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Zhang TM, Zhu XN, Qin SW, Guo XF, Xing XK, Zhao LF, Tan SK. Potential and application of abortive transcripts as a novel molecular marker of cancers. World J Exp Med 2024; 14:92343. [PMID: 38948416 PMCID: PMC11212745 DOI: 10.5493/wjem.v14.i2.92343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/25/2024] [Accepted: 05/14/2024] [Indexed: 06/19/2024] Open
Abstract
Abortive transcript (AT) is a 2-19 nt long non-coding RNA that is produced in the abortive initiation stage. Abortive initiation was found to be closely related to RNA polymerase through in vitro experiments. Therefore, the distribution of AT length and the scale of abortive initiation are correlated to the promoter, discriminator, and transcription initiation sequence, and can be affected by transcription elongation factors. AT plays an important role in the occurrence and development of various diseases. Here we summarize the discovery of AT, the factors responsible for AT formation, the detection methods and biological functions of AT, to provide new clues for finding potential targets in the early diagnosis and treatment of cancers.
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Affiliation(s)
- Tian-Miao Zhang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin 541199, Guangxi Zhuang Autonomous Region, China
| | - Xiao-Nian Zhu
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin 541199, Guangxi Zhuang Autonomous Region, China
| | - Shao-Wei Qin
- School of Leisure and Health, Guilin Tourism University, Guilin 541006, Guangxi Zhuang Autonomous Region, China
| | - Xue-Feng Guo
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin 541199, Guangxi Zhuang Autonomous Region, China
| | - Xue-Kun Xing
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin 541199, Guangxi Zhuang Autonomous Region, China
| | - Li-Feng Zhao
- School of Leisure and Health, Guilin Tourism University, Guilin 541006, Guangxi Zhuang Autonomous Region, China
| | - Sheng-Kui Tan
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin 541199, Guangxi Zhuang Autonomous Region, China
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Qin S, Wu H, Li C, Yang J, Yan W, He Z, Xing X, Zhang J, Xu X, Zhao L, Su X. Detection of Naturally occurring abortive transcripts by Base-Stacking Hybridization Assisted Ligation and PCR amplification. Biosens Bioelectron 2024; 251:116099. [PMID: 38330773 DOI: 10.1016/j.bios.2024.116099] [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: 11/22/2023] [Revised: 01/13/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
Abortive transcripts (ATs) refer to nascent 2-10 nucleotides (nt) RNAs released by RNA polymerases before synthesizing productive RNAs. The quantitative detection of ATs is important for studying transcription initiation and the biological function of ATs; however, no method is available for the qualitative and quantitative assessment of such ultra-short oligonucleotides (typically shorter than 11 nt) in vivo at present, even with the LNA probes, the detection limit can only reach 11 nt. Here, we demonstrated the base stacking hybridization assisted ligation (BSHAL) technique, combined with TaqMan-MGB qPCR, can detect 4-10 nt ATs with a specificity of nucleotide resolution and a sensitivity of approximately 10 pM. By this technique, we detected endogenous ATs in cell lines, mice plasmas, and mice liver tissues, respectively, and proved that naturally occurring ATs do exist. We found that the 8 nt ATs of HMSB and Gapdh could be used as reference ATs for data normalization in Homo and mouse respectively, and 8 nt ATs of Afp and Gpc3 were suitable for use as plasma biomarkers of Hepatocellular carcinoma in mouse, indicate ATs are promising biomarkers. This study offers opportunities to study ATs and other ultra-short oligonucleotides in biological samples.
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Affiliation(s)
- Shaowei Qin
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Haizhu Wu
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Cailin Li
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Jiarui Yang
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, The Johns Hopkins University, Baltimore, 21218, USA
| | - Weiwei Yan
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Zhigui He
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Xuekun Xing
- College of Public Health, Guilin Medical University, Guilin, 541199, China
| | - Jiayang Zhang
- College of Public Health, Guilin Medical University, Guilin, 541199, China
| | - Xianglin Xu
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China
| | - Lifeng Zhao
- School of Food and Health, Guilin Tourism University, Guilin, 541006, China.
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation. J Bacteriol 2021; 203:JB.00512-20. [PMID: 33139481 DOI: 10.1128/jb.00512-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The fitness of an individual bacterial cell is highly dependent upon the temporal tuning of gene expression levels when subjected to different environmental cues. Kinetic regulation of transcription initiation is a key step in modulating the levels of transcribed genes to promote bacterial survival. The initiation phase encompasses the binding of RNA polymerase (RNAP) to promoter DNA and a series of coupled protein-DNA conformational changes prior to entry into processive elongation. The time required to complete the initiation phase can vary by orders of magnitude and is ultimately dictated by the DNA sequence of the promoter. In this review, we aim to provide the required background to understand how promoter sequence motifs may affect initiation kinetics during promoter recognition and binding, subsequent conformational changes which lead to DNA opening around the transcription start site, and promoter escape. By calculating the steady-state flux of RNA production as a function of these effects, we illustrate that the presence/absence of a consensus promoter motif cannot be used in isolation to make conclusions regarding promoter strength. Instead, the entire series of linked, sequence-dependent structural transitions must be considered holistically. Finally, we describe how individual transcription factors take advantage of the broad distribution of sequence-dependent basal kinetics to either increase or decrease RNA flux.
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Stumper SK, Ravi H, Friedman LJ, Mooney RA, Corrêa IR, Gershenson A, Landick R, Gelles J. Delayed inhibition mechanism for secondary channel factor regulation of ribosomal RNA transcription. eLife 2019; 8:40576. [PMID: 30720429 PMCID: PMC7028371 DOI: 10.7554/elife.40576] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 02/04/2019] [Indexed: 11/25/2022] Open
Abstract
RNA polymerases (RNAPs) contain a conserved ‘secondary channel’ which binds regulatory factors that modulate transcription initiation. In Escherichia coli, the secondary channel factors (SCFs) GreB and DksA both repress ribosomal RNA (rRNA) transcription, but SCF loading and repression mechanisms are unclear. We observed in vitro fluorescently labeled GreB molecules binding to single RNAPs and initiation of individual transcripts from an rRNA promoter. GreB arrived and departed from promoters only in complex with RNAP. GreB did not alter initial RNAP-promoter binding but instead blocked a step after conformational rearrangement of the initial RNAP-promoter complex. Strikingly, GreB-RNAP complexes never initiated at an rRNA promoter; only RNAP molecules arriving at the promoter without bound GreB produced transcript. The data reveal that a model SCF functions by a ‘delayed inhibition’ mechanism and suggest that rRNA promoters are inhibited by GreB/DksA because their short-lived RNAP complexes do not allow sufficient time for SCFs to dissociate.
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Affiliation(s)
- Sarah K Stumper
- Department of Biochemistry, Brandeis University, Waltham, United States
| | - Harini Ravi
- Department of Biochemistry, Brandeis University, Waltham, United States
| | - Larry J Friedman
- Department of Biochemistry, Brandeis University, Waltham, United States
| | - Rachel Anne Mooney
- Department of Biochemistry, University of Wisconsin, Madison, United States
| | | | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin, Madison, United States.,Department of Bacteriology, University of Wisconsin, Madison, United States
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, United States
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Sendy B, Lee DJ, Busby SJW, Bryant JA. RNA polymerase supply and flux through the lac operon in Escherichia coli. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2016.0080. [PMID: 27672157 PMCID: PMC5052750 DOI: 10.1098/rstb.2016.0080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2016] [Indexed: 11/12/2022] Open
Abstract
Chromatin immunoprecipitation, followed by quantification of immunoprecipitated DNA, can be used to measure RNA polymerase binding to any DNA segment in Escherichia coli. By calibrating measurements against the signal from a single RNA polymerase bound at a single promoter, we can calculate both promoter occupancy levels and the flux of transcribing RNA polymerase through transcription units. Here, we have applied the methodology to the E. coli lactose operon promoter. We confirm that promoter occupancy is limited by recruitment and that the supply of RNA polymerase to the lactose operon promoter depends on its location in the E. coli chromosome. Measurements of RNA polymerase binding to DNA segments within the lactose operon show that flux of RNA polymerase through the operon is low, with, on average, over 18 s elapsing between the passage of transcribing polymerases. Similar low levels of flux were found when semi-synthetic promoters were used to drive transcript initiation, even when the promoter elements were changed to ensure full occupancy of the promoter by RNA polymerase. This article is part of the themed issue ‘The new bacteriology’.
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Affiliation(s)
- Bandar Sendy
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - David J Lee
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Stephen J W Busby
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Jack A Bryant
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
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