1
|
Deyneko IV. BestCRM: An Exhaustive Search for Optimal Cis-Regulatory Modules in Promoters Accelerated by the Multidimensional Hash Function. Int J Mol Sci 2024; 25:1903. [PMID: 38339181 PMCID: PMC10856692 DOI: 10.3390/ijms25031903] [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: 12/01/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
The concept of cis-regulatory modules located in gene promoters represents today's vision of the organization of gene transcriptional regulation. Such modules are a combination of two or more single, short DNA motifs. The bioinformatic identification of such modules belongs to so-called NP-hard problems with extreme computational complexity, and therefore, simplifications, assumptions, and heuristics are usually deployed to tackle the problem. In practice, this requires, first, many parameters to be set before the search, and second, it leads to the identification of locally optimal results. Here, a novel method is presented, aimed at identifying the cis-regulatory elements in gene promoters based on an exhaustive search of all the feasible modules' configurations. All required parameters are automatically estimated using positive and negative datasets. To be computationally efficient, the search is accelerated using a multidimensional hash function, allowing the search to complete in a few hours on a regular laptop (for example, a CPU Intel i7, 3.2 GH, 32 Gb RAM). Tests on an established benchmark and real data show better performance of BestCRM compared to the available methods according to several metrics like specificity, sensitivity, AUC, etc. A great practical advantage of the method is its minimum number of input parameters-apart from positive and negative promoters, only a desired level of module presence in promoters is required.
Collapse
Affiliation(s)
- Igor V Deyneko
- K.A. Timiryazev Institute of Plant Physiology RAS, 35 Botanicheskaya Str., Moscow 127276, Russia
| |
Collapse
|
2
|
Yang Y, Li X, Li C, Zhang H, Tuerxun Z, Hui F, Li J, Liu Z, Chen G, Cai D, Chen X, Li B. Isolation and Functional Characterization of a Constitutive Promoter in Upland Cotton ( Gossypium hirsutum L.). Int J Mol Sci 2024; 25:1917. [PMID: 38339199 PMCID: PMC10855717 DOI: 10.3390/ijms25031917] [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: 12/05/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Multiple cis-acting elements are present in promoter sequences that play critical regulatory roles in gene transcription and expression. In this study, we isolated the cotton FDH (Fiddlehead) gene promoter (pGhFDH) using a real-time reverse transcription-PCR (qRT-PCR) expression analysis and performed a cis-acting elements prediction analysis. The plant expression vector pGhFDH::GUS was constructed using the Gateway approach and was used for the genetic transformation of Arabidopsis and upland cotton plants to obtain transgenic lines. Histochemical staining and a β-glucuronidase (GUS) activity assay showed that the GUS protein was detected in the roots, stems, leaves, inflorescences, and pods of transgenic Arabidopsis thaliana lines. Notably, high GUS activity was observed in different tissues. In the transgenic lines, high GUS activity was detected in different tissues such as leaves, stalks, buds, petals, androecium, endosperm, and fibers, where the pGhFDH-driven GUS expression levels were 3-10-fold higher compared to those under the CaMV 35S promoter at 10-30 days post-anthesis (DPA) during fiber development. The results indicate that pGhFDH can be used as an endogenous constitutive promoter to drive the expression of target genes in various cotton tissues to facilitate functional genomic studies and accelerate cotton molecular breeding.
Collapse
Affiliation(s)
- Yang Yang
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Xiaorong Li
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Chenyu Li
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China
| | - Hui Zhang
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Zumuremu Tuerxun
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Fengjiao Hui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
| | - Juan Li
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Zhigang Liu
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Guo Chen
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Darun Cai
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Xunji Chen
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Bo Li
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| |
Collapse
|
3
|
Zhang X, Li X, Tan F, Yu N, Pei H. STAT1 Inhibits MiR-181a Expression to Suppress Colorectal Cancer Cell Proliferation Through PTEN/Akt. J Cell Biochem 2017; 118:3435-3443. [PMID: 28322462 DOI: 10.1002/jcb.26000] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 03/17/2017] [Indexed: 11/08/2022]
Abstract
Signal transducers and activators of transcription 1 (STAT1) exhibits tumor-suppressor properties by inhibiting oncogenic pathways and promoting tumor immunosurveillance. MicroRNAs, a group of non-coding endogenous ones, may regulate gene expression and plays specific roles in tumorigenesis. Recently, miR-181a has been reported to be associated with poor prognosis of colorectal cancer (CRC). Using human colorectal cancer cell lines, we demonstrated that STAT1 suppresses both LoVo and SW480 cell growth by down-regulating miR-181a. STAT1 regulates the expression of miR-181a through binding to the elements in the miR-181a's promoter region. Further, we revealed that miR-181a accelerates CRC cell proliferation through phosphatase and tensin homolog on chromosome ten (PTEN). In addition, PTEN protein was upregulated in response to STAT1 overexpression or miR-181a inhibition, downregulated in response to STAT1 knockdown or miR-181a overexpression. Without changes on the AKT protein level, p-AKT was downregulated by STAT1 overexpression or miR-181a inhibition while upregulated by STAT1 knockdown or miR-181a overexpression, indicating PTEN/Akt pathway activated in STAT1/miR-181a regulation of CRC cell proliferation. Taken together, our findings shed new light on the STAT1/miR-181a/PTEN pathway in colorectal cancer and add new insight regarding the carcinogenesis of colorectal cancer. J. Cell. Biochem. 118: 3435-3443, 2017. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Xingwen Zhang
- Department of Gastrointestinal Surgery, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China.,Department of Emergency, Hunan Provincial People's Hospital, P.R. China
| | - Xiang Li
- Department of Emergency, Hunan Provincial People's Hospital, P.R. China
| | - Fengbo Tan
- Department of Gastrointestinal Surgery, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
| | - Nanhui Yu
- Department of Gastrointestinal Surgery, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
| | - Haiping Pei
- Department of Gastrointestinal Surgery, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
| |
Collapse
|
4
|
Deyneko IV, Kasnitz N, Leschner S, Weiss S. Composing a Tumor Specific Bacterial Promoter. PLoS One 2016; 11:e0155338. [PMID: 27171245 PMCID: PMC4865170 DOI: 10.1371/journal.pone.0155338] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/27/2016] [Indexed: 12/12/2022] Open
Abstract
Systemically applied Salmonella enterica spp. have been shown to invade and colonize neoplastic tissues where it retards the growth of many tumors. This offers the possibility to use the bacteria as a vehicle for the tumor specific delivery of therapeutic molecules. Specificity of such delivery is solely depending on promoter sequences that control the production of a target molecule. We have established the functional structure of bacterial promoters that are transcriptionally active exclusively in tumor tissues after systemic application. We observed that the specific transcriptional activation is accomplished by a combination of a weak basal promoter and a strong FNR binding site. This represents a minimal set of control elements required for such activation. In natural promoters, additional DNA remodeling elements are found that alter the level of transcription quantitatively. Inefficiency of the basal promoter ensures the absence of transcription outside tumors. As a proof of concept, we compiled an artificial promoter sequence from individual motifs representing FNR and basal promoter and showed specific activation in a tumor microenvironment. Our results open possibilities for the generation of promoters with an adjusted level of expression of target proteins in particular for applications in bacterial tumor therapy.
Collapse
Affiliation(s)
- Igor V. Deyneko
- Molecular Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- * E-mail:
| | - Nadine Kasnitz
- Molecular Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sara Leschner
- Molecular Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Siegfried Weiss
- Molecular Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute of Immunology, Medical School Hannover, Hannover, Germany
| |
Collapse
|
5
|
Nuclear factor-κB–dependent microRNA-130a upregulation promotes cervical cancer cell growth by targeting phosphatase and tensin homolog. Arch Biochem Biophys 2016; 598:57-65. [DOI: 10.1016/j.abb.2016.03.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/17/2016] [Accepted: 03/19/2016] [Indexed: 12/13/2022]
|
6
|
Ponomarenko MP, Arkova O, Rasskazov D, Ponomarenko P, Savinkova L, Kolchanov N. Candidate SNP Markers of Gender-Biased Autoimmune Complications of Monogenic Diseases Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters. Front Immunol 2016; 7:130. [PMID: 27092142 PMCID: PMC4819121 DOI: 10.3389/fimmu.2016.00130] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 03/21/2016] [Indexed: 12/17/2022] Open
Abstract
Some variations of human genome [for example, single nucleotide polymorphisms (SNPs)] are markers of hereditary diseases and drug responses. Analysis of them can help to improve treatment. Computer-based analysis of millions of SNPs in the 1000 Genomes project makes a search for SNP markers more targeted. Here, we combined two computer-based approaches: DNA sequence analysis and keyword search in databases. In the binding sites for TATA-binding protein (TBP) in human gene promoters, we found candidate SNP markers of gender-biased autoimmune diseases, including rs1143627 [cachexia in rheumatoid arthritis (double prevalence among women)]; rs11557611 [demyelinating diseases (thrice more prevalent among young white women than among non-white individuals)]; rs17231520 and rs569033466 [both: atherosclerosis comorbid with related diseases (double prevalence among women)]; rs563763767 [Hughes syndrome-related thrombosis (lethal during pregnancy)]; rs2814778 [autoimmune diseases (excluding multiple sclerosis and rheumatoid arthritis) underlying hypergammaglobulinemia in women]; rs72661131 and rs562962093 (both: preterm delivery in pregnant diabetic women); and rs35518301, rs34166473, rs34500389, rs33981098, rs33980857, rs397509430, rs34598529, rs33931746, rs281864525, and rs63750953 (all: autoimmune diseases underlying hypergammaglobulinemia in women). Validation of these predicted candidate SNP markers using the clinical standards may advance personalized medicine.
Collapse
Affiliation(s)
- Mikhail P. Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Olga Arkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Dmitry Rasskazov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | | | - Ludmila Savinkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Nikolay Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| |
Collapse
|
7
|
Arkova OV, Ponomarenko MP, Rasskazov DA, Drachkova IA, Arshinova TV, Ponomarenko PM, Savinkova LK, Kolchanov NA. Obesity-related known and candidate SNP markers can significantly change affinity of TATA-binding protein for human gene promoters. BMC Genomics 2015; 16 Suppl 13:S5. [PMID: 26694100 PMCID: PMC4686794 DOI: 10.1186/1471-2164-16-s13-s5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Obesity affects quality of life and life expectancy and is associated with cardiovascular disorders, cancer, diabetes, reproductive disorders in women, prostate diseases in men, and congenital anomalies in children. The use of single nucleotide polymorphism (SNP) markers of diseases and drug responses (i.e., significant differences of personal genomes of patients from the reference human genome) can help physicians to improve treatment. Clinical research can validate SNP markers via genotyping of patients and demonstration that SNP alleles are significantly more frequent in patients than in healthy people. The search for biomedical SNP markers of interest can be accelerated by computer-based analysis of hundreds of millions of SNPs in the 1000 Genomes project because of selection of the most meaningful candidate SNP markers and elimination of neutral SNPs. RESULTS We cross-validated the output of two computer-based methods: DNA sequence analysis using Web service SNP_TATA_Comparator and keyword search for articles on comorbidities of obesity. Near the sites binding to TATA-binding protein (TBP) in human gene promoters, we found 22 obesity-related candidate SNP markers, including rs10895068 (male breast cancer in obesity); rs35036378 (reduced risk of obesity after ovariectomy); rs201739205 (reduced risk of obesity-related cancers due to weight loss by diet/exercise in obese postmenopausal women); rs183433761 (obesity resistance during a high-fat diet); rs367732974 and rs549591993 (both: cardiovascular complications in obese patients with type 2 diabetes mellitus); rs200487063 and rs34104384 (both: obesity-caused hypertension); rs35518301, rs72661131, and rs562962093 (all: obesity); and rs397509430, rs33980857, rs34598529, rs33931746, rs33981098, rs34500389, rs63750953, rs281864525, rs35518301, and rs34166473 (all: chronic inflammation in comorbidities of obesity). Using an electrophoretic mobility shift assay under nonequilibrium conditions, we empirically validated the statistical significance (α < 0.00025) of the differences in TBP affinity values between the minor and ancestral alleles of 4 out of the 22 SNPs: rs200487063, rs201381696, rs34104384, and rs183433761. We also measured half-life (t1/2), Gibbs free energy change (ΔG), and the association and dissociation rate constants, ka and kd, of the TBP-DNA complex for these SNPs. CONCLUSIONS Validation of the 22 candidate SNP markers by proper clinical protocols appears to have a strong rationale and may advance postgenomic predictive preventive personalized medicine.
Collapse
Affiliation(s)
- Olga V Arkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyeva Avenue, Novosibirsk 630090, Russia
| | - Mikhail P Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyeva Avenue, Novosibirsk 630090, Russia
- Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia
- Laboratory of Evolutionary Bioinformatics and Theoretical Genetics, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyev Avenue, Novosibirsk 630090, Russia
| | - Dmitry A Rasskazov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyeva Avenue, Novosibirsk 630090, Russia
| | - Irina A Drachkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyeva Avenue, Novosibirsk 630090, Russia
| | - Tatjana V Arshinova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyeva Avenue, Novosibirsk 630090, Russia
| | - Petr M Ponomarenko
- Children's Hospital Los Angeles, 4640 Hollywood Boulevard, University of Southern California, Los Angeles, CA 90027, USA
| | - Ludmila K Savinkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyeva Avenue, Novosibirsk 630090, Russia
| | - Nikolay A Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentyeva Avenue, Novosibirsk 630090, Russia
- Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia
| |
Collapse
|