene-pairs sharing promoter elements.
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Affiliation(s)
- Antti Häkkinen
- BioMediTech Institute and Department of Signal Processing, Tampere University of Technology, PO Box 553 33101, Tampere, Finland
| | - Samuel M D Oliveira
- BioMediTech Institute and Department of Signal Processing, Tampere University of Technology, PO Box 553 33101, Tampere, Finland
| | - Ramakanth Neeli-Venkata
- BioMediTech Institute and Department of Signal Processing, Tampere University of Technology, PO Box 553 33101, Tampere, Finland
| | - Andre S Ribeiro
- BioMediTech Institute and Department of Signal Processing, Tampere University of Technology, PO Box 553 33101, Tampere, Finland
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Wang Y, Zhang Y, Zhang C, Weng H, Li Y, Cai W, Xie M, Long Y, Ai Q, Liu Z, Du G, Wang S, Niu Y, Song F, Ozaki T, Bu Y. The gene pair PRR11 and SKA2 shares a NF-Y-regulated bidirectional promoter and contributes to lung cancer development. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1133-44. [PMID: 26162986 DOI: 10.1016/j.bbagrm.2015.07.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/03/2015] [Accepted: 07/06/2015] [Indexed: 12/21/2022]
Abstract
Head-to-head gene pairs represent a unique feature of gene organization in eukaryotes, accounting for >10% of genes in the human genome. Identification and functional analysis of such gene pairs is only in its infancy. Recently, we identified PRR11 as a novel cancer-related gene that is implicated in cell cycle and lung cancer. Here we demonstrate that PRR11 is oriented in a head-to-head configuration with its neighboring gene, SKA2. 5'-RACE assay revealed that the intergenic spacer region between the two genes is <500 bp. Serial luciferase reporter assays demonstrated that a minimal 80-bp intergenic region functions as a core bidirectional promoter to drive basal transcription in both the PRR11 and SKA2 orientations. EMSA and ChIP assays demonstrated that NF-Y binds to and directly transactivates the PRR11-SKA2 bidirectional promoter. SiRNA-mediated NF-Y depletion significantly downregulated PRR11 and SKA2 expression. Expression of both PRR11 and SKA2 was significantly upregulated in lung cancer. Expression of the two genes was highly correlated with each other and with NF-Y expression. Remarkably, high expression of both PRR11 and SKA2 was associated with poorer prognosis in lung cancer patients compared with high expression of one gene or low expression of both genes. Knockdown of PRR11 and/or SKA2 remarkably reduced cell proliferation, migration, and invasion in lung cancer cells. Thus, the PRR11-SKA2 bidirectional transcription unit, which is a novel direct target of NF-Y, is essential for the accelerated proliferation and motility of lung cancer cells and may represent a potential target in the diagnosis and/or treatment of human lung cancer.
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Affiliation(s)
- Yitao Wang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Chundong Zhang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Huali Weng
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Yi Li
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Wei Cai
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Mengyu Xie
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Yinjiang Long
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Qing Ai
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Zhu Liu
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Gang Du
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Sen Wang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Yulong Niu
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Fangzhou Song
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Toshinori Ozaki
- Laboratory of DNA Damage Signaling, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuohku, Chiba 260-8717, Japan
| | - Youquan Bu
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China.
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Zhang L, Ding Q, Wang P, Wang Z. An upstream promoter element blocks the reverse transcription of the mouse insulin-degrading enzyme gene. Biochem Biophys Res Commun 2012. [PMID: 23200833 DOI: 10.1016/j.bbrc.2012.11.052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Despite the prevalence of bidirectional promoters among the mammalian genomes, the majority of promoters are unidirectional. The mechanism through which unidirectional promoters are prevented from reverse transcription remains to be clarified. Here we investigate the transcriptional directionality of the mouse insulin-degrading enzyme (IDE) promoter, which contains a CpG island and has dispersed transcription initiation sites. Although IDE is unidirectionally transcribed according to its genomic context, the basic promoter region of mouse IDE has bidirectional transcriptional properties. The region between -219 and +133 of mouse IDE relative to its first transcription initiation site has bidirectional transcriptional activities, but the region between -350 and +133 can only be transcribed from the normal direction, implying that an upstream promoter element locating between -350 and -219 blocks the reverse transcription of mouse IDE. We further mapped this upstream promoter element to the region between -243 and -287. Promoter mutation analysis showed that the upstream promoter element contains two functional sub-regions. In conclusion, we identified an upstream promoter element which blocks the reverse transcription of mouse IDE. Our studies are suggestive for the transcriptional mechanism of bidirectional promoters in mammalian genomes.
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Affiliation(s)
- Lang Zhang
- Protein Science Key Laboratory of the Ministry of Education, Department of Biological Sciences and Biotechnology, School of Medicine, Tsinghua University, Beijing 100084, China.
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Ho MR, Tsai KW, Lin WC. A unified framework of overlapping genes: towards the origination and endogenic regulation. Genomics 2012; 100:231-9. [PMID: 22766524 DOI: 10.1016/j.ygeno.2012.06.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 06/21/2012] [Accepted: 06/25/2012] [Indexed: 11/27/2022]
Abstract
Overlapping genes are pairs of adjacent genes whose genomic regions partially overlap. They are notable by their potential intricate regulation, such as cis-regulation of nested gene-promoter configurations, and post-transcriptional regulation of natural antisense transcripts. The originations and consequent detailed regulation remain obscure. Herein, we propose a unified framework comprising biological classification rules followed by extensive analyses, namely, exon-sharing analysis, a human-mouse conservation study, and transcriptome analysis of hundreds of microarrays and transcriptome sequencing data (mRNA-Seq). We demonstrate that the tail-to-tail architecture would result from sharing functional elements in 3'-untranslated regions (3'-UTRs) of pre-existing genes. Dissimilarly, we illustrate that the other gene overlaps would originate from a new gene arising in a pre-existing gene locus. Interestingly, these types of coupled overlapping genes may influence each other synergistically or competitively during transcription, depending on the promoter configurations. This framework discloses distinctive characteristics of overlapping genes to be a foundation for a further comprehensive understanding of them.
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Affiliation(s)
- Meng-Ru Ho
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
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Lecanidou R, Papantonis A. Modeling bidirectional transcription using silkmoth chorion gene promoters. Organogenesis 2012; 6:54-8. [PMID: 20592866 DOI: 10.4161/org.6.1.10696] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2009] [Revised: 11/18/2009] [Accepted: 11/18/2009] [Indexed: 11/19/2022] Open
Abstract
Bidirectional transcription is an interesting feature of eukaryotic genomes; yet not all aspects of its mechanism are understood. Silkmoth choriogenesis is a model system for studying transcriptional regulation at the initiation level. As chorion genes comprise a large group of divergently transcribed gene pairs, we are presented with the possibility of investigating the intricacies of bidirectional transcription. Their well characterized 5' regulatory regions and expression profiles lay the foundation for investigating protein:protein and protein:DNA interactions, and RNA polymerase function during oocyte development. In this article we summarize current knowledge on chorion gene regulation and propose an approach to modeling bidirectional transcription using chorion promoters.
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Affiliation(s)
- Rena Lecanidou
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
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Liu B, Chen J, Shen B. Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs. BMC SYSTEMS BIOLOGY 2011; 5 Suppl 1:S2. [PMID: 21689477 PMCID: PMC3121118 DOI: 10.1186/1752-0509-5-s1-s2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Background Bi-directional gene pairs have received considerable attention for their prevalence in vertebrate genomes. However, their biological relevance and exact regulatory mechanism remain less understood. To study the inner properties of this gene organization and the difference between bi- and uni-directional genes, we conducted a genome-wide investigation in terms of their sequence composition, functional association and regulatory motif discovery. Results We identified 1210 bi-directional gene pairs based on the GRCh37 assembly data, accounting for 11.6% of all the human genes owning RNAs. CpG islands were detected in 98.42% of bi-directional promoters and 61.07% of unidirectional promoters. Functional enrichment analysis in GO and GeneGO both revealed that bi-directional genes tend to be associated with housekeeping functions in metabolism pathways and nuclear processes, and 46.84% of the pair members are involved in the same biological function. By fold-enrichment analysis, we characterized 73 and 43 putative transcription factor binding sites(TFBS) that preferentially occur in bi-directional promoters from TRANSFAC and JASPAR database respectively. By text mining, some of them were verified by individual experiments and several novel binding motifs were also identified. Conclusions Bi-directional promoters feature a significant enrichment of CpG-islands as well as a high GC content. We provided insight into the function constraints of bi-directional genes and found that paired genes are biased toward functional similarities. We hypothesized that the functional association underlies the co-expression of bi-directional genes. Furthermore, we proposed a set of putative regulatory motifs in the bi-directional promoters for further experimental studies to investigate transcriptional regulation of bi-directional genes.
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Affiliation(s)
- Bingchuan Liu
- Center for Systems Biology, Soochow University, Suzhou, China
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