1
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Liu WT, Chen CC, Ji DD, Tu WC. The cecropin-prophenoloxidase regulatory mechanism is a cross-species physiological function in mosquitoes. iScience 2022; 25:104478. [PMID: 35712072 PMCID: PMC9194137 DOI: 10.1016/j.isci.2022.104478] [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: 09/29/2021] [Revised: 04/06/2022] [Accepted: 05/25/2022] [Indexed: 11/06/2022] Open
Abstract
This study's aim was to investigate whether the cecropin-prophenoloxidase regulatory mechanism is a cross-species physiological function among mosquitoes. BLAST and phylogenetic analysis revealed that three mosquito cecropin Bs, namely Aedes albopictus cecropin B (Aalcec B), Armigeres subalbatus cecropin B2 (Ascec B2), and Culex quinquefasciatus cecropin B1 (Cqcec B1), play crucial roles in cuticle formation during pupal development via the regulation of prophenoloxidase 3 (PPO 3). The effects of cecropin B knockdown were rescued in a cross-species manner by injecting synthetic cecropin B peptide into pupae. Further investigations showed that these three cecropin B peptides bind to TTGG(A/C)A motifs within each of the PPO 3 DNA fragments obtained from these three mosquitoes. These results suggest that Aalcec B, Ascec B2, and Cqcec B1 each play an important role as a transcription factor in cuticle formation and that similar cecropin-prophenoloxidase regulatory mechanisms exist in multiple mosquito species. Cecropin B is able to regulate PPO 3 expression in the pupae Cecropin B binds to TTGG(A/C)A motifs within the PPO 3 DNA The knockdown of cecropin B was rescued by sequence-similar cecropin B peptides The cecropin B-prophenoloxidase 3 regulatory mechanism is conserved in mosquitoes
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2
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Nuclear factor I-C disrupts cellular homeostasis between autophagy and apoptosis via miR-200b-Ambra1 in neural tube defects. Cell Death Dis 2021; 13:17. [PMID: 34930914 PMCID: PMC8688449 DOI: 10.1038/s41419-021-04473-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/25/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023]
Abstract
Impaired autophagy and excessive apoptosis disrupt cellular homeostasis and contribute to neural tube defects (NTDs), which are a group of fatal and disabling birth defects caused by the failure of neural tube closure during early embryonic development. However, the regulatory mechanisms underlying NTDs and outcomes remain elusive. Here, we report the role of the transcription factor nuclear factor I-C (NFIC) in maintaining cellular homeostasis in NTDs. We demonstrated that abnormally elevated levels of NFIC in a mouse model of NTDs can interact with the miR-200b promoter, leading to the activation of the transcription of miR-200b, which plays a critical role in NTD formation, as reported in our previous study. Furthermore, miR-200b represses autophagy and triggers apoptosis by directly targeting the autophagy-related gene Ambra1 (Autophagy/Beclin1 regulator 1). Notably, miR-200b inhibitors mitigate the unexpected effects of NFIC on autophagy and apoptosis. Collectively, these results indicate that the NFIC-miR-200b-Ambra1 axis, which integrates transcription- and epigenome-regulated miRNAs and an autophagy regulator, disrupts cellular homeostasis during the closure of the neural tube, and may provide new insight into NTD pathogenesis.
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3
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Barnes SN, Wram CL, Mitchum MG, Baum TJ. The plant-parasitic cyst nematode effector GLAND4 is a DNA-binding protein. MOLECULAR PLANT PATHOLOGY 2018; 19:2263-2276. [PMID: 29719112 PMCID: PMC6637993 DOI: 10.1111/mpp.12697] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/23/2018] [Accepted: 04/30/2018] [Indexed: 05/24/2023]
Abstract
Cyst nematodes are plant pathogens that infect a wide range of economically important crops. One parasitic mechanism employed by cyst nematodes is the production and in planta delivery of effector proteins to modify plant cells and suppress defences to favour parasitism. This study focuses on GLAND4, an effector of Heterodera glycines and H. schachtii, the soybean and sugar beet cyst nematodes, respectively. We show that GLAND4 is recognized by the plant cellular machinery and is transported to the plant nucleus, an organelle for which little is known about plant nematode effector functions. We show that GLAND4 has DNA-binding ability and represses reporter gene expression in a plant transcriptional assay. One DNA fragment that binds to GLAND4 is localized in an Arabidopsis chromosomal region associated with the promoters of two lipid transfer protein genes (LTP). These LTPs have known defence functions and are down-regulated in the nematode feeding site. When expressed in Arabidopsis, the presence of GLAND4 causes the down-regulation of the two LTP genes in question, which is also associated with increased susceptibility to the plant-pathogenic bacterium Pseudomonas syringae. Furthermore, overexpression of one of the LTP genes reduces plant susceptibility to H. schachtii and P. syringae, confirming that LTP repression probably suppresses plant defences. This study makes GLAND4 one of a small subset of characterized plant nematode nuclear effectors and identifies GLAND4 as the first DNA-binding, plant-parasitic nematode effector.
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Affiliation(s)
- Stacey N. Barnes
- Plant Pathology & Microbiology DepartmentIowa State UniversityAmesIA 50011USA
| | - Catherine L. Wram
- Plant Pathology & Microbiology DepartmentIowa State UniversityAmesIA 50011USA
- Present address:
Department of Botany and Plant PathologyOregon State UniversityCorvallisOR 97330USA
| | - Melissa G. Mitchum
- Division of Plant Sciences and Bond Life Sciences CenterUniversity of MissouriColumbiaMO 65211USA
| | - Thomas J. Baum
- Plant Pathology & Microbiology DepartmentIowa State UniversityAmesIA 50011USA
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Krause MW, Love DC, Ghosh SK, Wang P, Yun S, Fukushige T, Hanover JA. Nutrient-Driven O-GlcNAcylation at Promoters Impacts Genome-Wide RNA Pol II Distribution. Front Endocrinol (Lausanne) 2018; 9:521. [PMID: 30250452 PMCID: PMC6139338 DOI: 10.3389/fendo.2018.00521] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/21/2018] [Indexed: 01/07/2023] Open
Abstract
Nutrient-driven O-GlcNAcylation has been linked to epigenetic regulation of gene expression in metazoans. In C. elegans, O-GlcNAc marks the promoters of over 800 developmental, metabolic, and stress-related genes; these O-GlcNAc marked genes show a strong 5', promoter-proximal bias in the distribution of RNA Polymerase II (Pol II). In response to starvation or feeding, the steady state distribution of O-GlcNAc at promoters remain nearly constant presumably due to dynamic cycling mediated by the transferase OGT-1 and the O-GlcNAcase OGA-1. However, in viable mutants lacking either of these enzymes of O-GlcNAc metabolism, the nutrient-responsive GlcNAcylation of promoters is dramatically altered. Blocked O-GlcNAc cycling leads to a striking nutrient-dependent accumulation of O-GlcNAc on RNA Pol II. O-GlcNAc cycling mutants also show an exaggerated, nutrient-responsive redistribution of promoter-proximal RNA Pol II isoforms and extensive transcriptional deregulation. Our findings suggest a complex interplay between the O-GlcNAc modification at promoters, the kinase-dependent "CTD-code," and co-factors regulating RNA Pol II dynamics. Nutrient-responsive O-GlcNAc cycling may buffer the transcriptional apparatus from dramatic swings in nutrient availability by modulating promoter activity to meet metabolic and developmental needs.
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Affiliation(s)
- Michael W. Krause
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Dona C. Love
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Salil K. Ghosh
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Peng Wang
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Sijung Yun
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Tetsunari Fukushige
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - John A. Hanover
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: John A. Hanover
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5
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Liu WT, Tu WC, Lin CH, Yang UC, Chen CC. Involvement of cecropin B in the formation of the Aedes aegypti mosquito cuticle. Sci Rep 2017; 7:16395. [PMID: 29180688 PMCID: PMC5703890 DOI: 10.1038/s41598-017-16625-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 11/15/2017] [Indexed: 01/13/2023] Open
Abstract
In this study, we found a mosquito antimicrobial peptide (AMP), Aedes aegypti cecropin B (Aacec B), was expressed constitutively in pupae. Knockdown in the pupae of Aacec B using double-stranded RNA (dsRNA) resulted in high mortality, the emergence of deformed adults and an impairment of pharate adult cuticle formation with fewer lamellae being deposited and the helicoidal pattern of the chitin microfibrils being disorganized. Simultaneous injection of Aacec B dsRNA and Aacec B peptide into pupae significantly reduced this mortality and no deformed adults then emerged. The expression levels of Ae. aegypti prophenoloxidase (AaPPO) 3 and AaPPO 4 were significantly reduced in the Aacec B knockdown pupae. Exogenous Aacec B peptide significantly enhanced the transcription of AaPPO 3 in pupae. Knockdown of AaPPO 3 in pupae caused effects similar to Aacec B-knockdown. The Aacec B peptide could be detected in both the cytoplasm and nuclei of pupal cells and was able to bind to the TTGG(A/C)A motif in AaPPO 3 DNA both in vitro and in vivo. These findings suggest that Aacec B plays a crucial role in pharate adult cuticle formation via the regulation of AaPPO 3 gene expression in pupae.
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Affiliation(s)
- Wei-Ting Liu
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, 112, Taiwan, ROC
| | - Wu-Chun Tu
- Department of Entomology, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Chao-Hsiung Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, 112, Taiwan, ROC
| | - Ueng-Cheng Yang
- Institute of Biomedical Informatics, National Yang-Ming University, National Yang-Ming University, Taipei, 112, Taiwan, ROC
| | - Cheng-Chen Chen
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, 112, Taiwan, ROC.
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6
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Reverse engineering highlights potential principles of large gene regulatory network design and learning. NPJ Syst Biol Appl 2017. [PMID: 28649444 PMCID: PMC5481436 DOI: 10.1038/s41540-017-0019-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Inferring transcriptional gene regulatory networks from transcriptomic datasets is a key challenge of systems biology, with potential impacts ranging from medicine to agronomy. There are several techniques used presently to experimentally assay transcription factors to target relationships, defining important information about real gene regulatory networks connections. These techniques include classical ChIP-seq, yeast one-hybrid, or more recently, DAP-seq or target technologies. These techniques are usually used to validate algorithm predictions. Here, we developed a reverse engineering approach based on mathematical and computer simulation to evaluate the impact that this prior knowledge on gene regulatory networks may have on training machine learning algorithms. First, we developed a gene regulatory networks-simulating engine called FRANK (Fast Randomizing Algorithm for Network Knowledge) that is able to simulate large gene regulatory networks (containing 104 genes) with characteristics of gene regulatory networks observed in vivo. FRANK also generates stable or oscillatory gene expression directly produced by the simulated gene regulatory networks. The development of FRANK leads to important general conclusions concerning the design of large and stable gene regulatory networks harboring scale free properties (built ex nihilo). In combination with supervised (accepting prior knowledge) support vector machine algorithm we (i) address biologically oriented questions concerning our capacity to accurately reconstruct gene regulatory networks and in particular we demonstrate that prior-knowledge structure is crucial for accurate learning, and (ii) draw conclusions to inform experimental design to performed learning able to solve gene regulatory networks in the future. By demonstrating that our predictions concerning the influence of the prior-knowledge structure on support vector machine learning capacity holds true on real data (Escherichia coli K14 network reconstruction using network and transcriptomic data), we show that the formalism used to build FRANK can to some extent be a reasonable model for gene regulatory networks in real cells. This work by Carré et al addresses central questions in biology, which are: how very large gene regulatory networks (GRNs) are organized, generate stable gene expression, and can be learnt using machine learning algorithms? In this work authors developed an algorithm able to simulate large GRNs. From these networks they simulate stable or oscillating gene expression and highlights some mathematical rules controlling such a collective (several thousands of genes) behavior. They discuss consequent hypothesis concerning the organization of GRNs in real cells. Using this simulation tool, authors also demonstrate that it’s likely possible to computationally learn GRNs from transcriptomic data and prior knowledge on the network (actual known connections issued from Yeast One Hybrid or ChIP Seq for instance). They particularly highlight the crucial importance of the prior knowledge structure in their capacity to learn large GRNs.
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7
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Romanovskaya EV, Vikhnina MV, Grishina TV, Ivanov MP, Leonova LE, Tsvetkova EV. Transcription factors of the NF1 family: Possible mechanisms of inducible gene expression in the evolutionary lineage of multicellular animals. J EVOL BIOCHEM PHYS+ 2017. [DOI: 10.1134/s123456781702001x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Yang L, Orenstein Y, Jolma A, Yin Y, Taipale J, Shamir R, Rohs R. Transcription factor family-specific DNA shape readout revealed by quantitative specificity models. Mol Syst Biol 2017; 13:910. [PMID: 28167566 PMCID: PMC5327724 DOI: 10.15252/msb.20167238] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Transcription factors (TFs) achieve DNA‐binding specificity through contacts with functional groups of bases (base readout) and readout of structural properties of the double helix (shape readout). Currently, it remains unclear whether DNA shape readout is utilized by only a few selected TF families, or whether this mechanism is used extensively by most TF families. We resequenced data from previously published HT‐SELEX experiments, the most extensive mammalian TF–DNA binding data available to date. Using these data, we demonstrated the contributions of DNA shape readout across diverse TF families and its importance in core motif‐flanking regions. Statistical machine‐learning models combined with feature‐selection techniques helped to reveal the nucleotide position‐dependent DNA shape readout in TF‐binding sites and the TF family‐specific position dependence. Based on these results, we proposed novel DNA shape logos to visualize the DNA shape preferences of TFs. Overall, this work suggests a way of obtaining mechanistic insights into TF–DNA binding without relying on experimentally solved all‐atom structures.
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Affiliation(s)
- Lin Yang
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA, USA
| | - Yaron Orenstein
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Arttu Jolma
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Yimeng Yin
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jussi Taipale
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Remo Rohs
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA, USA
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9
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Yang Y, Chi Y, Wang Z, Zhou Y, Fan B, Chen Z. Functional analysis of structurally related soybean GmWRKY58 and GmWRKY76 in plant growth and development. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4727-42. [PMID: 27335454 PMCID: PMC4973743 DOI: 10.1093/jxb/erw252] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
WRKY transcription factors constitute a large protein superfamily with a predominant role in plant stress responses. In this study we report that two structurally related soybean WRKY proteins, GmWRKY58 and GmWRKY76, play a critical role in plant growth and flowering. GmWRKY58 and GmWRKY76 are both Group III WRKY proteins with a C2HC zinc finger domain and are close homologs of AtWRKY70 and AtWRKY54, two well-characterized Arabidopsis WRKY proteins with an important role in plant responses to biotic and abiotic stresses. GmWRKY58 and GmWRKY76 are both localized to the nucleus, recognize the TTGACC W-box sequence with a high specificity, and function as transcriptional activators in both yeast and plant cells. Expression of GmWRKY58 and GmWRKY76 was detected at low levels in roots, stem, leaves, flowers, and pods. Expression of the two genes in leaves increased substantially during the first 4 weeks after germination but steadily declined thereafter with increased age. To determine their biological functions, transgenic Arabidopsis plants were generated overexpressing GmWRKY58 or GmWRKY76 Unlike AtWRKY70 and AtWRKY54, overexpression of GmWRKY58 or GmWRKY76 had no effect on disease resistance and only small effects on abiotic stress tolerance of the transgenic plants. Significantly, transgenic Arabidopsis plants overexpressing GmWRKY58 or GmWRKY76 flowered substantially earlier than control plants and this early flowering phenotype was associated with increased expression of several flowering-promoting genes, some of which are enriched in W-box sequences in their promoters recognized by GmWRKY58 and GmWRKY76. In addition, virus-induced silencing of GmWRKY58 and GmWRKY76 in soybean resulted in stunted plants with reduced leaf expansion and terminated stem growth. These results provide strong evidence for functional divergence among close structural homologs of WRKY proteins from different plant species.
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Affiliation(s)
- Yan Yang
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou 310058, China
| | - Yingjun Chi
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou 310058, China
| | - Ze Wang
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou 310058, China
| | - Yuan Zhou
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou 310058, China
| | - Baofang Fan
- Department of Botany and Plant Pathology, 915W. State Street, Purdue University, West Lafayette, IN 47907, USA
| | - Zhixiang Chen
- Department of Horticulture, Zijingang Campus, 866 Yuhangtang Road, Zhejiang University, Hangzhou 310058, China Department of Botany and Plant Pathology, 915W. State Street, Purdue University, West Lafayette, IN 47907, USA
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10
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He X, Tillo D, Vierstra J, Syed KS, Deng C, Ray GJ, Stamatoyannopoulos J, FitzGerald PC, Vinson C. Methylated Cytosines Mutate to Transcription Factor Binding Sites that Drive Tetrapod Evolution. Genome Biol Evol 2015; 7:3155-69. [PMID: 26507798 PMCID: PMC4994754 DOI: 10.1093/gbe/evv205] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In mammals, the cytosine in CG dinucleotides is typically methylated producing
5-methylcytosine (5mC), a chemically less stable form of cytosine that can spontaneously
deaminate to thymidine resulting in a T•G mismatched base pair. Unlike other eukaryotes
that efficiently repair this mismatched base pair back to C•G, in mammals, 5mCG
deamination is mutagenic, sometimes producing TG dinucleotides, explaining the depletion
of CG dinucleotides in mammalian genomes. It was suggested that new TG dinucleotides
generate genetic diversity that may be critical for evolutionary change. We tested this
conjecture by examining the DNA sequence properties of regulatory sequences identified by
DNase I hypersensitive sites (DHSs) in human and mouse genomes. We hypothesized that the
new TG dinucleotides generate transcription factor binding sites (TFBS) that become
tissue-specific DHSs (TS-DHSs). We find that 8-mers containing the CG dinucleotide are
enriched in DHSs in both species. However, 8-mers containing a TG and no CG dinucleotide
are preferentially enriched in TS-DHSs when compared with 8-mers with neither a TG nor a
CG dinucleotide. The most enriched 8-mer with a TG and no CG dinucleotide in
tissue-specific regulatory regions in both genomes is the AP-1 motif
(TGAC/GTCAN), and we find evidence that
TG dinucleotides in the AP-1 motif arose from CG dinucleotides. Additional TS-DHS-enriched
TFBS containing the TG/CA dinucleotide are the E-Box motif
(GCAGCTGC), the NF-1 motif (GGCA—TGCC), and the
GR (glucocorticoid receptor) motif (G-ACA—TGT-C). Our results support the
suggestion that cytosine methylation is mutagenic in tetrapods producing TG dinucleotides
that create TFBS that drive evolution.
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Affiliation(s)
- Ximiao He
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Desiree Tillo
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jeff Vierstra
- Department of Genome Sciences, University of Washington
| | - Khund-Sayeed Syed
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Callie Deng
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - G Jordan Ray
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Peter C FitzGerald
- Genome Analysis Unit, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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11
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MacNeil LT, Pons C, Arda HE, Giese GE, Myers CL, Walhout AJM. Transcription Factor Activity Mapping of a Tissue-Specific in vivo Gene Regulatory Network. Cell Syst 2015; 1:152-162. [PMID: 26430702 DOI: 10.1016/j.cels.2015.08.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A wealth of physical interaction data between transcription factors (TFs) and DNA has been generated, but these interactions often do not have apparent regulatory consequences. Thus, equating physical interaction data with gene regulatory networks (GRNs) is problematic. Here, we comprehensively assay TF activity, rather than binding, to construct a network of gene regulatory interactions in the C. elegans intestine. By manually observing the in vivo tissue-specific knockdown of 921 TFs on a panel of 19 fluorescent transcriptional reporters, we identified a GRN of 411 interactions between 19 promoters and 177 TFs. This GRN shows only modest overlap with physical interactions, indicating that many regulatory interactions are indirect. We applied nested effects modeling to uncover information flow between TFs in the intestine that converges on a small set of physical TF-promoter interactions. We found numerous cell nonautonomous regulatory interactions, illustrating tissue-to-tissue communication. Altogether, our study illuminates the complexity of gene regulation in the context of a living animal.
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Affiliation(s)
- Lesley T MacNeil
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA ; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Carles Pons
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA
| | - H Efsun Arda
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA ; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Gabrielle E Giese
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA
| | - Albertha J M Walhout
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA ; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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12
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Nussinov R, Tsai CJ, Liu J. Principles of allosteric interactions in cell signaling. J Am Chem Soc 2014; 136:17692-701. [PMID: 25474128 PMCID: PMC4291754 DOI: 10.1021/ja510028c] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Indexed: 02/07/2023]
Abstract
Linking cell signaling events to the fundamental physicochemical basis of the conformational behavior of single molecules and ultimately to cellular function is a key challenge facing the life sciences. Here we outline the emerging principles of allosteric interactions in cell signaling, with emphasis on the following points. (1) Allosteric efficacy is not a function of the chemical composition of the allosteric pocket but reflects the extent of the population shift between the inactive and active states. That is, the allosteric effect is determined by the extent of preferred binding, not by the overall binding affinity. (2) Coupling between the allosteric and active sites does not decide the allosteric effect; however, it does define the propagation pathways, the allosteric binding sites, and key on-path residues. (3) Atoms of allosteric effectors can act as "driver" or "anchor" and create attractive "pulling" or repulsive "pushing" interactions. Deciphering, quantifying, and integrating the multiple co-occurring events present daunting challenges to our scientific community.
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Affiliation(s)
- Ruth Nussinov
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research,
National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler
Institute of Molecular Medicine, Department of Human Genetics and
Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chung-Jung Tsai
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research,
National Cancer Institute, Frederick, Maryland 21702, United States
| | - Jin Liu
- Department
of Biophysics, University of Texas Southwestern
Medical Center, 5323
Harry Hines Boulevard, Dallas, Texas 75390, United
States
- Department
of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4),
and Center for Scientific Computation, Southern
Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275, United
States
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13
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Afek A, Lukatsky DB. Positive and negative design for nonconsensus protein-DNA binding affinity in the vicinity of functional binding sites. Biophys J 2014; 105:1653-60. [PMID: 24094406 DOI: 10.1016/j.bpj.2013.08.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Revised: 08/04/2013] [Accepted: 08/26/2013] [Indexed: 01/01/2023] Open
Abstract
Recent experiments provide an unprecedented view of protein-DNA binding in yeast and human genomes at single-nucleotide resolution. These measurements, performed over large cell populations, show quite generally that sequence-specific transcription regulators with well-defined protein-DNA consensus motifs bind only a fraction among all consensus motifs present in the genome. Alternatively, proteins in vivo often bind DNA regions lacking known consensus sequences. The rules determining whether a consensus motif is functional remain incompletely understood. Here we predict that genomic background surrounding specific protein-DNA binding motifs statistically modulates the binding of sequence-specific transcription regulators to these motifs. In particular, we show that nonconsensus protein-DNA binding in yeast is statistically enhanced, on average, around functional Reb1 motifs that are bound as compared to nonfunctional Reb1 motifs that are unbound. The landscape of nonconsensus protein-DNA binding around functional CTCF motifs in human demonstrates a more complex behavior. In particular, human genomic regions characterized by the highest CTCF occupancy, show statistically reduced level of nonconsensus protein-DNA binding. Our findings suggest that nonconsensus protein-DNA binding is fine-tuned around functional binding sites using a variety of design strategies.
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Affiliation(s)
- Ariel Afek
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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14
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Reinke V, Krause M, Okkema P. Transcriptional regulation of gene expression in C. elegans. ACTA ACUST UNITED AC 2013:1-34. [PMID: 23801596 DOI: 10.1895/wormbook.1.45.2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protein coding gene sequences are converted to mRNA by the highly regulated process of transcription. The precise temporal and spatial control of transcription for many genes is an essential part of development in metazoans. Thus, understanding the molecular mechanisms underlying transcriptional control is essential to understanding cell fate determination during embryogenesis, post-embryonic development, many environmental interactions, and disease-related processes. Studies of transcriptional regulation in C. elegans exploit its genomic simplicity and physical characteristics to define regulatory events with single-cell and minute-time-scale resolution. When combined with the genetics of the system, C. elegans offers a unique and powerful vantage point from which to study how chromatin-associated proteins and their modifications interact with transcription factors and their binding sites to yield precise control of gene expression through transcriptional regulation.
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Affiliation(s)
- Valerie Reinke
- Department of Genetics, Yale University, New Haven, CT 06520, USA.
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15
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Ihuegbu NE, Stormo GD, Buhler J. Fast, sensitive discovery of conserved genome-wide motifs. J Comput Biol 2012; 19:139-47. [PMID: 22300316 DOI: 10.1089/cmb.2011.0249] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Regulatory sites that control gene expression are essential to the proper functioning of cells, and identifying them is critical for modeling regulatory networks. We have developed Magma (Multiple Aligner of Genomic Multiple Alignments), a software tool for multiple species, multiple gene motif discovery. Magma identifies putative regulatory sites that are conserved across multiple species and occur near multiple genes throughout a reference genome. Magma takes as input multiple alignments that can include gaps. It uses efficient clustering methods that make it about 70 times faster than PhyloNet, a previous program for this task, with slightly greater sensitivity. We ran Magma on all non-coding DNA conserved between Caenorhabditis elegans and five additional species, about 70 Mbp in total, in <4 h. We obtained 2,309 motifs with lengths of 6-20 bp, each occurring at least 10 times throughout the genome, which collectively covered about 566 kbp of the genomes, approximately 0.8% of the input. Predicted sites occurred in all types of non-coding sequence but were especially enriched in the promoter regions. Comparisons to several experimental datasets show that Magma motifs correspond to a variety of known regulatory motifs.
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Affiliation(s)
- Nnamdi E Ihuegbu
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri 63108, USA
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16
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Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2012; 2:469-81. [PMID: 22540038 PMCID: PMC3337475 DOI: 10.1534/g3.111.001081] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 02/06/2012] [Indexed: 01/30/2023]
Abstract
Transcriptional regulation, a primary mechanism for controlling the development of multicellular organisms, is carried out by transcription factors (TFs) that recognize and bind to their cognate binding sites. In Caenorhabditis elegans, our knowledge of which genes are regulated by which TFs, through binding to specific sites, is still very limited. To expand our knowledge about the C. elegans regulatory network, we performed a comprehensive analysis of the C. elegans, Caenorhabditis briggsae, and Caenorhabditis remanei genomes to identify regulatory elements that are conserved in all genomes. Our analysis identified 4959 elements that are significantly conserved across the genomes and that each occur multiple times within each genome, both hallmarks of functional regulatory sites. Our motifs show significant matches to known core promoter elements, TF binding sites, splice sites, and poly-A signals as well as many putative regulatory sites. Many of the motifs are significantly correlated with various types of experimental data, including gene expression patterns, tissue-specific expression patterns, and binding site location analysis as well as enrichment in specific functional classes of genes. Many can also be significantly associated with specific TFs. Combinations of motif occurrences allow us to predict the location of cis-regulatory modules and we show that many of them significantly overlap experimentally determined enhancers. We provide access to the predicted binding sites, their associated motifs, and the predicted cis-regulatory modules across the whole genome through a web-accessible database and as tracks for genome browsers.
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17
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Van Nostrand EL, Kim SK. Seeing elegance in gene regulatory networks of the worm. Curr Opin Genet Dev 2011; 21:776-86. [PMID: 21963133 DOI: 10.1016/j.gde.2011.08.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 08/19/2011] [Indexed: 01/09/2023]
Abstract
There has been a recent explosion in the wealth of genomic data available to C. elegans researchers, as efforts to characterize gene expression and its regulators at a molecular level have borne significant fruit. Detailed measurement of gene expression at a variety of developmental stages, and in numerous individual tissues, has dramatically increased our understanding of cell-type-specific gene expression networks. Characterization of the targets of transcription factors, chromatin-binding proteins, and miRNAs has provided genome-wide insights into the mechanisms governing gene expression. Development of new techniques have allowed this characterization to begin to shift from whole-organism studies to tissue-level, and even single-cell-level profiling, creating a first glimpse into gene regulatory circuits at the single-cell level in a living organism. Integration of these datasets has yielded novel insights into evolution, gene expression regulation, and the link between sequence and phenotype.
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Affiliation(s)
- Eric L Van Nostrand
- Department of Genetics, Stanford University Medical Center, Stanford, CA, USA
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18
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Tabuchi TM, Deplancke B, Osato N, Zhu LJ, Barrasa MI, Harrison MM, Horvitz HR, Walhout AJM, Hagstrom KA. Chromosome-biased binding and gene regulation by the Caenorhabditis elegans DRM complex. PLoS Genet 2011; 7:e1002074. [PMID: 21589891 PMCID: PMC3093354 DOI: 10.1371/journal.pgen.1002074] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 03/25/2011] [Indexed: 01/28/2023] Open
Abstract
DRM is a conserved transcription factor complex that includes E2F/DP and pRB family proteins and plays important roles in development and cancer. Here we describe new aspects of DRM binding and function revealed through genome-wide analyses of the Caenorhabditis elegans DRM subunit LIN-54. We show that LIN-54 DNA-binding activity recruits DRM to promoters enriched for adjacent putative E2F/DP and LIN-54 binding sites, suggesting that these two DNA-binding moieties together direct DRM to its target genes. Chromatin immunoprecipitation and gene expression profiling reveals conserved roles for DRM in regulating genes involved in cell division, development, and reproduction. We find that LIN-54 promotes expression of reproduction genes in the germline, but prevents ectopic activation of germline-specific genes in embryonic soma. Strikingly, C. elegans DRM does not act uniformly throughout the genome: the DRM recruitment motif, DRM binding, and DRM-regulated embryonic genes are all under-represented on the X chromosome. However, germline genes down-regulated in lin-54 mutants are over-represented on the X chromosome. We discuss models for how loss of autosome-bound DRM may enhance germline X chromosome silencing. We propose that autosome-enriched binding of DRM arose in C. elegans as a consequence of germline X chromosome silencing and the evolutionary redistribution of germline-expressed and essential target genes to autosomes. Sex chromosome gene regulation may thus have profound evolutionary effects on genome organization and transcriptional regulatory networks.
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Affiliation(s)
- Tomoko M. Tabuchi
- Program in Molecular Medicine and Program in Cell Dynamics, University of
Massachusetts Medical School, Worcester, Massachusetts, United States of
America
| | - Bart Deplancke
- Program in Gene Function and Expression and Program in Molecular
Medicine, University of Massachusetts Medical School, Worcester, Massachusetts,
United States of America
| | - Naoki Osato
- Program in Gene Function and Expression and Program in Molecular
Medicine, University of Massachusetts Medical School, Worcester, Massachusetts,
United States of America
| | - Lihua J. Zhu
- Program in Gene Function and Expression and Program in Molecular
Medicine, University of Massachusetts Medical School, Worcester, Massachusetts,
United States of America
| | - M. Inmaculada Barrasa
- Program in Gene Function and Expression and Program in Molecular
Medicine, University of Massachusetts Medical School, Worcester, Massachusetts,
United States of America
| | - Melissa M. Harrison
- Howard Hughes Medical Institute, Department of Biology, Massachusetts
Institute of Technology, Cambridge, Massachusetts, United States of
America
| | - H. Robert Horvitz
- Howard Hughes Medical Institute, Department of Biology, Massachusetts
Institute of Technology, Cambridge, Massachusetts, United States of
America
| | - Albertha J. M. Walhout
- Program in Gene Function and Expression and Program in Molecular
Medicine, University of Massachusetts Medical School, Worcester, Massachusetts,
United States of America
| | - Kirsten A. Hagstrom
- Program in Molecular Medicine and Program in Cell Dynamics, University of
Massachusetts Medical School, Worcester, Massachusetts, United States of
America
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19
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Abstract
The Caenorhabditis elegans hermaphrodite is a complex multicellular animal that is composed of 959 somatic cells. The C. elegans genome contains ∼20,000 protein-coding genes, 940 of which encode regulatory transcription factors (TFs). In addition, the worm genome encodes more than 100 microRNAs and many other regulatory RNA and protein molecules. Most C. elegans genes are subject to regulatory control, most likely by multiple regulators, and combined, this dictates the activation or repression of the gene and corresponding protein in the relevant cells and under the appropriate conditions. A major goal in C. elegans research is to determine the spatiotemporal expression pattern of each gene throughout development and in response to different signals, and to determine how this expression pattern is accomplished. Gene regulatory networks describe physical and/or functional interactions between genes and their regulators that result in specific spatiotemporal gene expression. Such regulators can act at transcriptional or post-transcriptional levels. Here, I will discuss the methods that can be used to delineate gene regulatory networks in C. elegans. I will mostly focus on gene-centered yeast one-hybrid (Y1H) assays that are used to map interactions between non-coding genic regions, such as promoters, and regulatory TFs. The approaches discussed here are not only relevant to C. elegans biology, but can also be applied to other model organisms and humans.
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Affiliation(s)
- Albertha J.M. Walhout
- Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Phone: 508-856-4364
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20
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Gaudet J, McGhee JD. Recent advances in understanding the molecular mechanisms regulating C. elegans transcription. Dev Dyn 2010; 239:1388-404. [PMID: 20175193 DOI: 10.1002/dvdy.22246] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
We review recent studies that have advanced our understanding of the molecular mechanisms regulating transcription in the nematode C. elegans. Topics covered include: (i) general properties of C. elegans promoters; (ii) transcription factors and transcription factor combinations involved in cell fate specification and cell differentiation; (iii) new roles for general transcription factors; (iv) nucleosome positioning in C. elegans "chromatin"; and (v) some characteristics of histone variants and histone modifications and their possible roles in controlling C. elegans transcription.
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Affiliation(s)
- Jeb Gaudet
- Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Alberta, Canada
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21
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Identification of hookworm DAF-16/FOXO response elements and direct gene targets. PLoS One 2010; 5:e12289. [PMID: 20808816 PMCID: PMC2924398 DOI: 10.1371/journal.pone.0012289] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 07/29/2010] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The infective stage of the parasitic nematode hookworm is developmentally arrested in the environment and needs to infect a specific host to complete its life cycle. The canine hookworm (Ancylostoma caninum) is an excellent model for investigating human hookworm infections. The transcription factor of A. caninum, Ac-DAF-16, which has a characteristic fork head or "winged helix" DNA binding domain (DBD), has been implicated in the resumption of hookworm development in the host. However, the precise roles of Ac-DAF-16 in hookworm parasitism and its downstream targets are unknown. In the present study, we combined molecular techniques and bioinformatics to identify a group of Ac-DAF-16 binding sites and target genes. METHODOLOGY/PRINCIPAL FINDINGS The DNA binding domain of Ac-DAF-16 was used to select genomic fragments by in vitro genomic selection. Twenty four bound genomic fragments were analyzed for the presence of the DAF-16 family binding element (DBE) and possible alternative Ac-DAF-16 bind motifs. The 22 genes linked to these genomic fragments were identified using bioinformatics tools and defined as candidate direct gene targets of Ac-DAF-16. Their developmental stage-specific expression patterns were examined. Also, a new putative DAF-16 binding element was identified. CONCLUSIONS/SIGNIFICANCE Our results show that Ac-DAF-16 is involved in diverse biological processes throughout hookworm development. Further investigation of these target genes will provide insights into the molecular basis by which Ac-DAF-16 regulates its downstream gene network in hookworm infection.
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22
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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.
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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
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23
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Pan Y, Tsai CJ, Ma B, Nussinov R. Mechanisms of transcription factor selectivity. Trends Genet 2010; 26:75-83. [PMID: 20074831 PMCID: PMC7316385 DOI: 10.1016/j.tig.2009.12.003] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 12/08/2009] [Accepted: 12/10/2009] [Indexed: 10/20/2022]
Abstract
The initiation of transcription is regulated by transcription factors (TFs) binding to DNA response elements (REs). How do TFs recognize specific binding sites among the many similar ones available in the genome? Recent research has illustrated that even a single nucleotide substitution can alter the selective binding of TFs to coregulators, that prior binding events can lead to selective DNA binding, and that selectivity is influenced by the availability of binding sites in the genome. Here, we combine structural insights with recent genomics screens to address the problem of TF-DNA interaction specificity. The emerging picture of selective binding site sequence recognition and TF activation involves three major factors: the cellular network, protein and DNA as dynamic conformational ensembles and the tight packing of multiple TFs and coregulators on stretches of regulatory DNA. The classification of TF recognition mechanisms based on these factors impacts our understanding of how transcription initiation is regulated.
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Affiliation(s)
- Yongping Pan
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA
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24
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Armstrong KR, Chamberlin HM. Coordinate regulation of gene expression in the C. elegans excretory cell by the POU domain protein CEH-6. Mol Genet Genomics 2009; 283:73-87. [PMID: 19921263 DOI: 10.1007/s00438-009-0497-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 10/23/2009] [Indexed: 11/24/2022]
Abstract
Excretory renal organs are critical in animals for osmoregulation and the elimination of waste. Renal organs across a range of species exhibit cellular and molecular similarities. For example, class III POU-homeodomain transcription factors are expressed in the renal organs of many invertebrates and vertebrates. However, the functional role for these factors is not well characterized. To better understand the role of class III POU-homeodomain proteins in animal excretory systems, we have characterized a set of genes expressed in the Caenorhabditis elegans excretory cell, and determined their regulation by the POU-III transcription factor CEH-6. Our molecular and biochemical studies show that CEH-6 regulates a subset of genes expressed in the excretory cell. Additionally, we find that the CEH-6-dependent genes share two molecular features: they contain at least one octamer regulatory element and they encode for transport and channel proteins. This work suggests that a role for POU-III factors in renal organs is to coordinate the expression of a set of functionally related genes.
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Affiliation(s)
- Kristin R Armstrong
- Department of Molecular Genetics, Ohio State University, 938 Biological Sciences Building, 484 W. 12th Avenue, Columbus, OH 43210, USA
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