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Savinkova LK, Sharypova EB, Kolchanov NA. On the Role of TATA Boxes and TATA-Binding Protein in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2023; 12:1000. [PMID: 36903861 PMCID: PMC10005294 DOI: 10.3390/plants12051000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/13/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
For transcription initiation by RNA polymerase II (Pol II), all eukaryotes require assembly of basal transcription machinery on the core promoter, a region located approximately in the locus spanning a transcription start site (-50; +50 bp). Although Pol II is a complex multi-subunit enzyme conserved among all eukaryotes, it cannot initiate transcription without the participation of many other proteins. Transcription initiation on TATA-containing promoters requires the assembly of the preinitiation complex; this process is triggered by an interaction of TATA-binding protein (TBP, a component of the general transcription factor TFIID (transcription factor II D)) with a TATA box. The interaction of TBP with various TATA boxes in plants, in particular Arabidopsis thaliana, has hardly been investigated, except for a few early studies that addressed the role of a TATA box and substitutions in it in plant transcription systems. This is despite the fact that the interaction of TBP with TATA boxes and their variants can be used to regulate transcription. In this review, we examine the roles of some general transcription factors in the assembly of the basal transcription complex, as well as functions of TATA boxes of the model plant A. thaliana. We review examples showing not only the involvement of TATA boxes in the initiation of transcription machinery assembly but also their indirect participation in plant adaptation to environmental conditions in responses to light and other phenomena. Examples of an influence of the expression levels of A. thaliana TBP1 and TBP2 on morphological traits of the plants are also examined. We summarize available functional data on these two early players that trigger the assembly of transcription machinery. This information will deepen the understanding of the mechanisms underlying transcription by Pol II in plants and will help to utilize the functions of the interaction of TBP with TATA boxes in practice.
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2
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Regulation of human ZNF687, a gene associated with Paget's disease of bone. Int J Biochem Cell Biol 2023; 154:106332. [PMID: 36372390 DOI: 10.1016/j.biocel.2022.106332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/31/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Mutations in Zinc finger 687 (ZNF687) were associated with Paget's disease of bone (PDB), a disease characterized by increased bone resorption and excessive bone formation. It was suggested that ZNF687 plays a role in bone differentiation and development. However, the mechanisms involved in ZNF687 regulation remain unknown. This study aimed to obtain novel knowledge regarding ZNF687 transcriptional and epigenetic regulation. Through in silico analysis, we hypothesized three ZNF687 promoter regions located upstream exon 1 A, 1B, and 1 C and denominated promoter regions 1, 2, and 3, respectively. Their functionality was confirmed by luciferase activity assays and positive/negative regulatory regions were identified using promoter deletions constructs. In silico analysis revealed a high density of CpG islands in these promoter regions and in vitro methylation suppressed promoters' activity. Using bioinformatic approaches, bone-associated transcription factor binding sites containing CpG dinucleotides were identified, including those for NFκB, PU.1, DLX5, and SOX9. By co-transfection in HEK293 and hFOB cells, we found that DLX5 specifically activated ZNF687 promoter region 1, and its methylation impaired DLX5-driven promoter stimulation. NFκB repressed and activated promoter regions 1 and 2, respectively, and these activities were affected by methylation. PU.1 induced ZNF687 promoter region 1 which was affected by methylation. SOX9 differentially regulated ZNF687 promoters in HEK293 and hFOB cells that were impaired after methylation. In conclusion, this study provides novel insights into ZNF687 regulation by demonstrating that NFκB, PU.1, DLX5, and SOX9 are regulators of ZNF687 promoters, and DNA methylation influences their activity. The contribution of the dysregulation of these mechanisms in PDB should be further elucidated.
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Santana JF, Collins GS, Parida M, Luse DS, Price D. Differential dependencies of human RNA polymerase II promoters on TBP, TAF1, TFIIB and XPB. Nucleic Acids Res 2022; 50:9127-9148. [PMID: 35947745 PMCID: PMC9458433 DOI: 10.1093/nar/gkac678] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/08/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022] Open
Abstract
The effects of rapid acute depletion of components of RNA polymerase II (Pol II) general transcription factors (GTFs) that are thought to be critical for formation of preinitiation complexes (PICs) and initiation in vitro were quantified in HAP1 cells using precision nuclear run-on sequencing (PRO-Seq). The average dependencies for each factor across >70 000 promoters varied widely even though levels of depletions were similar. Some of the effects could be attributed to the presence or absence of core promoter elements such as the upstream TBP-specificity motif or downstream G-rich sequences, but some dependencies anti-correlated with such sequences. While depletion of TBP had a large effect on most Pol III promoters only a small fraction of Pol II promoters were similarly affected. TFIIB depletion had the largest general effect on Pol II and also correlated with apparent termination defects downstream of genes. Our results demonstrate that promoter activity is combinatorially influenced by recruitment of TFIID and sequence-specific transcription factors. They also suggest that interaction of the preinitiation complex (PIC) with nucleosomes can affect activity and that recruitment of TFIID containing TBP only plays a positive role at a subset of promoters.
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Affiliation(s)
- Juan F Santana
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Geoffrey S Collins
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Mrutyunjaya Parida
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Donal S Luse
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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Nizamuddin S, Koidl S, Bhuiyan T, Werner TV, Biniossek M, Bonvin AMJJ, Lassmann S, Timmers HT. Integrating quantitative proteomics with accurate genome profiling of transcription factors by greenCUT&RUN. Nucleic Acids Res 2021; 49:e49. [PMID: 33524153 PMCID: PMC8136828 DOI: 10.1093/nar/gkab038] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/08/2021] [Accepted: 01/16/2021] [Indexed: 11/14/2022] Open
Abstract
Genome-wide localization of chromatin and transcription regulators can be detected by a variety of techniques. Here, we describe a novel method 'greenCUT&RUN' for genome-wide profiling of transcription regulators, which has a very high sensitivity, resolution, accuracy and reproducibility, whilst assuring specificity. Our strategy begins with tagging of the protein of interest with GFP and utilizes a GFP-specific nanobody fused to MNase to profile genome-wide binding events. By using a GFP-nanobody the greenCUT&RUN approach eliminates antibody dependency and variability. Robust genomic profiles were obtained with greenCUT&RUN, which are accurate and unbiased towards open chromatin. By integrating greenCUT&RUN with nanobody-based affinity purification mass spectrometry, 'piggy-back' DNA binding events can be identified on a genomic scale. The unique design of greenCUT&RUN grants target protein flexibility and yields high resolution footprints. In addition, greenCUT&RUN allows rapid profiling of mutants of chromatin and transcription proteins. In conclusion, greenCUT&RUN is a widely applicable and versatile genome-mapping technique.
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Affiliation(s)
- Sheikh Nizamuddin
- Department of Urology, Medical Center-University of Freiburg, 79016 Freiburg, Germany
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Stefanie Koidl
- Department of Urology, Medical Center-University of Freiburg, 79016 Freiburg, Germany
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Tanja Bhuiyan
- Department of Urology, Medical Center-University of Freiburg, 79016 Freiburg, Germany
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Tamara V Werner
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Institute for Surgical Pathology, Medical Center-University of Freiburg, 79016 Freiburg, Germany
| | - Martin L Biniossek
- Institute for Molecular Medicine and Cell Research, Medical Center-University of Freiburg, 79016 Freiburg, Germany
| | - Alexandre M J J Bonvin
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht 3584CH, the Netherlands
| | - Silke Lassmann
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Institute for Surgical Pathology, Medical Center-University of Freiburg, 79016 Freiburg, Germany
| | - HThMarc Timmers
- Department of Urology, Medical Center-University of Freiburg, 79016 Freiburg, Germany
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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Oubounyt M, Louadi Z, Tayara H, Chong KT. DeePromoter: Robust Promoter Predictor Using Deep Learning. Front Genet 2019; 10:286. [PMID: 31024615 PMCID: PMC6460014 DOI: 10.3389/fgene.2019.00286] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 03/15/2019] [Indexed: 12/11/2022] Open
Abstract
The promoter region is located near the transcription start sites and regulates transcription initiation of the gene by controlling the binding of RNA polymerase. Thus, promoter region recognition is an important area of interest in the field of bioinformatics. Numerous tools for promoter prediction were proposed. However, the reliability of these tools still needs to be improved. In this work, we propose a robust deep learning model, called DeePromoter, to analyze the characteristics of the short eukaryotic promoter sequences, and accurately recognize the human and mouse promoter sequences. DeePromoter combines a convolutional neural network (CNN) and a long short-term memory (LSTM). Additionally, instead of using non-promoter regions of the genome as a negative set, we derive a more challenging negative set from the promoter sequences. The proposed negative set reconstruction method improves the discrimination ability and significantly reduces the number of false positive predictions. Consequently, DeePromoter outperforms the previously proposed promoter prediction tools. In addition, a web-server for promoter prediction is developed based on the proposed methods and made available at https://home.jbnu.ac.kr/NSCL/deepromoter.htm.
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Affiliation(s)
- Mhaned Oubounyt
- Department of Information and Electronics Engineering, Chonbuk National University, Jeonju, South Korea
| | - Zakaria Louadi
- Department of Information and Electronics Engineering, Chonbuk National University, Jeonju, South Korea
| | - Hilal Tayara
- Department of Information and Electronics Engineering, Chonbuk National University, Jeonju, South Korea
| | - Kil To Chong
- Advanced Research Center of Information and Electronics Engineering, Chonbuk National University, Jeonju, South Korea
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Das S, Bansal M. Variation of gene expression in plants is influenced by gene architecture and structural properties of promoters. PLoS One 2019; 14:e0212678. [PMID: 30908494 PMCID: PMC6433290 DOI: 10.1371/journal.pone.0212678] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 02/07/2019] [Indexed: 12/03/2022] Open
Abstract
In higher eukaryotes, gene architecture and structural properties of promoters have emerged as significant factors influencing variation in number of transcripts (expression level) and specificity of gene expression in a tissue (expression breadth), which eventually shape the phenotype. In this study, transcriptome data of different tissue types at various developmental stages of A. thaliana, O. sativa, S. bicolor and Z. mays have been used to understand the relationship between properties of gene components and its expression. Our findings indicate that in plants, among all gene architecture and structural properties of promoters, compactness of genes in terms of intron content is significantly linked to gene expression level and breadth, whereas in human an exactly opposite scenario is seen. In plants, for the first time we have carried out a quantitative estimation of effect of a particular trait on expression level and breadth, by using multiple regression analysis and it confirms that intron content of primary transcript (as %) is a powerful determinant of expression breadth. Similarly, further regression analysis revealed that among structural properties of the promoters, stability is negatively linked to expression breadth, while DNase1 sensitivity strongly governs gene expression breadth in monocots and gene expression level in dicots. In addition, promoter regions of tissue specific genes are found to be enriched with TATA box and Y-patch motifs. Finally, multi copy orthologous genes in plants are found to be longer, highly regulated and tissue specific.
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Affiliation(s)
- Sanjukta Das
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
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Mezquita-Pla J. Gordon H. Dixon's trace in my personal career and the quantic jump experienced in regulatory information. Syst Biol Reprod Med 2018; 64:448-468. [PMID: 30136864 DOI: 10.1080/19396368.2018.1503752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Even before Rosalin Franklin had discovered the DNA double helix, in her impressive X-ray diffraction image pattern, Erwin Schröedinger, described, in his excellent book, What is Life, how the finding of aperiodic crystals in biological systems surprised him (an aperiodic crystal, which, in my opinion is the material carrier of life). In the 21st century and still far from being able to define life, we are attending to a quick acceleration of knowledge on regulatory information. With the discovery of new codes and punctuation marks, we will greatly increase our understanding in front of an impressive avalanche of genomic sequences. Trifonov et al. defined a genetic code as a widespread DNA sequence pattern that carries a message with an impact on biology. These patterns are largely captured in transcribed messages that give meaning and identity to the particular cells. In this review, I will go through my personal career in and after my years of work in the laboratory of Gordon H. Dixon, extending toward the impressive acquisition of new knowledge on regulatory information and genetic codes provided by remarkable scientists in the field. Abbreviations: CA II: carbonic anhydridase II (chicken); Car2: carbonic anhydridase 2 (mouse); CpG islands: short (>0.5 kb) stretches of DNA with a G+C content ≥55%; DNMT1: DNA methyltransferases 1; DNMT3b: DNA methyltransferases 3B; DSB: double-strand DNA breaks; ERT: endogenous retrotransposon; ERV: endogenous retroviruses; ES cells: embryonic stem cells; GAPDH: glyceraldehide phosphate dehydrogenase; H1: histone H1; HATs: histone acetyltransferases; HDACs: histone deacetylases; H3K4me3: histone 3 trimethylated at lys 4; H3K79me2: histone 3 dimethylated at lys 79; HMG: high mobility group proteins; HMT: histone methyltransferase; HP1: heterochromatin protein 1; HR: homologous recombination; HSE: heat-shock element; ICRs: imprinted control regions; IRF: interferon regulatory factor; LDH-A/-B: lactate dehydrogenase A/B; LTR: long terminal repeats; MeCP2: methyl CpG binding protein 2; OCT4: octamer-binding transcription factor 4; PAF1: RNA Polymerase II associated factor 1; piRNA: PIWI-interacting RNA; poly(A) tails: poly-adenine tails; PRC2: polycomb repressive complex 2; PTMs: post-translational modifications; SIRT 1: sirtuin 1, silent information regulator; STAT3: signal transducer and activator of transcription; tRNAs: transfer RNA; tRFs: tRNA-derived fragments; TSS: transcription start site; TE: transposable elements; UB I: polyubiquitin I; UB II: polyubiquitin II; UBE 2N: ubiquitin conjugating enzyme E2N; 5'-UTR: 5'-untranslated sequences; 3'-UTR: 3'-untranslated sequences.
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Affiliation(s)
- Jovita Mezquita-Pla
- a Molecular Genetics and Control of Pluripotency Laboratory, Department of Biomedicine, IDIBAPS, Faculty of Medicine , University of Barcelona , Catalonia , Spain
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8
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Li G, Liu Y, Liu C, Su Z, Ren S, Wang Y, Deng T, Huang D, Tian Y, Qiu Y. Genome-wide analyses of long noncoding RNA expression profiles correlated with radioresistance in nasopharyngeal carcinoma via next-generation deep sequencing. BMC Cancer 2016; 16:719. [PMID: 27599611 PMCID: PMC5012053 DOI: 10.1186/s12885-016-2755-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 08/31/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Radioresistance is one of the major factors limiting the therapeutic efficacy and prognosis of patients with nasopharyngeal carcinoma (NPC). Accumulating evidence has suggested that aberrant expression of long noncoding RNAs (lncRNAs) contributes to cancer progression. Therefore, here we identified lncRNAs associated with radioresistance in NPC. METHODS The differential expression profiles of lncRNAs associated with NPC radioresistance were constructed by next-generation deep sequencing by comparing radioresistant NPC cells with their parental cells. LncRNA-related mRNAs were predicted and analyzed using bioinformatics algorithms compared with the mRNA profiles related to radioresistance obtained in our previous study. Several lncRNAs and associated mRNAs were validated in established NPC radioresistant cell models and NPC tissues. RESULTS By comparison between radioresistant CNE-2-Rs and parental CNE-2 cells by next-generation deep sequencing, a total of 781 known lncRNAs and 2054 novel lncRNAs were annotated. The top five upregulated and downregulated known/novel lncRNAs were detected using quantitative real-time reverse transcription-polymerase chain reaction, and 7/10 known lncRNAs and 3/10 novel lncRNAs were demonstrated to have significant differential expression trends that were the same as those predicted by deep sequencing. From the prediction process, 13 pairs of lncRNAs and their associated genes were acquired, and the prediction trends of three pairs were validated in both radioresistant CNE-2-Rs and 6-10B-Rs cell lines, including lncRNA n373932 and SLITRK5, n409627 and PRSS12, and n386034 and RIMKLB. LncRNA n373932 and its related SLITRK5 showed dramatic expression changes in post-irradiation radioresistant cells and a negative expression correlation in NPC tissues (R = -0.595, p < 0.05). CONCLUSIONS Our study provides an overview of the expression profiles of radioresistant lncRNAs and potentially related mRNAs, which will facilitate future investigations into the function of lncRNAs in NPC radioresistance.
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Affiliation(s)
- Guo Li
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China.,Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China
| | - Yong Liu
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China.,Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China
| | - Chao Liu
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China.,Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China
| | - Zhongwu Su
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China.,Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China
| | - Shuling Ren
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China.,Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China
| | - Yunyun Wang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China.,Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China
| | - Tengbo Deng
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China.,Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China
| | - Donghai Huang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China.,Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China
| | - Yongquan Tian
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China.,Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China
| | - Yuanzheng Qiu
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road, Changsha, 410008, Hunan, China. .,Otolaryngology Major Disease Research Key Laboratory of Hunan Province, Xiangya Road, Changsha, 410008, Hunan, China.
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Mejía-Guerra MK, Li W, Galeano NF, Vidal M, Gray J, Doseff AI, Grotewold E. Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites. THE PLANT CELL 2015; 27:3309-20. [PMID: 26628745 PMCID: PMC4707454 DOI: 10.1105/tpc.15.00630] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/11/2015] [Indexed: 05/03/2023]
Abstract
Core promoters are crucial for gene regulation, providing blueprints for the assembly of transcriptional machinery at transcription start sites (TSSs). Empirically, TSSs define the coordinates of core promoters and other regulatory sequences. Thus, experimental TSS identification provides an essential step in the characterization of promoters and their features. Here, we describe the application of CAGE (cap analysis of gene expression) to identify genome-wide TSSs used in root and shoot tissues of two maize (Zea mays) inbred lines (B73 and Mo17). Our studies indicate that most TSS clusters are sharp in maize, similar to mice, but distinct from Arabidopsis thaliana, Drosophila melanogaster, or zebra fish, in which a majority of genes have broad-shaped TSS clusters. We established that ∼38% of maize promoters are characterized by a broader TATA-motif consensus, and this motif is significantly enriched in genes with sharp TSSs. A noteworthy plasticity in TSS usage between tissues and inbreds was uncovered, with ∼1500 genes showing significantly different dominant TSSs, sometimes affecting protein sequence by providing alternate translation initiation codons. We experimentally characterized instances in which this differential TSS utilization results in protein isoforms with additional domains or targeted to distinct subcellular compartments. These results provide important insights into TSS selection and gene expression in an agronomically important crop.
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Affiliation(s)
- María Katherine Mejía-Guerra
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210 Molecular Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, Ohio 43210
| | - Wei Li
- Department of Physiology and Cell Biology, 305B Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210 Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Narmer F Galeano
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210 Instituto de Investigación en Microbiología y Biotecnología Agroindustrial, Universidad Católica de Manizales, Carrera 23 No 60-63 Manizales, Colombia
| | - Mabel Vidal
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210
| | - John Gray
- Department of Biological Sciences, University of Toledo, Toledo, Ohio 43606
| | - Andrea I Doseff
- Department of Physiology and Cell Biology, 305B Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210 Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Erich Grotewold
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210 Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
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Abstract
With current advances in genomics, several technological processes have been generated, resulting in improvement in different segments of molecular research involving prokaryotic and eukaryotic systems. A widely used contribution is the identification of new genes and their functions, which has led to the elucidation of several issues concerning cell regulation and interactions. For this, increase in the knowledge generated from the identification of promoters becomes considerably relevant, especially considering that to generate new technological processes, such as genetically modified organisms, the availability of promoters that regulate the expression of new genes is still limited. Considering that this issue is essential for biotechnologists, this paper presents an updated review of promoters, from their structure to expression, and focuses on the knowledge already available in eukaryotic systems. Information on current promoters and methodologies available for studying their expression are also reported.
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Arhondakis S, Auletta F, Bernardi G. Isochores and the regulation of gene expression in the human genome. Genome Biol Evol 2012; 3:1080-9. [PMID: 21979159 PMCID: PMC3227402 DOI: 10.1093/gbe/evr017] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
It is well established that changes in the phenotype depend much more on changes in gene expression than on changes in protein-coding genes, and that cis-regulatory sequences and chromatin structure are two major factors influencing gene expression. Here, we investigated these factors at the genome-wide level by focusing on the trinucleotide patterns in the 0.1- to 25-kb regions flanking the human genes that are present in the GC-poorest L1 and GC-richest H3 isochore families, the other families exhibiting intermediate patterns. We could show 1) that the trinucleotide patterns of the 25-kb gene-flanking regions are representative of the very different patterns already reported for the whole isochores from the L1 and H3 families and, expectedly, identical in upstream and downstream locations; 2) that the patterns of the 0.1- to 0.5-kb regions in the L1 and H3 isochores are remarkably more divergent and more specific when compared with those of the 25-kb regions, as well as different in the upstream and downstream locations; and 3) that these patterns fade into the 25-kb patterns around 5kb in both upstream and downstream locations. The 25-kb findings indicate differences in nucleosome positioning and density in different isochore families, those of the 0.1- to 0.5-kb sequences indicate differences in the transcription factors that bind upstream and downstream of genes. These results indicate differences in the regulation of genes located in different isochore families, a point of functional and evolutionary relevance.
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Affiliation(s)
- Stilianos Arhondakis
- Bioinformatics and Medical Informatics Team, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
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12
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Koch F, Fenouil R, Gut M, Cauchy P, Albert TK, Zacarias-Cabeza J, Spicuglia S, de la Chapelle AL, Heidemann M, Hintermair C, Eick D, Gut I, Ferrier P, Andrau JC. Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Nat Struct Mol Biol 2011; 18:956-63. [PMID: 21765417 DOI: 10.1038/nsmb.2085] [Citation(s) in RCA: 241] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 05/12/2011] [Indexed: 11/09/2022]
Abstract
Recent work has shown that RNA polymerase (Pol) II can be recruited to and transcribe distal regulatory regions. Here we analyzed transcription initiation and elongation through genome-wide localization of Pol II, general transcription factors (GTFs) and active chromatin in developing T cells. We show that Pol II and GTFs are recruited to known T cell-specific enhancers. We extend this observation to many new putative enhancers, a majority of which can be transcribed with or without polyadenylation. Importantly, we also identify genomic features called transcriptional initiation platforms (TIPs) that are characterized by large areas of Pol II and GTF recruitment at promoters, intergenic and intragenic regions. TIPs show variable widths (0.4-10 kb) and correlate with high CpG content and increased tissue specificity at promoters. Finally, we also report differential recruitment of TFIID and other GTFs at promoters and enhancers. Overall, we propose that TIPs represent important new regulatory hallmarks of the genome.
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Affiliation(s)
- Frederic Koch
- Centre d'Immunologie de Marseille-Luminy, Université Aix-Marseille, Campus de Luminy, Marseille, France
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Bernard V, Brunaud V, Lecharny A. TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation. BMC Genomics 2010; 11:166. [PMID: 20222994 PMCID: PMC2842252 DOI: 10.1186/1471-2164-11-166] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 03/12/2010] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The TATA-box and TATA-variants are regulatory elements involved in the formation of a transcription initiation complex. Both have been conserved throughout evolution in a restricted region close to the Transcription Start Site (TSS). However, less than half of the genes in model organisms studied so far have been found to contain either one of these elements. Indeed different core-promoter elements are involved in the recruitment of the TATA-box-binding protein. Here we assessed the possibility of identifying novel functional motifs in plant genes, sharing the TATA-box topological constraints. RESULTS We developed an ab-initio approach considering the preferential location of motifs relative to the TSS. We identified motifs observed at the TATA-box expected location and conserved in both Arabidopsis thaliana and Oryza sativa promoters. We identified TC-elements within non-TA-rich promoters 30 bases upstream of the TSS. As with the TATA-box and TATA-variant sequences, it was possible to construct a unique distance graph with the TC-element sequences. The structural and functional features of TC-element-containing genes were distinct from those of TATA-box- or TATA-variant-containing genes. Arabidopsis thaliana transcriptome analysis revealed that TATA-box-containing genes were generally those showing relatively high levels of expression and that TC-element-containing genes were generally those expressed in specific conditions. CONCLUSIONS Our observations suggest that the TC-elements might constitute a class of novel regulatory elements participating towards the complex modulation of gene expression in plants.
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Affiliation(s)
- Virginie Bernard
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165-CNRS 8114-UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, France
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Vidaković M, Gluch A, Qiao J, Oumard A, Frisch M, Poznanović G, Bode J. PARP-1 expression in the mouse is controlled by an autoregulatory loop: PARP-1 binding to an upstream S/MAR element and to a novel recognition motif in its promoter suppresses transcription. J Mol Biol 2009; 388:730-50. [PMID: 19303024 DOI: 10.1016/j.jmb.2009.03.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 02/26/2009] [Accepted: 03/09/2009] [Indexed: 11/16/2022]
Abstract
This work identifies central components of a feedback mechanism for the expression of mouse poly(ADP-ribose) polymerase-1 (PARP-1). Using the stress-induced duplex destabilization algorithm, multiple base-unpairing regions (BURs) could be localized in the 5' region of the mouse PARP-1 gene (muPARP-1). Some of these could be identified as scaffold/matrix-attachment regions (S/MARs), suggesting an S/MAR-mediated transcriptional regulation. PARP-1 binding to the most proximal element, S/MAR 1, and to three consensus motifs, AGGCC, in its own promoter (basepairs -956 to +100), could be traced by electrophoretic mobility-shift assay. The AGGCC-complementary GGCCT motif was detected by cis-diammine-dichloro platinum cross-linking and functionally characterized by the effects of site-directed mutagenesis on its performance in wild type (PARP-1(+/+)) and PARP-1 knockout cells (PARP-1(-/-)). Mutation of the central AGGCC tract at basepairs -554 to -550 prevented PARP-1/promoter interactions, whereby muPARP-1 expression became up-regulated. Transfection of a series of reporter gene constructs with or without S/MAR 1 (basepairs -1523 to -1007) and the more distant S/MAR 2 (basepairs -8373 to -6880), into PARP-1(+/+) as well as PARP-1(-/-) cells, revealed an additional, major level of muPARP-1 promoter down-regulation, triggered by PARP-1 binding to S/MAR 1. We conclude that S/MAR 1 represents an upstream control element that acts in conjunction with the muPARP-1 promoter. These interactions are part of a negative autoregulatory loop.
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Affiliation(s)
- Melita Vidaković
- Helmholtz Centre for Infection Research, Epigenetic Regulation, Braunschweig, Germany
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Yamamoto YY, Ichida H, Abe T, Suzuki Y, Sugano S, Obokata J. Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis. Nucleic Acids Res 2007; 35:6219-26. [PMID: 17855401 PMCID: PMC2094075 DOI: 10.1093/nar/gkm685] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mammalian promoters are categorized into TATA and CpG-related groups, and they have complementary roles associated with differentiated transcriptional characteristics. While the TATA box is also found in plant promoters, it is not known if CpG-type promoters exist in plants. Plant promoters contain Y Patches (pyrimidine patches) in the core promoter region, and the ubiquity of these beyond higher plants is not understood as well. Sets of promoter sequences were utilized for the analysis of local distribution of short sequences (LDSS), and approximately one thousand octamer sequences have been identified as promoter constituents from Arabidopsis, rice, human and mouse, respectively. Based on their localization profiles, the identified octamer sequences were classified into several major groups, REG (Regulatory Element Group), TATA box, Inr (Initiator), Kozak, CpG and Y Patch. Comparison of the four species has revealed three categories: (i) shared groups found in both plants and mammals (TATA box), (ii) common groups found in both kingdoms but the utilized sequence is differentiated (REG, Inr and Kozak) and (iii) specific groups found in either plants or mammals (CpG and Y Patch). Our comparative LDSS analysis has identified conservation and differentiation of promoter architectures between higher plants and mammals.
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Deng Y, Ni J, Zhang C. Development of computations in bioscience and bioinformatics and its application: review of the Symposium of Computations in Bioinformatics and Bioscience (SCBB06). BMC Bioinformatics 2006; 7 Suppl 4:S1. [PMID: 17217501 PMCID: PMC1780134 DOI: 10.1186/1471-2105-7-s4-s1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The first symposium of computations in bioinformatics and bioscience (SCBB06) was held in Hangzhou, China on June 21–22, 2006. Twenty-six peer-reviewed papers were selected for publication in this special issue of BMC Bioinformatics. These papers cover a broad range of topics including bioinformatics theories, algorithms, applications and tool development. The main technical topics contain gene expression analysis, sequence analysis, genome analysis, phylogenetic analysis, gene function prediction, molecular interaction and system biology, genetics and population study, immune strategy, protein structure prediction and proteomics.
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Affiliation(s)
- Youping Deng
- Department of Biological Sciences, University of SouthernMississippi, Hattiesburg, MS 39406, USA
| | - Jun Ni
- Department of Computer Science, the University of Iowa, Iowa City, IA 52242, USA
| | - Chaoyang Zhang
- School of Computing, University of Southern Mississippi,Hattiesburg, MS 39406, USA
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