1
|
Trerotola M, Antolini L, Beni L, Guerra E, Spadaccini M, Verzulli D, Moschella A, Alberti S. A deterministic code for transcription factor-DNA recognition through computation of binding interfaces. NAR Genom Bioinform 2022; 4:lqac008. [PMID: 35261972 PMCID: PMC8896162 DOI: 10.1093/nargab/lqac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/05/2021] [Accepted: 02/28/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
The recognition code between transcription factor (TF) amino acids and DNA bases remains poorly understood. Here, the determinants of TF amino acid-DNA base binding selectivity were identified through the analysis of crystals of TF-DNA complexes. Selective, high-frequency interactions were identified for the vast majority of amino acid side chains (‘structural code’). DNA binding specificities were then independently assessed by meta-analysis of random-mutagenesis studies of Zn finger-target DNA sequences. Selective, high-frequency interactions were identified for the majority of mutagenized residues (‘mutagenesis code’). The structural code and the mutagenesis code were shown to match to a striking level of accuracy (P = 3.1 × 10−33), suggesting the identification of fundamental rules of TF binding to DNA bases. Additional insight was gained by showing a geometry-dictated choice among DNA-binding TF residues with overlapping specificity. These findings indicate the existence of a DNA recognition mode whereby the physical-chemical characteristics of the interacting residues play a deterministic role. The discovery of this DNA recognition code advances our knowledge on fundamental features of regulation of gene expression and is expected to pave the way for integration with higher-order complexity approaches.
Collapse
Affiliation(s)
- Marco Trerotola
- Laboratory of Cancer Pathology, Center for Advanced Studies and Technology (CAST), University “G. D’ Annunzio”, Via L. Polacchi 11, 66100 Chieti, Italy
- Department of Medical, Oral and Biotechnological Sciences, University “G. d’Annunzio”, 66100 Chieti, Italy
| | - Laura Antolini
- Center for Biostatistics, Department of Clinical Medicine, Prevention and Biotechnology, University of Milano-Bicocca, 20052 Monza, Italy
| | - Laura Beni
- Laboratory of Cancer Pathology, Center for Advanced Studies and Technology (CAST), University “G. D’ Annunzio”, Via L. Polacchi 11, 66100 Chieti, Italy
| | - Emanuela Guerra
- Laboratory of Cancer Pathology, Center for Advanced Studies and Technology (CAST), University “G. D’ Annunzio”, Via L. Polacchi 11, 66100 Chieti, Italy
- Department of Medical, Oral and Biotechnological Sciences, University “G. d’Annunzio”, 66100 Chieti, Italy
| | | | - Damiano Verzulli
- Unit of Informatics, University “G. d’Annunzio”, 66100 Chieti, Italy
| | - Antonino Moschella
- Unit of Medical Genetics, Department of Biomedical Sciences - BIOMORF, University of Messina, via Consolare Valeria, 98125 Messina, Italy
| | - Saverio Alberti
- Laboratory of Cancer Pathology, Center for Advanced Studies and Technology (CAST), University “G. D’ Annunzio”, Via L. Polacchi 11, 66100 Chieti, Italy
- Unit of Medical Genetics, Department of Biomedical Sciences - BIOMORF, University of Messina, via Consolare Valeria, 98125 Messina, Italy
| |
Collapse
|
2
|
Daimiel L, Micó V, Valls RM, Pedret A, Motilva MJ, Rubió L, Fitó M, Farrás M, Covas MI, Solá R, Ordovás JM. Impact of Phenol-Enriched Virgin Olive Oils on the Postprandial Levels of Circulating microRNAs Related to Cardiovascular Disease. Mol Nutr Food Res 2020; 64:e2000049. [PMID: 32562310 PMCID: PMC7507201 DOI: 10.1002/mnfr.202000049] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/06/2020] [Indexed: 12/19/2022]
Abstract
SCOPE We investigate the postprandial modulation of cardiovascular-related microRNAs elicited by extra virgin olive oil (EVOOs) containing different levels of their own polyphenols. METHODS AND RESULTS It is randomized, postprandial, parallel, double-blind study. Twelve healthy participants consumed 30 mL of EVOO containing low (L-EVOO; 250 mg total phenols kg-1 of oil), medium (M-EVOO; 500 mg total phenols kg-1 of oil), and high (H-EVOO; 750 mg total phenols kg-1 of oil) enriched EVOOs. Postprandial plasma microRNAs levels are analyzed by real-time quantitative PCR. The results show that L-EVOO intake is associated with decreased let-7e-5p and miR-328a-3p levels and increased miR-17-5p and miR-20a-5p, concentrations. M-EVOO decreases plasma let-7e-5p and increases miR-17-5p, miR-20a-5p, and miR-192-5p levels. Finally, H-EVOO decreases let-7e-5p, miR-10a-5p, miR-21-5p, and miR-26b-5p levels. CONCLUSION During the postprandial state, the levels of let-7e-5p decrease with EVOO regardless of polyphenol content suggesting a general response to the fatty acid composition of EVOO or/and the presence of at least 250 mg polyphenol kg-1 olive oil. Moreover, the miR-17-92 cluster increases by low and medium polyphenol content suggesting a role in fatty acid metabolism and nutrient sensing. Thus, postprandial modulation of circulating microRNAs levels could be a potential mechanism for the cardiovascular benefits associated with EVOO intake.
Collapse
Affiliation(s)
- Lidia Daimiel
- Nutritional Control of the Epigenome GroupInstituto Madrileño de EstudiosAvanzados (IMDEA) Food InstituteCEI UAM+CSICMadrid28049Spain
| | - Víctor Micó
- Nutritional Control of the Epigenome GroupInstituto Madrileño de EstudiosAvanzados (IMDEA) Food InstituteCEI UAM+CSICMadrid28049Spain
| | - Rosa M Valls
- Functional NutritionOxidation and Cardiovascular Disease Research GroupUniversitat Rovira i VirgiliHospital Universitari Sant JoanEURECATReus43204Spain
| | - Anna Pedret
- Functional NutritionOxidation and Cardiovascular Disease Research GroupUniversitat Rovira i VirgiliHospital Universitari Sant JoanEURECATReus43204Spain
| | - María José Motilva
- Food Technology DepartmentAgrotecnio CenterEscola Tècnica Superior d'Enginyeria AgràriaUniversity of LleidaLleida25198Spain
- Present address:
Instituto de Ciencias de la Vid y del Vino‐ICVV (CSIC‐Consejo Superior de Investigaciones CientíficasUniversidad de La Rioja, Gobierno de La Rioja)Finca La Grajera, Ctra. de Burgos Km. 6 (LO‐20 ‐ salida 13)Logroño (La Rioja)26007Spain
| | - Laura Rubió
- Instituto de Ciencias de la Vid y del Vino‐ICVV(CSIC‐Consejo Superior de Investigaciones Científicas, Universidad de La Rioja, Gobierno de La Rioja)Finca La Grajera, Ctra. de Burgos Km. 6 (LO‐20 – salida 13)LogroñoLa Rioja26007Spain
| | - Montse Fitó
- Cardiovascular Risk and Nutrition (Regicor Study Group)Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain. CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN)Institute of Health Carlos IIIMadrid28029Spain
| | - Marta Farrás
- Cardiovascular Risk and Nutrition (Regicor Study Group)Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain. CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN)Institute of Health Carlos IIIMadrid28029Spain
| | - María Isabel Covas
- Cardiovascular Risk and Nutrition (Regicor Study Group)Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain. CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN)Institute of Health Carlos IIIMadrid28029Spain
| | - Rosa Solá
- Functional NutritionOxidation and Cardiovascular Disease Research GroupUniversitat Rovira i VirgiliHospital Universitari Sant JoanEURECATReus43204Spain
| | - José M. Ordovás
- Nutritional Genomics and Epigenomics GroupInstituto Madrileño de Estudios Avanzados (IMDEA) Food InstituteCEI UAM+CSICMadrid28049Spain
- Jean Mayer U.S. Department of Agriculture Human Nutrition Research Center on AgingTufts University School of MedicineBostonMA02111USA
| |
Collapse
|
3
|
Singh S, Jangid RK, Crowder A, Groves AK. Foxi3 transcription factor activity is mediated by a C-terminal transactivation domain and regulated by the Protein Phosphatase 2A (PP2A) complex. Sci Rep 2018; 8:17249. [PMID: 30467319 PMCID: PMC6250667 DOI: 10.1038/s41598-018-35390-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/02/2018] [Indexed: 01/20/2023] Open
Abstract
The Forkhead box (FOX) family consists of at least 19 subgroups of transcription factors which are characterized by the presence of an evolutionary conserved ‘forkhead’ or ‘winged-helix’ DNA-binding domain. Despite having a conserved core DNA binding domain, FOX proteins display remarkable functional diversity and are involved in many developmental and cell specific processes. In the present study, we focus on a poorly characterized member of the Forkhead family, Foxi3, which plays a critical role in the development of the inner ear and jaw. We show that Foxi3 contains at least two important functional domains, a nuclear localization sequence (NLS) and a C-terminal transactivation domain (TAD), and that it directly binds its targets in a sequence specific manner. We also show that the transcriptional activity of Foxi3 is regulated by phosphorylation, and that the activity of Foxi3 can be attenuated by its physical interaction with the protein phosphatase 2A (PP2A) complex.
Collapse
Affiliation(s)
- Sunita Singh
- Department of Neuroscience, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Rahul K Jangid
- Department of Neuroscience, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Alyssa Crowder
- Department of Neuroscience, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Andrew K Groves
- Department of Neuroscience, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. .,Program in Developmental Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| |
Collapse
|
4
|
Zhao W, Bachhav B, McWhite C, Segatori L. A yeast selection system for the detection of proteasomal activation. Protein Eng Des Sel 2018; 31:437-445. [PMID: 30989230 DOI: 10.1093/protein/gzz006] [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: 12/10/2018] [Revised: 03/05/2019] [Accepted: 03/21/2019] [Indexed: 11/13/2022] Open
Abstract
The ubiquitin proteasome system (UPS) is a complex cellular machinery that catalyzes degradation of misfolded or damaged proteins and regulates turnover of native proteins in eukaryotic cells, thus playing a crucial role in maintaining protein homeostasis. The UPS has emerged as a drug target for a diverse range of diseases characterized by accumulation of misfolded or aggregated proteins. While enhancement of UPS activity is widely recognized as a promising strategy to prevent accumulation of aberrant, off-pathway protein conformations and ameliorate the phenotypes of a wide range of protein misfolding diseases, the molecular mechanisms underlying activation of proteasomal degradation are poorly characterized. We report the development of a yeast selection platform for genome-wide selection of UPS activators. We engineered the Saccharomyces cerevisiae selection marker orotidine-5'-phosphate decarboxylase (URA3) to function as a substrate of proteasomal degradation through fusion to UPS-sensitive tags. The resulting UPS-sensitive URA3 variant links UPS activity to cell growth. The yeast selection platform reported in this study will open the way to high-throughput, genome-wide studies aimed at identifying modulators of UPS function that might provide novel target for therapeutic applications.
Collapse
Affiliation(s)
- Wenting Zhao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston TX, USA
| | - Bhagyashree Bachhav
- Department of Chemical and Biomolecular Engineering, Rice University, Houston TX, USA
| | - Claire McWhite
- Department of BioSciences, Rice University, Houston TX, USA
| | - Laura Segatori
- Department of Chemical and Biomolecular Engineering, Rice University, Houston TX, USA.,Department of BioSciences, Rice University, Houston TX, USA.,Department of Bioengineering, Rice University, Houston TX, USA
| |
Collapse
|
5
|
Znf385C mediates a novel p53-dependent transcriptional switch to control timing of facial bone formation. Dev Biol 2015; 400:23-32. [DOI: 10.1016/j.ydbio.2015.01.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 01/12/2015] [Indexed: 11/18/2022]
|
6
|
Chuang HN, Hsiao KM, Chang HY, Wu CC, Pan H. The homeobox transcription factor Irxl1 negatively regulates MyoD expression and myoblast differentiation. FEBS J 2014; 281:2990-3003. [PMID: 24814716 DOI: 10.1111/febs.12837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 04/07/2014] [Accepted: 04/30/2014] [Indexed: 11/29/2022]
Abstract
Irxl1/Mkx (Iroquois homeobox-like 1/Mohawk) encodes a member of the TALE subfamily of homeodomain proteins. It is expressed in multiple mesoderm-derived tissues and has recently been shown to regulate tendon differentiation during mouse embryonic development. Previously we showed that knockdown of Irxl1 in zebrafish caused a deficit in neural crest cells which consequently resulted in deformation of craniofacial muscles and arch cartilages. Here, we further demonstrate that loss of Irxl1 function results in deformed somites with disordered muscle fibers and myotendinous junctions. Because expression of myoD is increased in the somites of Irxl1 knockdown morphants, we test whether Irxl1 negatively regulates myoD expression. When stable C2C12 myoblasts overexpressing Irxl1/Mkx were induced to differentiate, myotube formation was inhibited and protein levels of myoD and myosin heavy chain were decreased accordingly. A series of deletion constructs of myoD promoter fragments were tested by luciferase reporter assays, which identified a promoter fragment that is necessary and sufficient for Irxl1-mediated repression. Direct interaction of Irxl1 and myoD promoter was subsequently elucidated by yeast one-hybrid assays, electrophoretic mobility shift assays and chromatin immunoprecipitation analysis. Furthermore, mouse Mkx also binds to and represses myoD promoter. These results indicate that Irxl1/Mkx can repress myoD expression through direct binding to its promoter and may thus play a negative regulatory role in muscle differentiation.
Collapse
Affiliation(s)
- Han-Ni Chuang
- Department of Life Science and Institute of Molecular Biology, National Chung Cheng University, Chia-Yi, Taiwan; Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | | | | | | | | |
Collapse
|
7
|
Edlund RK, Ohyama T, Kantarci H, Riley BB, Groves AK. Foxi transcription factors promote pharyngeal arch development by regulating formation of FGF signaling centers. Dev Biol 2014; 390:1-13. [PMID: 24650709 DOI: 10.1016/j.ydbio.2014.03.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 03/10/2014] [Indexed: 01/12/2023]
Abstract
The bones of the vertebrate face develop from transient embryonic branchial arches that are populated by cranial neural crest cells. We have characterized a mouse mutant for the Forkhead family transcription factor Foxi3, which is expressed in branchial ectoderm and endoderm. Foxi3 mutant mice are not viable and display severe branchial arch-derived facial skeleton defects, including absence of all but the most distal tip of the mandible and complete absence of the inner, middle and external ear structures. Although cranial neural crest cells of Foxi3 mutants are able to migrate, populate the branchial arches, and display some elements of correct proximo-distal patterning, they succumb to apoptosis from embryonic day 9.75 onwards. We show this cell death correlates with a delay in expression of Fgf8 in branchial arch ectoderm and a failure of neural crest cells in the arches to express FGF-responsive genes. Zebrafish foxi1 is also expressed in branchial arch ectoderm and endoderm, and morpholino knock-down of foxi1 also causes apoptosis of neural crest in the branchial arches. We show that heat shock induction of fgf3 in zebrafish arch tissue can rescue cell death in foxi1 morphants. Our results suggest that Foxi3 may play a role in the establishment of signaling centers in the branchial arches that are required for neural crest survival, patterning and the subsequent development of branchial arch derivatives.
Collapse
Affiliation(s)
- Renée K Edlund
- Program in Developmental Biology, Baylor College of Medicine, BCM295, 1 Baylor Plaza, Houston TX 77030
| | - Takahiro Ohyama
- Division of Cell Biology and Genetics, House Research Institute, 2100 W 3rd St., Los Angeles, CA 90057
| | - Husniye Kantarci
- Biology Department, Texas A&M University, College Station, TX 77843-3258
| | - Bruce B Riley
- Biology Department, Texas A&M University, College Station, TX 77843-3258
| | - Andrew K Groves
- Program in Developmental Biology, Baylor College of Medicine, BCM295, 1 Baylor Plaza, Houston TX 77030.,Department of Molecular and Human Genetics, Baylor College of Medicine, BCM295, 1 Baylor Plaza, Houston TX 77030.,Department of Neuroscience, Baylor College of Medicine, BCM295, 1 Baylor Plaza, Houston TX 77030
| |
Collapse
|
8
|
Yang TH, Wu WS. Inferring functional transcription factor-gene binding pairs by integrating transcription factor binding data with transcription factor knockout data. BMC SYSTEMS BIOLOGY 2013; 7 Suppl 6:S13. [PMID: 24565265 PMCID: PMC4029220 DOI: 10.1186/1752-0509-7-s6-s13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Background Chromatin immunoprecipitation (ChIP) experiments are now the most comprehensive experimental approaches for mapping the binding of transcription factors (TFs) to their target genes. However, ChIP data alone is insufficient for identifying functional binding target genes of TFs for two reasons. First, there is an inherent high false positive/negative rate in ChIP-chip or ChIP-seq experiments. Second, binding signals in the ChIP data do not necessarily imply functionality. Methods It is known that ChIP-chip data and TF knockout (TFKO) data reveal complementary information on gene regulation. While ChIP-chip data can provide TF-gene binding pairs, TFKO data can provide TF-gene regulation pairs. Therefore, we propose a novel network approach for identifying functional TF-gene binding pairs by integrating the ChIP-chip data with the TFKO data. In our method, a TF-gene binding pair from the ChIP-chip data is regarded to be functional if it also has high confident curated TFKO TF-gene regulatory relation or deduced hypostatic TF-gene regulatory relation. Results and conclusions We first validated our method on a gathered ground truth set. Then we applied our method to the ChIP-chip data to identify functional TF-gene binding pairs. The biological significance of our identified functional TF-gene binding pairs was shown by assessing their functional enrichment, the prevalence of protein-protein interaction, and expression coherence. Our results outperformed the results of three existing methods across all measures. And our identified functional targets of TFs also showed statistical significance over the randomly assigned TF-gene pairs. We also showed that our method is dataset independent and can apply to ChIP-seq data and the E. coli genome. Finally, we provided an example showing the biological applicability of our notion.
Collapse
|
9
|
Armas P, Margarit E, Mouguelar VS, Allende ML, Calcaterra NB. Beyond the binding site: in vivo identification of tbx2, smarca5 and wnt5b as molecular targets of CNBP during embryonic development. PLoS One 2013; 8:e63234. [PMID: 23667590 PMCID: PMC3646763 DOI: 10.1371/journal.pone.0063234] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 04/01/2013] [Indexed: 12/30/2022] Open
Abstract
CNBP is a nucleic acid chaperone implicated in vertebrate craniofacial development, as well as in myotonic dystrophy type 2 (DM2) and sporadic inclusion body myositis (sIBM) human muscle diseases. CNBP is highly conserved among vertebrates and has been implicated in transcriptional regulation; however, its DNA binding sites and molecular targets remain elusive. The main goal of this work was to identify CNBP DNA binding sites that might reveal target genes involved in vertebrate embryonic development. To accomplish this, we used a recently described yeast one-hybrid assay to identify DNA sequences bound in vivo by CNBP. Bioinformatic analyses revealed that these sequences are G-enriched and show high frequency of putative G-quadruplex DNA secondary structure. Moreover, an in silico approach enabled us to establish the CNBP DNA-binding site and to predict CNBP putative targets based on gene ontology terms and synexpression with CNBP. The direct interaction between CNBP and candidate genes was proved by EMSA and ChIP assays. Besides, the role of CNBP upon the identified genes was validated in loss-of-function experiments in developing zebrafish. We successfully confirmed that CNBP up-regulates tbx2b and smarca5, and down-regulates wnt5b gene expression. The highly stringent strategy used in this work allowed us to identify new CNBP target genes functionally important in different contexts of vertebrate embryonic development. Furthermore, it represents a novel approach toward understanding the biological function and regulatory networks involving CNBP in the biology of vertebrates.
Collapse
Affiliation(s)
- Pablo Armas
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, (S2000FHQ) Rosario, Argentina
| | - Ezequiel Margarit
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, (S2000FHQ) Rosario, Argentina
| | - Valeria S. Mouguelar
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, (S2000FHQ) Rosario, Argentina
| | - Miguel L. Allende
- FONDAP Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Nora B. Calcaterra
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, (S2000FHQ) Rosario, Argentina
- * E-mail:
| |
Collapse
|
10
|
Wang X, Du B, Liu M, Sun N, Qi X. <i>Arabidopsis</i> Transcription Factor WRKY33 Is Involved in Drought by Directly Regulating the Expression of <i>CesA8</i>. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ajps.2013.46a004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
11
|
Shaffer HA, Rood MK, Kashlan B, Chang EIL, Doyle DF, Azizi B. BAPJ69-4A: A yeast two-hybrid strain for both positive and negative genetic selection. J Microbiol Methods 2012; 91:22-9. [DOI: 10.1016/j.mimet.2012.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 07/01/2012] [Accepted: 07/02/2012] [Indexed: 10/28/2022]
|
12
|
Milla LA, Cortés CR, Hodar C, Oñate MG, Cambiazo V, Burgess SM, Palma V. Yeast-based assay identifies novel Shh/Gli target genes in vertebrate development. BMC Genomics 2012; 13:2. [PMID: 22214306 PMCID: PMC3285088 DOI: 10.1186/1471-2164-13-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 01/03/2012] [Indexed: 01/07/2023] Open
Abstract
Background The increasing number of developmental events and molecular mechanisms associated with the Hedgehog (Hh) pathway from Drosophila to vertebrates, suggest that gene regulation is crucial for diverse cellular responses, including target genes not yet described. Although several high-throughput, genome-wide approaches have yielded information at the genomic, transcriptional and proteomic levels, the specificity of Gli binding sites related to direct target gene activation still remain elusive. This study aims to identify novel putative targets of Gli transcription factors through a protein-DNA binding assay using yeast, and validating a subset of targets both in-vitro and in-vivo. Testing in different Hh/Gli gain- and loss-of-function scenarios we here identified known (e.g., ptc1) and novel Hh-regulated genes in zebrafish embryos. Results The combined yeast-based screening and MEME/MAST analysis were able to predict Gli transcription factor binding sites, and position mapping of these sequences upstream or in the first intron of promoters served to identify new putative target genes of Gli regulation. These candidates were validated by qPCR in combination with either the pharmacological Hh/Gli antagonist cyc or the agonist pur in Hh-responsive C3H10T1/2 cells. We also used small-hairpin RNAs against Gli proteins to evaluate targets and confirm specific Gli regulation their expression. Taking advantage of mutants that have been identified affecting different components of the Hh/Gli signaling system in the zebrafish model, we further analyzed specific novel candidates. Studying Hh function with pharmacological inhibition or activation complemented these genetic loss-of-function approaches. We provide evidence that in zebrafish embryos, Hh signaling regulates sfrp2, neo1, and c-myc expression in-vivo. Conclusion A recently described yeast-based screening allowed us to identify new Hh/Gli target genes, functionally important in different contexts of vertebrate embryonic development.
Collapse
Affiliation(s)
- Luis A Milla
- Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | | | | | | | | | | | | |
Collapse
|
13
|
Yan J, Burgess SM. Using a yeast inverse one-hybrid system to identify functional binding sites of transcription factors. Methods Mol Biol 2012; 786:275-290. [PMID: 21938633 DOI: 10.1007/978-1-61779-292-2_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Binding of transcription factors to promoters is a necessary step to initiate transcription. From an evolutionary standpoint, the regulatory proteins and their binding sites are considered to have molecularly coevolved. We developed an efficient yeast strategy, an "inverse one-hybrid system", to identify binding targets of transcription factors globally in a genome of interest. The technique consists of a yeast strain expressing a -transcription factor of interest mated to yeast containing a library of random genomic fragments cloned upstream of a reporter gene (URA3). Positive growth on media without uracil denotes a fragment being bound by the transcription factor, e.g., zebrafish FoxI1. The bound fragments in hundreds of positive clones are sequenced and retested for their binding activities using a colony PCR and sequencing strategy. The resulting tools allow for rapid and genomic-wide identification of transcriptional binding targets.
Collapse
Affiliation(s)
- Jizhou Yan
- Institute for Marine Biosystem and Neurosciences, Department of Hydrobiology, Shanghai Ocean University, College of Fisheries and Life Sciences, Lingang New City, Shanghai, China
| | | |
Collapse
|
14
|
Abstract
MicroRNAs (miRNAs) are a class of posttranscriptional regulators that have recently introduced an additional level of intricacy to our understanding of gene regulation. There are currently over 10,000 miRNAs that have been identified in a range of species including metazoa, mycetozoa, viridiplantae, and viruses, of which 940, to date, are found in humans. It is estimated that more than 60% of human protein-coding genes harbor miRNA target sites in their 3′ untranslated region and, thus, are potentially regulated by these molecules in health and disease. This review will first briefly describe the discovery, structure, and mode of function of miRNAs in mammalian cells, before elaborating on their roles and significance during development and pathogenesis in the various mammalian organs, while attempting to reconcile their functions with our existing knowledge of their targets. Finally, we will summarize some of the advances made in utilizing miRNAs in therapeutics.
Collapse
Affiliation(s)
- Danish Sayed
- Cardiovascular Research Institute, Department of Cell Biology and Molecular Medicine, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - Maha Abdellatif
- Cardiovascular Research Institute, Department of Cell Biology and Molecular Medicine, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| |
Collapse
|
15
|
Xie Z, Hu S, Qian J, Blackshaw S, Zhu H. Systematic characterization of protein-DNA interactions. Cell Mol Life Sci 2011; 68:1657-68. [PMID: 21207099 PMCID: PMC11115113 DOI: 10.1007/s00018-010-0617-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 11/29/2010] [Accepted: 12/16/2010] [Indexed: 12/13/2022]
Abstract
Sequence-specific protein-DNA interactions (PDIs) are critical for regulating many cellular processes, including transcription, DNA replication, repair, and rearrangement. We review recent experimental advances in high-throughput technologies designed to characterize PDIs and discuss recent studies that use these tools, including ChIP-chip/seq, SELEX-based approaches, yeast one-hybrid, bacterial one-hybrid, protein binding microarray, and protein microarray. The results of these studies have challenged some long-standing concepts of PDI and provide valuable insights into the complex transcriptional regulatory networks.
Collapse
Affiliation(s)
- Zhi Xie
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Present Address: The Center for Human Immunology, National Institutes of Health, Bethesda, MD USA
| | - Shaohui Hu
- The Center for High-Throughput Biology, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD USA
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Seth Blackshaw
- The Center for High-Throughput Biology, Johns Hopkins University School of Medicine, Baltimore, MD USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Heng Zhu
- The Center for High-Throughput Biology, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD USA
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Room 333, BRB, 733 N. Broadway, 21205 Baltimore, MD USA
| |
Collapse
|
16
|
Pan Y, Nussinov R. Lysine120 interactions with p53 response elements can allosterically direct p53 organization. PLoS Comput Biol 2010; 6:e1000878. [PMID: 20700496 PMCID: PMC2916859 DOI: 10.1371/journal.pcbi.1000878] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2010] [Accepted: 07/08/2010] [Indexed: 01/02/2023] Open
Abstract
p53 can serve as a paradigm in studies aiming to figure out how allosteric perturbations in transcription factors (TFs) triggered by small changes in DNA response element (RE) sequences, can spell selectivity in co-factor recruitment. p53-REs are 20-base pair (bp) DNA segments specifying diverse functions. They may be located near the transcription start sites or thousands of bps away in the genome. Their number has been estimated to be in the thousands, and they all share a common motif. A key question is then how does the p53 protein recognize a particular p53-RE sequence among all the similar ones? Here, representative p53-REs regulating diverse functions including cell cycle arrest, DNA repair, and apoptosis were simulated in explicit solvent. Among the major interactions between p53 and its REs involving Lys120, Arg280 and Arg248, the bps interacting with Lys120 vary while the interacting partners of other residues are less so. We observe that each p53-RE quarter site sequence has a unique pattern of interactions with p53 Lys120. The allosteric, DNA sequence-induced conformational and dynamic changes of the altered Lys120 interactions are amplified by the perturbation of other p53-DNA interactions. The combined subtle RE sequence-specific allosteric effects propagate in the p53 and in the DNA. The resulting amplified allosteric effects far away are reflected in changes in the overall p53 organization and in the p53 surface topology and residue fluctuations which play key roles in selective co-factor recruitment. As such, these observations suggest how similar p53-RE sequences can spell the preferred co-factor binding, which is the key to the selective gene transactivation and consequently different functional effects.
Collapse
Affiliation(s)
- Yongping Pan
- Basic Science Program, Science Applications International Corporation-Frederick, Inc., Center for Cancer Research Nanobiology Program, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Ruth Nussinov
- Basic Science Program, Science Applications International Corporation-Frederick, Inc., Center for Cancer Research Nanobiology Program, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
17
|
Pan Y, Nussinov R. Preferred drifting along the DNA major groove and cooperative anchoring of the p53 core domain: mechanisms and scenarios. J Mol Recognit 2010; 23:232-40. [PMID: 19856322 DOI: 10.1002/jmr.990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
While the importance of specific p53-DNA binding is broadly accepted, the recognition process is still not fully understood. Figuring out the initial tetrameric p53-DNA association and the swift and cooperative search for specific binding sites is crucial for understanding the transactivation mechanism and selectivity. To gain insight into the p53-DNA binding process, here we have carried out explicit solvent molecular dynamic (MD) simulations of several p53 core domain-DNA conformations with the p53 and the DNA separated by varying distances. p53 approached the DNA, bound non-specifically, and quickly drifted along the DNA surface to find the major groove, cooperatively anchoring in a way similar to the specific binding observed in the crystal structure. Electrostatics was the major driving force behind the p53 movement. Mechanistically, this is a cooperative process: key residues, particularly Lys120 and Arg280 acted as sensors; upon finding their hydrogen-bonding partners, they lock in, anchoring p53 into the major groove. Concomitantly, the DNA adopted a conformation that facilitated p53 easy access. The initial non-specific core domain-DNA contacts assist in shifting the DNA and the p53 substrates toward conformations "ready" for specific major groove binding, with subsequent optimization of the interactions. This work is an invited contribution for the special issue of the Journal of Molecular Recognition dedicated to Professor Martin Karplus.
Collapse
Affiliation(s)
- Yongping Pan
- Basic Research Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA
| | | |
Collapse
|
18
|
Georges AB, Benayoun BA, Caburet S, Veitia RA. Generic binding sites, generic DNA‐binding domains: where does specific promoter recognition come from? FASEB J 2009; 24:346-56. [DOI: 10.1096/fj.09-142117] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Adrien B. Georges
- Unité Mixte de Recherche 7592‐Centre National de la Recherche ScientifiqueInstitut Jacques MonodParisFrance
| | - Berenice A. Benayoun
- Unité Mixte de Recherche 7592‐Centre National de la Recherche ScientifiqueInstitut Jacques MonodParisFrance
| | - Sandrine Caburet
- Unité Mixte de Recherche 7592‐Centre National de la Recherche ScientifiqueInstitut Jacques MonodParisFrance
| | - Reiner A. Veitia
- Unité Mixte de Recherche 7592‐Centre National de la Recherche ScientifiqueInstitut Jacques MonodParisFrance
| |
Collapse
|
19
|
Pan Y, Nussinov R. Cooperativity dominates the genomic organization of p53-response elements: a mechanistic view. PLoS Comput Biol 2009; 5:e1000448. [PMID: 19629163 PMCID: PMC2705680 DOI: 10.1371/journal.pcbi.1000448] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Accepted: 06/24/2009] [Indexed: 11/18/2022] Open
Abstract
p53-response elements (p53-REs) are organized as two repeats of a palindromic DNA segment spaced by 0 to 20 base pairs (bp). Several experiments indicate that in the vast majority of the human p53-REs there are no spacers between the two repeats; those with spacers, particularly with sizes beyond two nucleotides, are rare. This raises the question of what it indicates about the factors determining the p53-RE genomic organization. Clearly, given the double helical DNA conformation, the orientation of two p53 core domain dimers with respect to each other will vary depending on the spacer size: a small spacer of 0 to 2 bps will lead to the closest p53 dimer-dimer orientation; a 10-bp spacer will locate the p53 dimers on the same DNA face but necessitate DNA looping; while a 5-bp spacer will position the p53 dimers on opposite DNA faces. Here, via conformational analysis we show that when there are 0-2 bp spacers, p53-DNA binding is cooperative; however, cooperativity is greatly diminished when there are spacers with sizes beyond 2 bp. Cooperative binding is broadly recognized to be crucial for biological processes, including transcriptional regulation. Our results clearly indicate that cooperativity of the p53-DNA association dominates the genomic organization of the p53-REs, raising questions of the structural organization and functional roles of p53-REs with larger spacers. We further propose that a dynamic landscape scenario of p53 and p53-REs can better explain the selectivity of the degenerate p53-REs. Our conclusions bear on the evolutionary preference of the p53-RE organization and as such, are expected to have broad implications to other multimeric transcription factor response element organization.
Collapse
Affiliation(s)
- Yongping Pan
- Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, Maryland, United States of America
| | - Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
| |
Collapse
|
20
|
Mitsuda N, Ohme-Takagi M. Functional analysis of transcription factors in Arabidopsis. PLANT & CELL PHYSIOLOGY 2009; 50:1232-48. [PMID: 19478073 PMCID: PMC2709548 DOI: 10.1093/pcp/pcp075] [Citation(s) in RCA: 182] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Accepted: 05/26/2009] [Indexed: 05/17/2023]
Abstract
Transcription factors (TFs) regulate the expression of genes at the transcriptional level. Modification of TF activity dynamically alters the transcriptome, which leads to metabolic and phenotypic changes. Thus, functional analysis of TFs using 'omics-based' methodologies is one of the most important areas of the post-genome era. In this mini-review, we present an overview of Arabidopsis TFs and introduce strategies for the functional analysis of plant TFs, which include both traditional and recently developed technologies. These strategies can be assigned to five categories: bioinformatic analysis; analysis of molecular function; expression analysis; phenotype analysis; and network analysis for the description of entire transcriptional regulatory networks.
Collapse
Affiliation(s)
| | - Masaru Ohme-Takagi
- Research Institute of Genome-Based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), Central 4, Higashi 1-1-1, Tsukuba, 305-8562 Japan
| |
Collapse
|
21
|
Middelbos IS, Vester BM, Karr-Lilienthal LK, Schook LB, Swanson KS. Age and diet affect gene expression profile in canine skeletal muscle. PLoS One 2009; 4:e4481. [PMID: 19221602 PMCID: PMC2637985 DOI: 10.1371/journal.pone.0004481] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Accepted: 01/07/2009] [Indexed: 11/19/2022] Open
Abstract
We evaluated gene transcription in canine skeletal muscle (biceps femoris) using microarray analysis to identify effects of age and diet on gene expression. Twelve female beagles were used (six 1-year olds and six 12-year olds) and they were fed one of two experimental diets for 12 months. One diet contained primarily plant-based protein sources (PPB), whereas the second diet contained primarily animal-based protein sources (APB). Affymetrix GeneChip Canine Genome Arrays were used to hybridize extracted RNA. Age had the greatest effect on gene transcription (262 differentially expressed genes), whereas the effect of diet was relatively small (22 differentially expressed genes). Effects of age (regardless of diet) were most notable on genes related to metabolism, cell cycle and cell development, and transcription function. All these genes were predominantly down-regulated in geriatric dogs. Age-affected genes that were differentially expressed on only one of two diets were primarily noted in the PPB diet group (144/165 genes). Again, genes related to cell cycle (22/35) and metabolism (15/19) had predominantly decreased transcription in geriatric dogs, but 6/8 genes related to muscle development had increased expression. Effects of diet on muscle gene expression were mostly noted in geriatric dogs, but no consistent patterns in transcription were observed. The insight these data provide into gene expression profiles of canine skeletal muscle as affected by age, could serve as a foundation for future research pertaining to age-related muscle diseases.
Collapse
Affiliation(s)
- Ingmar S. Middelbos
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Brittany M. Vester
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Lisa K. Karr-Lilienthal
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Lawrence B. Schook
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
- Division of Nutritional Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Kelly S. Swanson
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
- Division of Nutritional Sciences, University of Illinois, Urbana, Illinois, United States of America
- Department of Veterinary Clinical Medicine, University of Illinois, Urbana, Illinois, United States of America
| |
Collapse
|
22
|
Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
23
|
Smeenk L, van Heeringen SJ, Koeppel M, van Driel MA, Bartels SJJ, Akkers RC, Denissov S, Stunnenberg HG, Lohrum M. Characterization of genome-wide p53-binding sites upon stress response. Nucleic Acids Res 2008; 36:3639-54. [PMID: 18474530 PMCID: PMC2441782 DOI: 10.1093/nar/gkn232] [Citation(s) in RCA: 172] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The tumor suppressor p53 is a sequence-specific transcription factor, which regulates the expression of target genes involved in different stress responses. To understand p53's essential transcriptional functions, unbiased analysis of its DNA-binding repertoire is pivotal. In a genome-wide tiling ChIP-on-chip approach, we have identified and characterized 1546 binding sites of p53 upon Actinomycin D treatment. Among those binding sites were known as well as novel p53 target sites, which included regulatory regions of potentially novel transcripts. Using this collection of genome-wide binding sites, a new high-confidence algorithm was developed, p53scan, to identify the p53 consensus-binding motif. Strikingly, this motif was present in the majority of all bound sequences with 83% of all binding sites containing the motif. In the surrounding sequences of the binding sites, several motifs for potential regulatory cobinders were identified. Finally, we show that the majority of the genome-wide p53 target sites can also be bound by overexpressed p63 and p73 in vivo, suggesting that they can possibly play an important role at p53 binding sites. This emphasizes the possible interplay of p53 and its family members in the context of target gene binding. Our study greatly expands the known, experimentally validated p53 binding site repertoire and serves as a valuable knowledgebase for future research.
Collapse
Affiliation(s)
- Leonie Smeenk
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | | | | | | | | | | | | | | | | |
Collapse
|