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Bandyopadhyay D, Mishra PP. Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy. Front Mol Biosci 2021; 8:725541. [PMID: 34540899 PMCID: PMC8446445 DOI: 10.3389/fmolb.2021.725541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/30/2021] [Indexed: 12/02/2022] Open
Abstract
In addition to the canonical double helix form, DNA is known to be extrapolated into several other secondary structural patterns involving themselves in inter- and intramolecular type hydrogen bonding. The secondary structures of nucleic acids go through several stages of multiple, complex, and interconvertible heterogeneous conformations. The journey of DNA through these conformers has significant importance and has been monitored thoroughly to establish qualitative and quantitative information about the transition between the unfolded, folded, misfolded, and partially folded states. During this structural interconversion, there always exist specific populations of intermediates, which are short-lived or sometimes even do not accumulate within a heterogeneous population and are challenging to characterize using conventional ensemble techniques. The single-molecule FRET(sm-FRET) microspectroscopic method has the advantages to overcome these limitations and monitors biological phenomena transpiring at a measurable high rate and balanced stochastically over time. Thus, tracing the time trajectory of a particular molecule enables direct measurement of the rate constant of each transition step, including the intermediates that are hidden in the ensemble level due to their low concentrations. This review is focused on the advantages of the employment of single-molecule Forster's resonance energy transfer (sm-FRET), which is worthwhile to access the dynamic architecture and structural transition of various secondary structures that DNA adopts, without letting the donor of one molecule to cross-talk with the acceptor of any other. We have emphasized the studies performed to explore the states of folding and unfolding of several nucleic acid secondary structures, for example, the DNA hairpin, Holliday junction, G-quadruplex, and i-motif.
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Affiliation(s)
- Debolina Bandyopadhyay
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India
- HBNI, Mumbai, India
| | - Padmaja P. Mishra
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India
- HBNI, Mumbai, India
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2
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van der Westhuizen D, Slabber CA, Fernandes MA, Joubert DF, Kleinhans G, van der Westhuizen CJ, Stander A, Munro OQ, Bezuidenhout DI. A Cytotoxic Bis(1,2,3-triazol-5-ylidene)carbazolide Gold(III) Complex Targets DNA by Partial Intercalation. Chemistry 2021; 27:8295-8307. [PMID: 33822431 PMCID: PMC8251726 DOI: 10.1002/chem.202100598] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Indexed: 12/13/2022]
Abstract
The syntheses of bis(triazolium)carbazole precursors and their corresponding coinage metal (Au, Ag) complexes are reported. For alkylated triazolium salts, di- or tetranuclear complexes with bridging ligands were isolated, while the bis(aryl) analogue afforded a bis(carbene) AuI -CNC pincer complex suitable for oxidation to the redox-stable [AuIII (CNC)Cl]+ cation. Although the ligand salt and the [AuIII (CNC)Cl]+ complex were both notably cytotoxic toward the breast cancer cell line MDA-MB-231, the AuIII complex was somewhat more selective. Electrophoresis, viscometry, UV-vis, CD and LD spectroscopy suggest the cytotoxic [AuIII (CNC)Cl]+ complex behaves as a partial DNA intercalator. In silico screening indicated that the [AuIII (CNC)Cl]+ complex can target DNA three-way junctions with good specificity, several other regular B-DNA forms, and Z-DNA. Multiple hydrophobic π-type interactions involving T and A bases appear to be important for B-form DNA binding, while phosphate O⋅⋅⋅Au interactions evidently underpin Z-DNA binding. The CNC ligand effectively stabilizes the AuIII ion, preventing reduction in the presence of glutathione. Both the redox stability and DNA affinity of the hit compound might be key factors underpinning its cytotoxicity in vitro.
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Affiliation(s)
| | - Cathryn A. Slabber
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
| | - Manuel A. Fernandes
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
| | - Daniël F. Joubert
- Department of PhysiologyUniversity of Pretoria0031PretoriaSouth Africa
| | - George Kleinhans
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
- Chemistry DepartmentUniversity of Pretoria0028PretoriaSouth Africa
| | - C. Johan van der Westhuizen
- Chemistry DepartmentUniversity of Pretoria0028PretoriaSouth Africa
- Future Production: ChemicalsPharmaceutical Technologies Research GroupCouncil for Scientific and Industrial Research (CSIR)0184PretoriaSouth Africa
| | - André Stander
- Department of PhysiologyUniversity of Pretoria0031PretoriaSouth Africa
| | - Orde Q. Munro
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
| | - Daniela I. Bezuidenhout
- Molecular Sciences InstituteSchool of ChemistryUniversity of the Witwatersrand2050JohannesburgSouth Africa
- Laboratory of Inorganic ChemistryEnvironmental and Chemical EngineeringUniversity of Oulu3000OuluFinland
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3
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Cruciform Formable Sequences within Pou5f1 Enhancer Are Indispensable for Mouse ES Cell Integrity. Int J Mol Sci 2021; 22:ijms22073399. [PMID: 33810223 PMCID: PMC8036336 DOI: 10.3390/ijms22073399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 01/04/2023] Open
Abstract
DNA can adopt various structures besides the B-form. Among them, cruciform structures are formed on inverted repeat (IR) sequences. While cruciform formable IRs (CFIRs) are sometimes found in regulatory regions of transcription, their function in transcription remains elusive, especially in eukaryotes. We found a cluster of CFIRs within the mouse Pou5f1 enhancer. Here, we demonstrate that this cluster or some member(s) plays an active role in the transcriptional regulation of not only Pou5f1, but also Sox2, Nanog, Klf4 and Esrrb. To clarify in vivo function of the cluster, we performed genome editing using mouse ES cells, in which each of the CFIRs was altered to the corresponding mirror repeat sequence. The alterations reduced the level of the Pou5f1 transcript in the genome-edited cell lines, and elevated those of Sox2, Nanog, Klf4 and Esrrb. Furthermore, transcription of non-coding RNAs (ncRNAs) within the enhancer was also upregulated in the genome-edited cell lines, in a similar manner to Sox2, Nanog, Klf4 and Esrrb. These ncRNAs are hypothesized to control the expression of these four pluripotency genes. The CFIRs present in the Pou5f1 enhancer seem to be important to maintain the integrity of ES cells.
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Alamro H, Alzamel M, Iliopoulos CS, Pissis SP, Watts S. IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences. BMC Bioinformatics 2021; 22:51. [PMID: 33549041 PMCID: PMC7866733 DOI: 10.1186/s12859-021-03983-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 01/27/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND An inverted repeat is a DNA sequence followed downstream by its reverse complement, potentially with a gap in the centre. Inverted repeats are found in both prokaryotic and eukaryotic genomes and they have been linked with countless possible functions. Many international consortia provide a comprehensive description of common genetic variation making alternative sequence representations, such as IUPAC encoding, necessary for leveraging the full potential of such broad variation datasets. RESULTS We present IUPACPAL, an exact tool for efficient identification of inverted repeats in IUPAC-encoded DNA sequences allowing also for potential mismatches and gaps in the inverted repeats. CONCLUSION Within the parameters that were tested, our experimental results show that IUPACPAL compares favourably to a similar application packaged with EMBOSS. We show that IUPACPAL identifies many previously unidentified inverted repeats when compared with EMBOSS, and that this is also performed with orders of magnitude improved speed.
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Affiliation(s)
- Hayam Alamro
- Department of Informatics, King’s College London, 30 Aldwych, London, UK
- Department of Information Systems, Princess Nourah bint Abdulrahman University, Riyadh, Kingdom of Saudi Arabia
| | - Mai Alzamel
- Department of Informatics, King’s College London, 30 Aldwych, London, UK
- Computer Science Department, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | | | - Solon P. Pissis
- Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
- Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Steven Watts
- Department of Informatics, King’s College London, 30 Aldwych, London, UK
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5
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Long P, Zhang L, Huang B, Chen Q, Liu H. Integrating genome sequence and structural data for statistical learning to predict transcription factor binding sites. Nucleic Acids Res 2020; 48:12604-12617. [PMID: 33264415 PMCID: PMC7736823 DOI: 10.1093/nar/gkaa1134] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/18/2020] [Accepted: 11/10/2020] [Indexed: 01/11/2023] Open
Abstract
We report an approach to predict DNA specificity of the tetracycline repressor (TetR) family transcription regulators (TFRs). First, a genome sequence-based method was streamlined with quantitative P-values defined to filter out reliable predictions. Then, a framework was introduced to incorporate structural data and to train a statistical energy function to score the pairing between TFR and TFR binding site (TFBS) based on sequences. The predictions benchmarked against experiments, TFBSs for 29 out of 30 TFRs were correctly predicted by either the genome sequence-based or the statistical energy-based method. Using P-values or Z-scores as indicators, we estimate that 59.6% of TFRs are covered with relatively reliable predictions by at least one of the two methods, while only 28.7% are covered by the genome sequence-based method alone. Our approach predicts a large number of new TFBs which cannot be correctly retrieved from public databases such as FootprintDB. High-throughput experimental assays suggest that the statistical energy can model the TFBSs of a significant number of TFRs reliably. Thus the energy function may be applied to explore for new TFBSs in respective genomes. It is possible to extend our approach to other transcriptional factor families with sufficient structural information.
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Affiliation(s)
- Pengpeng Long
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Lu Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bin Huang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Quan Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui 230026, China
| | - Haiyan Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui 230026, China
- School of Data Science, University of Science and Technology of China, Hefei, Anhui 230026, China
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6
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A reference catalog of DNA palindromes in the human genome and their variations in 1000 Genomes. Hum Genome Var 2020; 7:40. [PMID: 33298903 PMCID: PMC7680136 DOI: 10.1038/s41439-020-00127-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/24/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023] Open
Abstract
A palindrome in DNA is like a palindrome in language, but when read backwards, it is a complement of the forward sequence; effectively, the two halves of a sequence complement each other from its midpoint like in a double strand of DNA. Palindromes are distributed throughout the human genome and play significant roles in gene expression and regulation. Palindromic mutations are linked to many human diseases, such as neuronal disorders, mental retardation, and various cancers. In this work, we computed and analyzed the palindromic sequences in the human genome and studied their conservation in personal genomes using 1000 Genomes data. We found that ~30% of the palindromes exhibit variation, some of which are caused by rare variants. The analysis of disease/trait-associated single-nucleotide polymorphisms in palindromic regions showed that disease-associated risk variants are 14 times more likely to be present in palindromic regions than in other regions. The catalog of palindromes in the reference genome and 1000 Genomes is being made available here with details on their variations in each individual genome to serve as a resource for future and retrospective whole-genome studies identifying statistically significant palindrome variations associated with diseases or traits and their roles in disease mechanisms.
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7
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Liu X, Wu X, Tan H, Xie B, Deng Y. Large inverted repeats identified by intra-specific comparison of mitochondrial genomes provide insights into the evolution of Agrocybe aegerita. Comput Struct Biotechnol J 2020; 18:2424-2437. [PMID: 33005305 PMCID: PMC7508693 DOI: 10.1016/j.csbj.2020.08.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 11/29/2022] Open
Abstract
Genomic structure and content of Agrocybe aegerita mitochondrial DNA contain essential information regarding the evolution of this gourmet mushroom. In this study, eight isolates of A. aegerita were sequenced and assembled into complete mitochondrial genomes. The mtDNA of the isolate Ag0067 contained two genotypes, both of which were quadripartite architecture consisting of two identical inverted repeats, separated by a small single-copy region and a large single-copy region. The only difference was opposite directions of the small single-copy region. The mtDNAs ranged from 116,329 bp to 134,035 bp, harboring two large identical inverted repeats. Genes of plasmid-origin were present in regions flanked by inverted repeat ID2. Most of the core genes evolved at a relatively low rate, whereas five tRNA genes located in corresponding regions of Ag0002:1-14000 and Ag0002:50001-61000 showed higher diversity. A long fragment inversion (10 Kb) was suggested to have occurred during the differentiation of two main clades, leading to two different gene orders. The number and distribution of the introns varied greatly among the A. aegerita mtDNAs. Fast invasion of short insertions likely resulted in the diversity of introns as well as other non-coding regions, increasing the variation of the mtDNAs. We raised a model about the evolution of the large repeats to explain the unusual features of A. aegerita mtDNAs. This study constructed quadripartite architecture of A. aegerita mtDNAs analogous to chloroplast DNA, proposed an interconversion model of the divergent mitochondrial genotypes with large inverted repeats. The findings could increase our knowledge of fungal evolution.
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Affiliation(s)
- Xinrui Liu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiaoping Wu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Hao Tan
- Mushroom Research Center, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China
- School of Bioengineering, Jiangnan University, Wuxi 214062, China
| | - Baogui Xie
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Youjin Deng
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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8
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Subramanian H, Gatenby RA. Evolutionary advantage of anti-parallel strand orientation of duplex DNA. Sci Rep 2020; 10:9883. [PMID: 32555277 PMCID: PMC7303137 DOI: 10.1038/s41598-020-66705-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 05/22/2020] [Indexed: 11/09/2022] Open
Abstract
DNA in all living systems shares common properties that are remarkably well suited to its function, suggesting refinement by evolution. However, DNA also shares some counter-intuitive properties which confer no obvious benefit, such as strand directionality and anti-parallel strand orientation, which together result in the complicated lagging strand replication. The evolutionary dynamics that led to these properties of DNA remain unknown but their universality suggests that they confer as yet unknown selective advantage to DNA. In this article, we identify an evolutionary advantage of anti-parallel strand orientation of duplex DNA, within a given set of plausible premises. The advantage stems from the increased rate of replication, achieved by dividing the DNA into predictable, independently and simultaneously replicating segments, as opposed to sequentially replicating the entire DNA, thereby parallelizing the replication process. We show that anti-parallel strand orientation is essential for such a replicative organization of DNA, given our premises, the most important of which is the assumption of the presence of sequence-dependent asymmetric cooperativity in DNA.
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Affiliation(s)
| | - Robert A Gatenby
- Integrated Mathematical Oncology Department, Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, 12902, USF Magnolia Dr, Tampa, Florida, USA
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9
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Ola M, O'Brien CE, Coughlan AY, Ma Q, Donovan PD, Wolfe KH, Butler G. Polymorphic centromere locations in the pathogenic yeast Candida parapsilosis. Genome Res 2020; 30:684-696. [PMID: 32424070 PMCID: PMC7263194 DOI: 10.1101/gr.257816.119] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/24/2020] [Indexed: 11/24/2022]
Abstract
Centromeres pose an evolutionary paradox: strongly conserved in function but rapidly changing in sequence and structure. However, in the absence of damage, centromere locations are usually conserved within a species. We report here that isolates of the pathogenic yeast species Candida parapsilosis show within-species polymorphism for the location of centromeres on two of its eight chromosomes. Its old centromeres have an inverted-repeat (IR) structure, whereas its new centromeres have no obvious structural features but are located within 30 kb of the old site. Centromeres can therefore move naturally from one chromosomal site to another, apparently spontaneously and in the absence of any significant changes in DNA sequence. Our observations are consistent with a model in which all centromeres are genetically determined, such as by the presence of short or long IRs or by the ability to form cruciforms. We also find that centromeres have been hotspots for genomic rearrangements in the C. parapsilosis clade.
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Affiliation(s)
- Mihaela Ola
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Caoimhe E O'Brien
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Aisling Y Coughlan
- School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Qinxi Ma
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Paul D Donovan
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kenneth H Wolfe
- School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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10
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Luo H, Gao F. DoriC 10.0: an updated database of replication origins in prokaryotic genomes including chromosomes and plasmids. Nucleic Acids Res 2020; 47:D74-D77. [PMID: 30364951 PMCID: PMC6323995 DOI: 10.1093/nar/gky1014] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 10/11/2018] [Indexed: 12/11/2022] Open
Abstract
DoriC, a database of replication origins, was initially created to present the bacterial oriCs predicted by Ori-Finder or determined by experiments in 2007. DoriC 5.0, an updated database of oriC regions in both bacterial and archaeal genomes, was published in the 2013 Nucleic Acids Research database issue. Now, the latest release DoriC 10, a large-scale update of replication origins in prokaryotic genomes including chromosomes and plasmids, has been presented with a completely redesigned user interface, which is freely available at http://tubic.org/doric/ and http://tubic.tju.edu.cn/doric/. In the current release, the database of DoriC has made significant improvements compared with version 5.0 as follows: (i) inclusion of oriCs on more bacterial chromosomes increased from 1633 to 7580; (ii) inclusion of oriCs on more archaeal chromosomes increased from 86 to 226; (iii) inclusion of 1209 plasmid replication origins retrieved from NCBI annotations or predicted by in silico analysis; (iv) inclusion of more replication origin elements on bacterial chromosomes including DnaA-trio motifs. Now, DoriC becomes the most complete and scalable database of replication origins in prokaryotic genomes, and facilitates the studies in large-scale oriC data mining, strand-biased analyses and replication origin predictions.
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Affiliation(s)
- Hao Luo
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
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11
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Silva SR, Pinheiro DG, Penha HA, Płachno BJ, Michael TP, Meer EJ, Miranda VFO, Varani AM. Intraspecific Variation within the Utricularia amethystina Species Morphotypes Based on Chloroplast Genomes. Int J Mol Sci 2019; 20:E6130. [PMID: 31817365 PMCID: PMC6940893 DOI: 10.3390/ijms20246130] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/09/2019] [Accepted: 11/27/2019] [Indexed: 01/09/2023] Open
Abstract
Utricularia amethystina Salzm. ex A.St.-Hil. & Girard (Lentibulariaceae) is a highly polymorphic carnivorous plant taxonomically rearranged many times throughout history. Herein, the complete chloroplast genomes (cpDNA) of three U. amethystina morphotypes: purple-, white-, and yellow-flowered, were sequenced, compared, and putative markers for systematic, populations, and evolutionary studies were uncovered. In addition, RNA-Seq and RNA-editing analysis were employed for functional cpDNA evaluation. The cpDNA of three U. amethystina morphotypes exhibits typical quadripartite structure. Fine-grained sequence comparison revealed a high degree of intraspecific genetic variability in all morphotypes, including an exclusive inversion in the psbM and petN genes in U. amethystina yellow. Phylogenetic analyses indicate that U. amethystina morphotypes are monophyletic. Furthermore, in contrast to the terrestrial Utricularia reniformis cpDNA, the U. amethystina morphotypes retain all the plastid NAD(P)H-dehydrogenase (ndh) complex genes. This observation supports the hypothesis that the ndhs in terrestrial Utricularia were independently lost and regained, also suggesting that different habitats (aquatic and terrestrial) are not related to the absence of Utricularia ndhs gene repertoire as previously assumed. Moreover, RNA-Seq analyses recovered similar patterns, including nonsynonymous RNA-editing sites (e.g., rps14 and petB). Collectively, our results bring new insights into the chloroplast genome architecture and evolution of the photosynthesis machinery in the Lentibulariaceae.
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Affiliation(s)
- Saura R. Silva
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Universidade Estadual Paulista (Unesp), Sao Paulo 14884-900, Brazil; (D.G.P.); (H.A.P.)
| | - Daniel G. Pinheiro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Universidade Estadual Paulista (Unesp), Sao Paulo 14884-900, Brazil; (D.G.P.); (H.A.P.)
| | - Helen A. Penha
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Universidade Estadual Paulista (Unesp), Sao Paulo 14884-900, Brazil; (D.G.P.); (H.A.P.)
| | - Bartosz J. Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, 30-387 Krakow, Poland;
| | | | | | - Vitor F. O. Miranda
- Departamento de Biologia Aplicada à Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Universidade Estadual Paulista (Unesp), Sao Paulo 14884-900, Brazil
| | - Alessandro M. Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Universidade Estadual Paulista (Unesp), Sao Paulo 14884-900, Brazil; (D.G.P.); (H.A.P.)
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12
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The Rich World of p53 DNA Binding Targets: The Role of DNA Structure. Int J Mol Sci 2019; 20:ijms20225605. [PMID: 31717504 PMCID: PMC6888028 DOI: 10.3390/ijms20225605] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/29/2019] [Accepted: 11/08/2019] [Indexed: 12/14/2022] Open
Abstract
The tumor suppressor functions of p53 and its roles in regulating the cell cycle, apoptosis, senescence, and metabolism are accomplished mainly by its interactions with DNA. p53 works as a transcription factor for a significant number of genes. Most p53 target genes contain so-called p53 response elements in their promoters, consisting of 20 bp long canonical consensus sequences. Compared to other transcription factors, which usually bind to one concrete and clearly defined DNA target, the p53 consensus sequence is not strict, but contains two repeats of a 5′RRRCWWGYYY3′ sequence; therefore it varies remarkably among target genes. Moreover, p53 binds also to DNA fragments that at least partially and often completely lack this consensus sequence. p53 also binds with high affinity to a variety of non-B DNA structures including Holliday junctions, cruciform structures, quadruplex DNA, triplex DNA, DNA loops, bulged DNA, and hemicatenane DNA. In this review, we summarize information of the interactions of p53 with various DNA targets and discuss the functional consequences of the rich world of p53 DNA binding targets for its complex regulatory functions.
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13
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Abstract
Animal and plant centromeres are embedded in repetitive "satellite" DNA, but are thought to be epigenetically specified. To define genetic characteristics of centromeres, we surveyed satellite DNA from diverse eukaryotes and identified variation in <10-bp dyad symmetries predicted to adopt non-B-form conformations. Organisms lacking centromeric dyad symmetries had binding sites for sequence-specific DNA-binding proteins with DNA-bending activity. For example, human and mouse centromeres are depleted for dyad symmetries, but are enriched for non-B-form DNA and are associated with binding sites for the conserved DNA-binding protein CENP-B, which is required for artificial centromere function but is paradoxically nonessential. We also detected dyad symmetries and predicted non-B-form DNA structures at neocentromeres, which form at ectopic loci. We propose that centromeres form at non-B-form DNA because of dyad symmetries or are strengthened by sequence-specific DNA binding proteins. This may resolve the CENP-B paradox and provide a general basis for centromere specification.
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Affiliation(s)
- Sivakanthan Kasinathan
- Medical Scientist Training Program, University of Washington School of Medicine, Seattle, WA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA.,Howard Hughes Medical Institute, Seattle, WA
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14
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Miura O, Ogake T, Yoneyama H, Kikuchi Y, Ohyama T. A strong structural correlation between short inverted repeat sequences and the polyadenylation signal in yeast and nucleosome exclusion by these inverted repeats. Curr Genet 2018; 65:575-590. [PMID: 30498953 PMCID: PMC6420913 DOI: 10.1007/s00294-018-0907-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 11/22/2022]
Abstract
DNA sequences that read the same from 5′ to 3′ in either strand are called inverted repeat sequences or simply IRs. They are found throughout a wide variety of genomes, from prokaryotes to eukaryotes. Despite extensive research, their in vivo functions, if any, remain unclear. Using Saccharomyces cerevisiae, we performed genome-wide analyses for the distribution, occurrence frequency, sequence characteristics and relevance to chromatin structure, for the IRs that reportedly have a cruciform-forming potential. Here, we provide the first comprehensive map of these IRs in the S. cerevisiae genome. The statistically significant enrichment of the IRs was found in the close vicinity of the DNA positions corresponding to polyadenylation [poly(A)] sites and ~ 30 to ~ 60 bp downstream of start codon-coding sites (referred to as ‘start codons’). In the former, ApT- or TpA-rich IRs and A-tract- or T-tract-rich IRs are enriched, while in the latter, different IRs are enriched. Furthermore, we found a strong structural correlation between the former IRs and the poly(A) signal. In the chromatin formed on the gene end regions, the majority of the IRs causes low nucleosome occupancy. The IRs in the region ~ 30 to ~ 60 bp downstream of start codons are located in the + 1 nucleosomes. In contrast, fewer IRs are present in the adjacent region downstream of start codons. The current study suggests that the IRs play similar roles in Escherichia coli and S. cerevisiae to regulate or complete transcription at the RNA level.
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Affiliation(s)
- Osamu Miura
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Toshihiro Ogake
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Hiroki Yoneyama
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Yo Kikuchi
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Takashi Ohyama
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan. .,Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.
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15
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Complex Analyses of Short Inverted Repeats in All Sequenced Chloroplast DNAs. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1097018. [PMID: 30140690 PMCID: PMC6081594 DOI: 10.1155/2018/1097018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/19/2018] [Accepted: 07/12/2018] [Indexed: 01/14/2023]
Abstract
Chloroplasts are key organelles in the management of oxygen in algae and plants and are therefore crucial for all living beings that consume oxygen. Chloroplasts typically contain a circular DNA molecule with nucleus-independent replication and heredity. Using "palindrome analyser" we performed complete analyses of short inverted repeats (S-IRs) in all chloroplast DNAs (cpDNAs) available from the NCBI genome database. Our results provide basic parameters of cpDNAs including comparative information on localization, frequency, and differences in S-IR presence. In a total of 2,565 cpDNA sequences available, the average frequency of S-IRs in cpDNA genomes is 45 S-IRs/per kbp, significantly higher than that found in mitochondrial DNA sequences. The frequency of S-IRs in cpDNAs generally decreased with S-IR length, but not for S-IRs 15, 22, 24, or 27 bp long, which are significantly more abundant than S-IRs with other lengths. These results point to the importance of specific S-IRs in cpDNA genomes. Moreover, comparison by Levenshtein distance of S-IR similarities showed that a limited number of S-IR sequences are shared in the majority of cpDNAs. S-IRs are not located randomly in cpDNAs, but are length-dependently enriched in specific locations, including the repeat region, stem, introns, and tRNA regions. The highest enrichment was found for 12 bp and longer S-IRs in the stem-loop region followed by 12 bp and longer S-IRs located before the repeat region. On the other hand, S-IRs are relatively rare in rRNA sequences and around introns. These data show nonrandom and conserved arrangements of S-IRs in chloroplast genomes.
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16
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Carr CE, Marky LA. Increased Flexibility between Stems of Intramolecular Three-Way Junctions by the Insertion of Bulges. Biophys J 2018; 114:2764-2774. [PMID: 29925014 PMCID: PMC6026347 DOI: 10.1016/j.bpj.2018.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/25/2018] [Accepted: 05/01/2018] [Indexed: 12/20/2022] Open
Abstract
Intramolecular junctions are a ubiquitous structure within DNA and RNA; three-way junctions in particular have high strain around the junction because of the lack of flexibility, preventing the junctions from adopting conformations that would allow for optimal folding. In this work, we used a combination of calorimetric and spectroscopic techniques to study the unfolding of four intramolecular three-way junctions. The control three-way junction, 3H, has the sequence d(GAAATTGCGCT5GCGCGTGCT5GCACAATTTC), which has three arms of different sequences. We studied three other three-way junctions in which one (2HS1H), two (HS12HS1), and three (HS1HS1HS1) cytosine bulges were placed at the junction to allow the arms to adopt a wider range of conformations that may potentially relieve strain. Through calorimetric studies, it was concluded that bulges produce only minor effects on the enthalpic and thermal stability at physiological salt concentrations for 2HS1H and HS1HS1HS1. HS12HS1 displays the strongest effect, with the GTGC stem lacking a defined transition. In addition to unfolding thermodynamics, the differential binding of counterions, water, and protons was determined. It was found that with each bulge, there was a large increase in the binding of counterions; this correlated with a decrease in the immobilization of structural water molecules. The increase in counterion uptake upon folding likely displaces binding of structural water, which is measured by the osmotic stress method, in favor of electrostricted waters. The cytosine bulges do not affect the binding of protons; this finding indicates that the bulges are not forming base-triplet stacks. These results indicate that bulges in junctions do not affect the unfolding profile or the enthalpy of oligonucleotides but do affect the number and amount of molecules immobilized by the junction.
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Affiliation(s)
- Carolyn E Carr
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska
| | - Luis A Marky
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska.
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17
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Lavi B, Levy Karin E, Pupko T, Hazkani-Covo E. The Prevalence and Evolutionary Conservation of Inverted Repeats in Proteobacteria. Genome Biol Evol 2018; 10:918-927. [PMID: 29608719 PMCID: PMC5941160 DOI: 10.1093/gbe/evy044] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2018] [Indexed: 12/11/2022] Open
Abstract
Perfect short inverted repeats (IRs) are known to be enriched in a variety of bacterial and eukaryotic genomes. Currently, it is unclear whether perfect IRs are conserved over evolutionary time scales. In this study, we aimed to characterize the prevalence and evolutionary conservation of IRs across 20 proteobacterial strains. We first identified IRs in Escherichia coli K-12 substr MG1655 and showed that they are overabundant. We next aimed to test whether this overabundance is reflected in the conservation of IRs over evolutionary time scales. To this end, for each perfect IR identified in E. coli MG1655, we collected orthologous sequences from related proteobacterial genomes. We next quantified the evolutionary conservation of these IRs, that is, the presence of the exact same IR across orthologous regions. We observed high conservation of perfect IRs: out of the 234 examined orthologous regions, 145 were more conserved than expected, which is statistically significant even after correcting for multiple testing. Our results together with previous experimental findings support a model in which imperfect IRs are corrected to perfect IRs in a preferential manner via a template switching mechanism.
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Affiliation(s)
- Bar Lavi
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel
| | - Eli Levy Karin
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
- Department of Molecular Biology & Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
| | - Einat Hazkani-Covo
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel
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18
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Miura O, Ogake T, Ohyama T. Requirement or exclusion of inverted repeat sequences with cruciform-forming potential in Escherichia coli revealed by genome-wide analyses. Curr Genet 2018; 64:945-958. [PMID: 29484452 PMCID: PMC6060812 DOI: 10.1007/s00294-018-0815-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/16/2018] [Accepted: 02/19/2018] [Indexed: 12/31/2022]
Abstract
Inverted repeat (IR) sequences are DNA sequences that read the same from 5' to 3' in each strand. Some IRs can form cruciforms under the stress of negative supercoiling, and these IRs are widely found in genomes. However, their biological significance remains unclear. The aim of the current study is to explore this issue further. We constructed the first Escherichia coli genome-wide comprehensive map of IRs with cruciform-forming potential. Based on the map, we performed detailed and quantitative analyses. Here, we report that IRs with cruciform-forming potential are statistically enriched in the following five regions: the adjacent regions downstream of the stop codon-coding sites (referred to as the stop codons), on and around the positions corresponding to mRNA ends (referred to as the gene ends), ~ 20 to ~45 bp upstream of the start codon-coding sites (referred to as the start codons) within the 5'-UTR (untranslated region), ~ 25 to ~ 60 bp downstream of the start codons, and promoter regions. For the adjacent regions downstream of the stop codons and on and around the gene ends, most of the IRs with a repeat unit length of ≥ 8 bp and a spacer size of ≤ 8 bp were parts of the intrinsic terminators, regardless of the location, and presumably used for Rho-independent transcription termination. In contrast, fewer IRs were present in the small region preceding the start codons. In E. coli, IRs with cruciform-forming potential are actively placed or excluded in the regulatory regions for the initiation and termination of transcription and translation, indicating their deep involvement or influence in these processes.
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Affiliation(s)
- Osamu Miura
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Toshihiro Ogake
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Takashi Ohyama
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.
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19
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Shi J, Li X, Dong M, Graham M, Yadav N, Liang C. JNSViewer-A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures. PLoS One 2017; 12:e0179040. [PMID: 28582416 PMCID: PMC5459502 DOI: 10.1371/journal.pone.0179040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/23/2017] [Indexed: 11/19/2022] Open
Abstract
Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html.
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Affiliation(s)
- Jieming Shi
- Department of Biology, Miami University, Oxford, Ohio, United States of America
| | - Xi Li
- Department of Biology, Miami University, Oxford, Ohio, United States of America
- College of Information Science and Engineering, Guangxi University for Nationalities, Nanning, Guangxi, China
| | - Min Dong
- Department of Biology, Miami University, Oxford, Ohio, United States of America
- Department of Automation, Xiamen University, Fujian, China
| | - Mitchell Graham
- Department of Biology, Miami University, Oxford, Ohio, United States of America
| | - Nehul Yadav
- Department of Biology, Miami University, Oxford, Ohio, United States of America
| | - Chun Liang
- Department of Biology, Miami University, Oxford, Ohio, United States of America
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20
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Ohsaki K, Ohgaki Y, Shimizu N. Amplification of a transgene within a long array of replication origins favors higher gene expression in animal cells. PLoS One 2017; 12:e0175585. [PMID: 28403180 PMCID: PMC5389822 DOI: 10.1371/journal.pone.0175585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/28/2017] [Indexed: 11/27/2022] Open
Abstract
Plasmids with both a mammalian replication initiation region (IR) and a matrix attachment region (MAR) are spontaneously amplified in transfected cells, and generate extrachromosomal double minute (DM) or chromosomal homogeneously staining region (HSR). We previously isolated the shortest core IR (G5) required for gene amplification. In this study, we ligated the G5 DNA to create direct or inverted repeats, mixed the repeats with an expression plasmid, and transfected the mixture into human COLO 320DM or hamster CHO DG44 cells. Consequently, we found that the transfected sequence generated DMs or HSR where, surprisingly, the plasmid sequence was embedded within a long stretch of G5 sequences. The amplified structure from the direct G5 repeats was stable, whereas that from the inverted repeats was not. The amplification might be explained by the efficient replication/multimerization of the G5 repeat and recombination with the co-transfected plasmid in an extrachromosomal context. The product might then be integrated into a chromosome arm to generate a HSR. The expression from the plasmid within the long G5 array was much higher than that from a simple plasmid repeat. Because G5 is a core IR that favors gene expression, a long array of G5 provides an excellent environment for gene expression from the embedded plasmid.
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Affiliation(s)
- Kiwamu Ohsaki
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, Japan
| | - Yusuke Ohgaki
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, Japan
| | - Noriaki Shimizu
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, Japan
- * E-mail:
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21
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Brázda V, Coufal J. Recognition of Local DNA Structures by p53 Protein. Int J Mol Sci 2017; 18:ijms18020375. [PMID: 28208646 PMCID: PMC5343910 DOI: 10.3390/ijms18020375] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 02/03/2017] [Indexed: 02/06/2023] Open
Abstract
p53 plays critical roles in regulating cell cycle, apoptosis, senescence and metabolism and is commonly mutated in human cancer. These roles are achieved by interaction with other proteins, but particularly by interaction with DNA. As a transcription factor, p53 is well known to bind consensus target sequences in linear B-DNA. Recent findings indicate that p53 binds with higher affinity to target sequences that form cruciform DNA structure. Moreover, p53 binds very tightly to non-B DNA structures and local DNA structures are increasingly recognized to influence the activity of wild-type and mutant p53. Apart from cruciform structures, p53 binds to quadruplex DNA, triplex DNA, DNA loops, bulged DNA and hemicatenane DNA. In this review, we describe local DNA structures and summarize information about interactions of p53 with these structural DNA motifs. These recent data provide important insights into the complexity of the p53 pathway and the functional consequences of wild-type and mutant p53 activation in normal and tumor cells.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Jan Coufal
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
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22
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Molin WT, Wright AA, Lawton-Rauh A, Saski CA. The unique genomic landscape surrounding the EPSPS gene in glyphosate resistant Amaranthus palmeri: a repetitive path to resistance. BMC Genomics 2017; 18:91. [PMID: 28095770 PMCID: PMC5240378 DOI: 10.1186/s12864-016-3336-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 11/23/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The expanding number and global distributions of herbicide resistant weedy species threaten food, fuel, fiber and bioproduct sustainability and agroecosystem longevity. Amongst the most competitive weeds, Amaranthus palmeri S. Wats has rapidly evolved resistance to glyphosate primarily through massive amplification and insertion of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene across the genome. Increased EPSPS gene copy numbers results in higher titers of the EPSPS enzyme, the target of glyphosate, and confers resistance to glyphosate treatment. To understand the genomic unit and mechanism of EPSPS gene copy number proliferation, we developed and used a bacterial artificial chromosome (BAC) library from a highly resistant biotype to sequence the local genomic landscape flanking the EPSPS gene. RESULTS By sequencing overlapping BACs, a 297 kb sequence was generated, hereafter referred to as the "EPSPS cassette." This region included several putative genes, dense clusters of tandem and inverted repeats, putative helitron and autonomous replication sequences, and regulatory elements. Whole genome shotgun sequencing (WGS) of two biotypes exhibiting high and no resistance to glyphosate was performed to compare genomic representation across the EPSPS cassette. Mapping of sequences for both biotypes to the reference EPSPS cassette revealed significant differences in upstream and downstream sequences relative to EPSPS with regard to both repetitive units and coding content between these biotypes. The differences in sequence may have resulted from a compounded-building mechanism such as repetitive transpositional events. The association of putative helitron sequences with the cassette suggests a possible amplification and distribution mechanism. Flow cytometry revealed that the EPSPS cassette added measurable genomic content. CONCLUSIONS The adoption of glyphosate resistant cropping systems in major crops such as corn, soybean, cotton and canola coupled with excessive use of glyphosate herbicide has led to evolved glyphosate resistance in several important weeds. In Amaranthus palmeri, the amplification of the EPSPS cassette, characterized by a complex array of repetitive elements and putative helitron sequences, suggests an adaptive structural genomic mechanism that drives amplification and distribution around the genome. The added genomic content not found in glyphosate sensitive plants may be driving evolution through genome expansion.
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Affiliation(s)
- William T Molin
- United States Department of Agriculture, Crop Production Systems Research Unit, Stoneville, MS, USA.
| | - Alice A Wright
- United States Department of Agriculture, Crop Production Systems Research Unit, Stoneville, MS, USA
| | - Amy Lawton-Rauh
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Christopher A Saski
- Institute of Translational Genomics, Genomics and Computational Biology Lab, Clemson University, Clemson, SC, USA.
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23
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Subramanian S, Chaparala S, Avali V, Ganapathiraju MK. A pilot study on the prevalence of DNA palindromes in breast cancer genomes. BMC Med Genomics 2016; 9:73. [PMID: 28117658 PMCID: PMC5260791 DOI: 10.1186/s12920-016-0232-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background DNA palindromes are a unique pattern of repeat sequences that are present in the human genome. It consists of a sequence of nucleotides in which the second half is the complement of the first half but appearing in reverse order. These palindromic sequences may have a significant role in DNA replication, transcription and gene regulation processes. They occur frequently in human cancers by clustering at specific locations of the genome that undergo gene amplification and tumorigenesis. Moreover, some studies showed that palindromes are clustered in amplified regions of breast cancer genomes especially in chromosomes (chr) 8 and 11. With the large number of personal genomes and cancer genomes becoming available, it is now possible to study their association to diseases using computational methods. Here, we conducted a pilot study on chromosomes 8 and 11 of cancer genomes to identify computationally the differentially occurring palindromes. Methods We processed 69 breast cancer genomes from The Cancer Genome Atlas including serum-normal and tumor genomes, and 1000 Genomes to serve as control group. The Biological Language Modelling Toolkit (BLMT) computes palindromes in whole genomes. We developed a computational pipeline integrating BLMT to compute and compare prevalence of palindromes in personal genomes. Results We carried out a pilot study on chr 8 and chr 11 taking into account single nucleotide polymorphisms, insertions and deletions. Of all the palindromes that showed any variation in cancer genomes, 38% of what were near breast cancer genes happened to be the most differentiated palindromes in tumor (i.e. they ranked among the top 25% by our heuristic measure). Conclusions These results will shed light on the prevalence of palindromes in oncogenes and the mutations that are present in the palindromic regions that could contribute to genomic rearrangements, and breast cancer progression.
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Affiliation(s)
- Sandeep Subramanian
- Language Technologies Institute, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Srilakshmi Chaparala
- Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, Suite 522, Pittsburgh, PA, 15206, USA
| | - Viji Avali
- Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, Suite 522, Pittsburgh, PA, 15206, USA
| | - Madhavi K Ganapathiraju
- Department of Biomedical Informatics, University of Pittsburgh, 5607 Baum Blvd, Suite 522, Pittsburgh, PA, 15206, USA. .,Language Technologies Institute, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
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24
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Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GKJ, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O’Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, van’t Veer L, Tutt A, Knappskog S, Tan BKT, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature 2016; 534:47-54. [PMID: 27135926 PMCID: PMC4910866 DOI: 10.1038/nature17676] [Citation(s) in RCA: 1488] [Impact Index Per Article: 186.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 03/17/2016] [Indexed: 02/06/2023]
Abstract
We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.
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Affiliation(s)
- Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 9NB, UK
| | - Helen Davies
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | | | - Dominik Glodzik
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Xueqing Zou
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - Ludmil B. Alexandrov
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Sancha Martin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - David C. Wedge
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Peter Van Loo
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Department of Human Genetics, University of Leuven, B-3000 Leuven, Belgium
| | - Young Seok Ju
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Marcel Smid
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, Department of Medical Oncology, Rotterdam, The Netherlands
| | - Arie B Brinkman
- Radboud University, Department of Molecular Biology, Faculties of Science and Medicine, Nijmegen, Netherlands
| | - Sandro Morganella
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus,Hinxton, Cambridgeshire, CB10 1SD
| | - Miriam R. Aure
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radiumhospital
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ole Christian Lingjærde
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Computer Science, University of Oslo, Oslo, Norway
| | - Anita Langerød
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radiumhospital
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Markus Ringnér
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Sung-Min Ahn
- Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Incheon, South Korea
| | - Sandrine Boyault
- Translational Research Lab, Centre Léon Bérard, 28, rue Laënnec, 69373 Lyon Cedex 08, France
| | - Jane E. Brock
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115 USA
| | - Annegien Broeks
- The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Adam Butler
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Christine Desmedt
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Bd de Waterloo 121, B-1000 Brussels, Belgium
| | - Luc Dirix
- Translational Cancer Research Unit, Center for Oncological Research, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Serge Dronov
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - John A. Foekens
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, Department of Medical Oncology, Rotterdam, The Netherlands
| | - Moritz Gerstung
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Gerrit KJ Hooijer
- Department of Pathology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Se Jin Jang
- Department of Pathology, Asan Medical Center, College of Medicine, Ulsan University, South Korea
| | - David R. Jones
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Hyung-Yong Kim
- Department of Pathology, College of Medicine, Hanyang University, Seoul, South Korea
| | - Tari A. King
- Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065, United States
| | - Savitri Krishnamurthy
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030
| | - Hee Jin Lee
- Department of Pathology, Asan Medical Center, College of Medicine, Ulsan University, South Korea
| | - Jeong-Yeon Lee
- Institute for Bioengineering and Biopharmaceutical Research (IBBR), Hanyang University, Seoul, South Korea
| | - Yilong Li
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Stuart McLaren
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Andrew Menzies
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Ville Mustonen
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Sarah O’Meara
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Iris Pauporté
- Institut National du Cancer, Research Division, Clinical Research Department, 52 avenue Morizet, 92513 Boulogne-Billancourt, France
| | - Xavier Pivot
- University Hospital of Minjoz, INSERM UMR 1098, Bd Fleming, Besançon 25000, France
| | - Colin A. Purdie
- Pathology Department, Ninewells Hospital & Medical School, Dundee DD1 9SY, UK
| | - Keiran Raine
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - F. Germán Rodríguez-González
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, Department of Medical Oncology, Rotterdam, The Netherlands
| | - Gilles Romieu
- Oncologie Sénologie, ICM Institut Régional du Cancer, Montpellier, France
| | - Anieta M. Sieuwerts
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, Department of Medical Oncology, Rotterdam, The Netherlands
| | - Peter T Simpson
- The University of Queensland: UQ Centre for Clinical Research and School of Medicine, Brisbane, Australia
| | - Rebecca Shepherd
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Lucy Stebbings
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Olafur A Stefansson
- Cancer Research Laboratory, Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Jon Teague
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - Isabelle Treilleux
- Department of Pathology, Centre Léon Bérard, 28 rue Laënnec, 69373 Lyon Cédex 08, France
| | - Gert G. Van den Eynden
- Translational Cancer Research Unit, Center for Oncological Research, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Department of Pathology, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - Peter Vermeulen
- Translational Cancer Research Unit, Center for Oncological Research, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Department of Pathology, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - Anne Vincent-Salomon
- Institut Curie, Department of Pathology and INSERM U934, 26 rue d’Ulm, 75248 Paris Cedex 05, France
| | - Lucy Yates
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - Laura van’t Veer
- The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Andrew Tutt
- Breast Cancer Now Toby Research Unit, King’s College London
- Breast Cancer Now Toby Robin’s Research Centre, Institute of Cancer Research, London
| | - Stian Knappskog
- Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
- Department of Oncology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Benita Kiat Tee Tan
- National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610
- Singapore General Hospital, Outram Road, Singapore 169608
| | - Jos Jonkers
- The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Naoto T Ueno
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Bd de Waterloo 121, B-1000 Brussels, Belgium
| | - Alain Viari
- Equipe Erable, INRIA Grenoble-Rhône-Alpes, 655, Av. de l’Europe, 38330 Montbonnot-Saint Martin, France
- Synergie Lyon Cancer, Centre Léon Bérard, 28 rue Laënnec, Lyon Cedex 08, France
| | - P. Andrew Futreal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX, 77230
| | - Peter J Campbell
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Paul N. Span
- Department of Radiation Oncology, and department of Laboratory Medicine, Radboud university medical center, Nijmegen, the Netherlands
| | - Steven Van Laere
- Translational Cancer Research Unit, Center for Oncological Research, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Sunil R Lakhani
- The University of Queensland: UQ Centre for Clinical Research and School of Medicine, Brisbane, Australia
- Pathology Queensland, The Royal Brisbane and Women’s Hospital, Brisbane, Australia
| | - Jorunn E. Eyfjord
- Cancer Research Laboratory, Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Alastair M. Thompson
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, 1400 Pressler Street,Houston, Texas 77030
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus,Hinxton, Cambridgeshire, CB10 1SD
| | - Hendrik G Stunnenberg
- Radboud University, Department of Molecular Biology, Faculties of Science and Medicine, Nijmegen, Netherlands
| | - Marc J van de Vijver
- Department of Pathology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - John W.M. Martens
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, Department of Medical Oncology, Rotterdam, The Netherlands
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radiumhospital
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Andrea L. Richardson
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115 USA
- Dana-Farber Cancer Institute, Boston, MA 02215 USA
| | - Gu Kong
- Department of Pathology, College of Medicine, Hanyang University, Seoul, South Korea
| | - Gilles Thomas
- Synergie Lyon Cancer, Centre Léon Bérard, 28 rue Laënnec, Lyon Cedex 08, France
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25
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Kaushik M, Kaushik S, Roy K, Singh A, Mahendru S, Kumar M, Chaudhary S, Ahmed S, Kukreti S. A bouquet of DNA structures: Emerging diversity. Biochem Biophys Rep 2016; 5:388-395. [PMID: 28955846 PMCID: PMC5600441 DOI: 10.1016/j.bbrep.2016.01.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/28/2015] [Accepted: 01/22/2016] [Indexed: 11/29/2022] Open
Abstract
Structural polymorphism of DNA has constantly been evolving from the time of illustration of the double helical model of DNA by Watson and Crick. A variety of non-canonical DNA structures have constantly been documented across the globe. DNA attracted worldwide attention as a carrier of genetic information. In addition to the classical Watson–Crick duplex, DNA can actually adopt diverse structures during its active participation in cellular processes like replication, transcription, recombination and repair. Structures like hairpin, cruciform, triplex, G-triplex, quadruplex, i-motif and other alternative non-canonical DNA structures have been studied at length and have also shown their in vivo occurrence. This review mainly focuses on non-canonical structures adopted by DNA oligonucleotides which have certain prerequisites for their formation in terms of sequence, its length, number and orientation of strands along with varied solution conditions. This conformational polymorphism of DNA might be the basis of different functional properties of a specific set of DNA sequences, further giving some insights for various extremely complicated biological phenomena. Many of these structures have already shown their linkages with diseases like cancer and genetic disorders, hence making them an extremely striking target for structure-specific drug designing and therapeutic applications. DNA can adopt diverse range of structures other than classical Watson–Crick duplex. Discussion of alternate structures like hairpin, cruciform, triplex, quadruplex etc. This review gives some insights for the biological relevance of DNA structures.
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Affiliation(s)
- Mahima Kaushik
- Cluster Innovation Centre, University of Delhi, Delhi, India.,Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Shikha Kaushik
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Kapil Roy
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Anju Singh
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Swati Mahendru
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Mohan Kumar
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Swati Chaudhary
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Saami Ahmed
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Shrikant Kukreti
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
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26
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Abstract
This article reviews atomic force microscopy (AFM) studies of DNA structure and dynamics and protein-DNA complexes, including recent advances in the visualization of protein-DNA complexes with the use of cutting-edge, high-speed AFM. Special emphasis is given to direct nanoscale visualization of dynamics of protein-DNA complexes. In the area of DNA structure and dynamics, structural studies of local non-B conformations of DNA and the interplay of local and global DNA conformations are reviewed. The application of time-lapse AFM nanoscale imaging of DNA dynamics is illustrated by studies of Holliday junction branch migration. Structure and dynamics of protein-DNA interactions include problems related to site-specific DNA recombination, DNA replication, and DNA mismatch repair. Studies involving the structure and dynamics of chromatin are also described.
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Affiliation(s)
- Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025
| | - Luda S. Shlyakhtenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025
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27
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The linear plastid chromosomes of maize: terminal sequences, structures, and implications for DNA replication. Curr Genet 2015; 62:431-42. [PMID: 26650613 DOI: 10.1007/s00294-015-0548-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 11/15/2015] [Accepted: 11/22/2015] [Indexed: 01/13/2023]
Abstract
The structure of a chromosomal DNA molecule may influence the way in which it is replicated and inherited. For decades plastid DNA (ptDNA) was believed to be circular, with breakage invoked to explain linear forms found upon extraction from the cell. Recent evidence indicates that ptDNA in vivo consists of linear molecules with discrete termini, although these ends were not characterized. We report the sequences of two terminal regions, End1 and End2, for maize (Zea mays L.) ptDNA. We describe structural features of these terminal regions and similarities found in other plant ptDNAs. The terminal sequences are within inverted repeat regions (leading to four genomic isomers) and adjacent to origins of replication. Conceptually, stem-loop structures may be formed following melting of the double-stranded DNA ends. Exonuclease digestion indicates that the ends in maize are unobstructed, but tobacco (Nicotiana tabacum L.) ends may have a 5'-protein. If the terminal structure of ptDNA molecules influences the retention of ptDNA, the unprotected molecular ends in mature leaves of maize may be more susceptible to degradation in vivo than the protected ends in tobacco. The terminal sequences and cumulative GC skew profiles are nearly identical for maize, wheat (Triticum aestivum L.) and rice (Oryza sativa L.), with less similarity among other plants. The linear structure is now confirmed for maize ptDNA and inferred for other plants and suggests a virus-like recombination-dependent replication mechanism for ptDNA. Plastid transformation vectors containing the terminal sequences may increase the chances of success in generating transplastomic cereals.
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28
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Estupiñán M, Álvarez-García D, Barril X, Diaz P, Manresa A. In Silico/In Vivo Insights into the Functional and Evolutionary Pathway of Pseudomonas aeruginosa Oleate-Diol Synthase. Discovery of a New Bacterial Di-Heme Cytochrome C Peroxidase Subfamily. PLoS One 2015; 10:e0131462. [PMID: 26154497 PMCID: PMC4496055 DOI: 10.1371/journal.pone.0131462] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 06/02/2015] [Indexed: 12/14/2022] Open
Abstract
As previously reported, P. aeruginosa genes PA2077 and PA2078 code for 10S-DOX (10S-Dioxygenase) and 7,10-DS (7,10-Diol Synthase) enzymes involved in long-chain fatty acid oxygenation through the recently described oleate-diol synthase pathway. Analysis of the amino acid sequence of both enzymes revealed the presence of two heme-binding motifs (CXXCH) on each protein. Phylogenetic analysis showed the relation of both proteins to bacterial di-heme cytochrome c peroxidases (Ccps), similar to Xanthomonas sp. 35Y rubber oxidase RoxA. Structural homology modelling of PA2077 and PA2078 was achieved using RoxA (pdb 4b2n) as a template. From the 3D model obtained, presence of significant amino acid variations in the predicted heme-environment was found. Moreover, the presence of palindromic repeats located in enzyme-coding regions, acting as protein evolution elements, is reported here for the first time in P. aeruginosa genome. These observations and the constructed phylogenetic tree of the two proteins, allow the proposal of an evolutionary pathway for P. aeruginosa oleate-diol synthase operon. Taking together the in silico and in vivo results obtained we conclude that enzymes PA2077 and PA2078 are the first described members of a new subfamily of bacterial peroxidases, designated as Fatty acid-di-heme Cytochrome cperoxidases (FadCcp).
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Affiliation(s)
- Mónica Estupiñán
- Unitat de Microbiologia i Parasitologia Sanitàries, Facultat de Farmàcia, University of Barcelona, Barcelona, Spain
- Department of Microbiology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Daniel Álvarez-García
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), PCB-Edifici Hèlix Baldiri Reixac, Barcelona, Spain
| | - Xavier Barril
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), PCB-Edifici Hèlix Baldiri Reixac, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys, Barcelona, Spain
| | - Pilar Diaz
- Department of Microbiology, Faculty of Biology, University of Barcelona, Barcelona, Spain
- * E-mail:
| | - Angeles Manresa
- Unitat de Microbiologia i Parasitologia Sanitàries, Facultat de Farmàcia, University of Barcelona, Barcelona, Spain
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29
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Lu S, Wang G, Bacolla A, Zhao J, Spitser S, Vasquez KM. Short Inverted Repeats Are Hotspots for Genetic Instability: Relevance to Cancer Genomes. Cell Rep 2015; 10:1674-1680. [PMID: 25772355 DOI: 10.1016/j.celrep.2015.02.039] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 01/26/2015] [Accepted: 02/16/2015] [Indexed: 12/25/2022] Open
Abstract
Analyses of chromosomal aberrations in human genetic disorders have revealed that inverted repeat sequences (IRs) often co-localize with endogenous chromosomal instability and breakage hotspots. Approximately 80% of all IRs in the human genome are short (<100 bp), yet the mutagenic potential of such short cruciform-forming sequences has not been characterized. Here, we find that short IRs are enriched at translocation breakpoints in human cancer and stimulate the formation of DNA double-strand breaks (DSBs) and deletions in mammalian and yeast cells. We provide evidence for replication-related mechanisms of IR-induced genetic instability and a novel XPF cleavage-based mechanism independent of DNA replication. These discoveries implicate short IRs as endogenous sources of DNA breakage involved in disease etiology and suggest that these repeats represent a feature of genome plasticity that may contribute to the evolution of the human genome by providing a means for diversity within the population.
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Affiliation(s)
- Steve Lu
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin - Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard R1800, Austin, TX 78723, USA
| | - Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin - Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard R1800, Austin, TX 78723, USA
| | - Albino Bacolla
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin - Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard R1800, Austin, TX 78723, USA
| | - Junhua Zhao
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin - Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard R1800, Austin, TX 78723, USA
| | - Scott Spitser
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin - Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard R1800, Austin, TX 78723, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin - Dell Pediatric Research Institute, 1400 Barbara Jordan Boulevard R1800, Austin, TX 78723, USA.
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Ye C, Ji G, Li L, Liang C. detectIR: a novel program for detecting perfect and imperfect inverted repeats using complex numbers and vector calculation. PLoS One 2014; 9:e113349. [PMID: 25409465 PMCID: PMC4237412 DOI: 10.1371/journal.pone.0113349] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 10/22/2014] [Indexed: 11/19/2022] Open
Abstract
Inverted repeats are present in abundance in both prokaryotic and eukaryotic genomes and can form DNA secondary structures--hairpins and cruciforms that are involved in many important biological processes. Bioinformatics tools for efficient and accurate detection of inverted repeats are desirable, because existing tools are often less accurate and time consuming, sometimes incapable of dealing with genome-scale input data. Here, we present a MATLAB-based program called detectIR for the perfect and imperfect inverted repeat detection that utilizes complex numbers and vector calculation and allows genome-scale data inputs. A novel algorithm is adopted in detectIR to convert the conventional sequence string comparison in inverted repeat detection into vector calculation of complex numbers, allowing non-complementary pairs (mismatches) in the pairing stem and a non-palindromic spacer (loop or gaps) in the middle of inverted repeats. Compared with existing popular tools, our program performs with significantly higher accuracy and efficiency. Using genome sequence data from HIV-1, Arabidopsis thaliana, Homo sapiens and Zea mays for comparison, detectIR can find lots of inverted repeats missed by existing tools whose outputs often contain many invalid cases. detectIR is open source and its source code is freely available at: https://sourceforge.net/projects/detectir.
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Affiliation(s)
- Congting Ye
- Department of Automation, Xiamen University, Xiamen, Fujian 361005, China; Department of Biology, Miami University, Oxford, Ohio 45056, United States of America
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, Fujian 361005, China; Innovation Center for Cell Biology, Xiamen University, Xiamen, Fujian 361005, China
| | - Lei Li
- Department of Automation, Xiamen University, Xiamen, Fujian 361005, China; Department of Biology, Miami University, Oxford, Ohio 45056, United States of America
| | - Chun Liang
- Department of Biology, Miami University, Oxford, Ohio 45056, United States of America; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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31
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Sukackaite R, Jensen MR, Mas PJ, Blackledge M, Buonomo SB, Hart DJ. Structural and biophysical characterization of murine rif1 C terminus reveals high specificity for DNA cruciform structures. J Biol Chem 2014; 289:13903-11. [PMID: 24634216 DOI: 10.1074/jbc.m114.557843] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mammalian Rif1 is a key regulator of DNA replication timing, double-stranded DNA break repair, and replication fork restart. Dissecting the molecular functions of Rif1 is essential to understand how it regulates such diverse processes. However, Rif1 is a large protein that lacks well defined functional domains and is predicted to be largely intrinsically disordered; these features have hampered recombinant expression of Rif1 and subsequent functional characterization. Here we applied ESPRIT (expression of soluble proteins by random incremental truncation), an in vitro evolution-like approach, to identify high yielding soluble fragments encompassing conserved regions I and II (CRI and CRII) at the C-terminal region of murine Rif1. NMR analysis showed CRI to be intrinsically disordered, whereas CRII is partially folded. CRII binds cruciform DNA with high selectivity and micromolar affinity and thus represents a functional DNA binding domain. Mutational analysis revealed an α-helical region of CRII to be important for cruciform DNA binding and identified critical residues. Thus, we present the first structural study of the mammalian Rif1, identifying a domain that directly links its function to DNA binding. The high specificity of Rif1 for cruciform structures is significant given the role of this key protein in regulating origin firing and DNA repair.
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Affiliation(s)
- Rasa Sukackaite
- From the European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, 38042 France, the Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 France, the European Molecular Biology Laboratory, Monterotondo Outstation, Adriano Buzzati-Traverso Campus, Via Ramarini 32, 00015 Monterotondo, Italy
| | - Malene Ringkjøbing Jensen
- the University of Grenoble Alpes, Institut de Biologie Structurale (IBS), 6 rue Jules Horowitz, F-38027 Grenoble, France, CEA, DSV, IBS, 6 rue Jules Horowitz, F-38027 Grenoble, France, CNRS, IBS, 6 rue Jules Horowitz, F-38027 Grenoble, France, and
| | - Philippe J Mas
- From the European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, 38042 France, the Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 France
| | - Martin Blackledge
- the University of Grenoble Alpes, Institut de Biologie Structurale (IBS), 6 rue Jules Horowitz, F-38027 Grenoble, France, CEA, DSV, IBS, 6 rue Jules Horowitz, F-38027 Grenoble, France, CNRS, IBS, 6 rue Jules Horowitz, F-38027 Grenoble, France, and
| | - Sara B Buonomo
- the European Molecular Biology Laboratory, Monterotondo Outstation, Adriano Buzzati-Traverso Campus, Via Ramarini 32, 00015 Monterotondo, Italy
| | - Darren J Hart
- From the European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, 38042 France, the Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 France,
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32
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Völker J, Plum GE, Gindikin V, Klump HH, Breslauer KJ. Impact of bulge loop size on DNA triplet repeat domains: Implications for DNA repair and expansion. Biopolymers 2014; 101:1-12. [PMID: 23494673 PMCID: PMC3920904 DOI: 10.1002/bip.22236] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 03/05/2013] [Indexed: 11/12/2022]
Abstract
Repetitive DNA sequences exhibit complex structural and energy landscapes, populated by metastable, noncanonical states, that favor expansion and deletion events correlated with disease phenotypes. To probe the origins of such genotype-phenotype linkages, we report the impact of sequence and repeat number on properties of (CNG) repeat bulge loops. We find the stability of duplexes with a repeat bulge loop is controlled by two opposing effects; a loop junction-dependent destabilization of the underlying double helix, and a self-structure dependent stabilization of the repeat bulge loop. For small bulge loops, destabilization of the underlying double helix overwhelms any favorable contribution from loop self-structure. As bulge loop size increases, the stabilizing loop structure contribution dominates. The role of sequence on repeat loop stability can be understood in terms of its impact on the opposing influences of junction formation and loop structure. The nature of the bulge loop affects the thermodynamics of these two contributions differently, resulting in unique differences in repeat size-dependent minima in the overall enthalpy, entropy, and free energy changes. Our results define factors that control repeat bulge loop formation; knowledge required to understand how this helix imperfection is linked to DNA expansion, deletion, and disease phenotypes.
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Affiliation(s)
- Jens Völker
- Department of Chemistry and Chemical Biology, Rutgers, The
State University of New Jersey, 610 Taylor Rd, Piscataway, NJ 08854
| | - G. Eric Plum
- IBET, Inc., 1507 Chambers Road, Suite 301, Columbus, OH
43212
| | - Vera Gindikin
- Department of Chemistry and Chemical Biology, Rutgers, The
State University of New Jersey, 610 Taylor Rd, Piscataway, NJ 08854
| | - Horst H. Klump
- Department of Molecular and Cell Biology,
University of Cape Town, Private Bag, Rondebosch 7800, South Africa
| | - Kenneth J. Breslauer
- Department of Chemistry and Chemical Biology, Rutgers, The
State University of New Jersey, 610 Taylor Rd, Piscataway, NJ 08854
- The Cancer Institute of New Jersey, New Brunswick,
NJ 08901
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Sreeskandarajan S, Flowers MM, Karro JE, Liang C. A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences. ACTA ACUST UNITED AC 2013; 30:887-8. [PMID: 24215021 DOI: 10.1093/bioinformatics/btt651] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
SUMMARY Palindromic sequences, or inverted repeats (IRs), in DNA sequences involve important biological processes such as DNA-protein binding, DNA replication and DNA transposition. Development of bioinformatics tools that are capable of accurately detecting perfect IRs can enable genome-wide studies of IR patterns in both prokaryotes and eukaryotes. Different from conventional string-comparison approaches, we propose a novel algorithm that uses a cumulative score system based on a prime number representation of nucleotide bases. We then implemented this algorithm as a MATLAB-based program for perfect IR detection. In comparison with other existing tools, our program demonstrates a high accuracy in detecting nested and overlapping IRs. AVAILABILITY AND IMPLEMENTATION The source code is freely available on (http://bioinfolab.miamioh.edu/bioinfolab/palindrome.php) CONTACT liangc@miamioh.edu or karroje@miamioh.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sutharzan Sreeskandarajan
- Department of Biology, Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056, USA and State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Vasquez KM, Wang G. The yin and yang of repair mechanisms in DNA structure-induced genetic instability. Mutat Res 2013; 743-744:118-131. [PMID: 23219604 PMCID: PMC3661696 DOI: 10.1016/j.mrfmmm.2012.11.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 11/21/2012] [Accepted: 11/24/2012] [Indexed: 01/14/2023]
Abstract
DNA can adopt a variety of secondary structures that deviate from the canonical Watson-Crick B-DNA form. More than 10 types of non-canonical or non-B DNA secondary structures have been characterized, and the sequences that have the capacity to adopt such structures are very abundant in the human genome. Non-B DNA structures have been implicated in many important biological processes and can serve as sources of genetic instability, implicating them in disease and evolution. Non-B DNA conformations interact with a wide variety of proteins involved in replication, transcription, DNA repair, and chromatin architectural regulation. In this review, we will focus on the interactions of DNA repair proteins with non-B DNA and their roles in genetic instability, as the proteins and DNA involved in such interactions may represent plausible targets for selective therapeutic intervention.
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Affiliation(s)
- Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States.
| | - Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States
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Abstract
In addition to the canonical double helix, DNA can fold into various other inter- and intramolecular secondary structures. Although many such structures were long thought to be in vitro artefacts, bioinformatics demonstrates that DNA sequences capable of forming these structures are conserved throughout evolution, suggesting the existence of non-B-form DNA in vivo. In addition, genes whose products promote formation or resolution of these structures are found in diverse organisms, and a growing body of work suggests that the resolution of DNA secondary structures is critical for genome integrity. This Review focuses on emerging evidence relating to the characteristics of G-quadruplex structures and the possible influence of such structures on genomic stability and cellular processes, such as transcription.
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Taqi MM, Wärmländer SKTS, Yamskova O, Madani F, Bazov I, Luo J, Zubarev R, Verbeek D, Gräslund A, Bakalkin G. Conformation effects of CpG methylation on single-stranded DNA oligonucleotides: analysis of the opioid peptide dynorphin-coding sequences. PLoS One 2012; 7:e39605. [PMID: 22768096 PMCID: PMC3387154 DOI: 10.1371/journal.pone.0039605] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 05/23/2012] [Indexed: 11/19/2022] Open
Abstract
Single-stranded DNA (ssDNA) is characterized by high conformational flexibility that allows these molecules to adopt a variety of conformations. Here we used native polyacrylamide gel electrophoresis (PAGE), circular dichroism (CD) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy to show that cytosine methylation at CpG sites affects the conformational flexibility of short ssDNA molecules. The CpG containing 37-nucleotide PDYN (prodynorphin) fragments were used as model molecules. The presence of secondary DNA structures was evident from differences in oligonucleotide mobilities on PAGE, from CD spectra, and from formation of A-T, G-C, and non-canonical G-T base pairs observed by NMR spectroscopy. The oligonucleotides displayed secondary structures at 4°C, and some also at 37°C. Methylation at CpG sites prompted sequence-dependent formation of novel conformations, or shifted the equilibrium between different existing ssDNA conformations. The effects of methylation on gel mobility and base pairing were comparable in strength to the effects induced by point mutations in the DNA sequences. The conformational effects of methylation may be relevant for epigenetic regulatory events in a chromatin context, including DNA-protein or DNA-DNA recognition in the course of gene transcription, and DNA replication and recombination when double-stranded DNA is unwinded to ssDNA.
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Affiliation(s)
- Malik Mumtaz Taqi
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Sebastian K. T. S. Wärmländer
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Olga Yamskova
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Fatemeh Madani
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Igor Bazov
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Jinghui Luo
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Roman Zubarev
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Dineke Verbeek
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Georgy Bakalkin
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
- * E-mail:
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Forth S, Deufel C, Patel SS, Wang MD. Direct measurements of torque during Holliday junction migration. Biophys J 2011; 101:L5-7. [PMID: 21767475 DOI: 10.1016/j.bpj.2011.05.066] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Revised: 04/25/2011] [Accepted: 05/03/2011] [Indexed: 11/25/2022] Open
Abstract
DNA experiences torsional stress resulting from the activities of motor enzymes and bound proteins. The mechanisms by which this torsional stress is dissipated to maintain DNA structural integrity are not fully known. Here, we show that a Holliday junction can limit torsion by coupling rotation to translocation and torque to force. The torque required to mechanically migrate through individual junctions was found to be an order of magnitude smaller than that required to melt DNA. We also directly show that substantially more torque was required to migrate through even a single-base sequence heterology, which has important implications for the activity of junction-migrating enzymes.
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Brázda V, Laister RC, Jagelská EB, Arrowsmith C. Cruciform structures are a common DNA feature important for regulating biological processes. BMC Mol Biol 2011; 12:33. [PMID: 21816114 PMCID: PMC3176155 DOI: 10.1186/1471-2199-12-33] [Citation(s) in RCA: 178] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 08/05/2011] [Indexed: 04/10/2023] Open
Abstract
DNA cruciforms play an important role in the regulation of natural processes involving DNA. These structures are formed by inverted repeats, and their stability is enhanced by DNA supercoiling. Cruciform structures are fundamentally important for a wide range of biological processes, including replication, regulation of gene expression, nucleosome structure and recombination. They also have been implicated in the evolution and development of diseases including cancer, Werner's syndrome and others. Cruciform structures are targets for many architectural and regulatory proteins, such as histones H1 and H5, topoisomerase IIβ, HMG proteins, HU, p53, the proto-oncogene protein DEK and others. A number of DNA-binding proteins, such as the HMGB-box family members, Rad54, BRCA1 protein, as well as PARP-1 polymerase, possess weak sequence specific DNA binding yet bind preferentially to cruciform structures. Some of these proteins are, in fact, capable of inducing the formation of cruciform structures upon DNA binding. In this article, we review the protein families that are involved in interacting with and regulating cruciform structures, including (a) the junction-resolving enzymes, (b) DNA repair proteins and transcription factors, (c) proteins involved in replication and (d) chromatin-associated proteins. The prevalence of cruciform structures and their roles in protein interactions, epigenetic regulation and the maintenance of cell homeostasis are also discussed.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v,v,i,, Královopolská 135, Brno, 612 65, Czech Republic.
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Folded DNA in action: hairpin formation and biological functions in prokaryotes. Microbiol Mol Biol Rev 2011; 74:570-88. [PMID: 21119018 DOI: 10.1128/mmbr.00026-10] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Structured forms of DNA with intrastrand pairing are generated in several cellular processes and are involved in biological functions. These structures may arise on single-stranded DNA (ssDNA) produced during replication, bacterial conjugation, natural transformation, or viral infections. Furthermore, negatively supercoiled DNA can extrude inverted repeats as hairpins in structures called cruciforms. Whether they are on ssDNA or as cruciforms, hairpins can modify the access of proteins to DNA, and in some cases, they can be directly recognized by proteins. Folded DNAs have been found to play an important role in replication, transcription regulation, and recognition of the origins of transfer in conjugative elements. More recently, they were shown to be used as recombination sites. Many of these functions are found on mobile genetic elements likely to be single stranded, including viruses, plasmids, transposons, and integrons, thus giving some clues as to the manner in which they might have evolved. We review here, with special focus on prokaryotes, the functions in which DNA secondary structures play a role and the cellular processes giving rise to them. Finally, we attempt to shed light on the selective pressures leading to the acquisition of functions for DNA secondary structures.
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40
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Scott SA, Cohen N, Brandt T, Warburton PE, Edelmann L. Large inverted repeats within Xp11.2 are present at the breakpoints of isodicentric X chromosomes in Turner syndrome. Hum Mol Genet 2010; 19:3383-93. [PMID: 20570968 PMCID: PMC2916707 DOI: 10.1093/hmg/ddq250] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 06/03/2010] [Accepted: 06/14/2010] [Indexed: 02/01/2023] Open
Abstract
Turner syndrome (TS) results from whole or partial monosomy X and is mediated by haploinsufficiency of genes that normally escape X-inactivation. Although a 45,X karyotype is observed in half of all TS cases, the most frequent variant TS karyotype includes the isodicentric X chromosome alone [46,X,idic(X)(p11)] or as a mosaic [46,X,idic(X)(p11)/45,X]. Given the mechanism of idic(X)(p11) rearrangement is poorly understood and breakpoint sequence information is unknown, this study sought to investigate the molecular mechanism of idic(X)(p11) formation by determining their precise breakpoint intervals. Karyotype analysis and fluorescence in situ hybridization mapping of eight idic(X)(p11) cell lines and three unbalanced Xp11.2 translocation lines identified the majority of breakpoints within a 5 Mb region, from approximately 53 to 58 Mb, in Xp11.1-p11.22, clustering into four regions. To further refine the breakpoints, a high-resolution oligonucleotide microarray (average of approximately 350 bp) was designed and array-based comparative genomic hybridization (aCGH) was performed on all 11 idic(X)(p11) and Xp11.2 translocation lines. aCGH analyses identified all breakpoint regions, including an idic(X)(p11) line with two potential breakpoints, one breakpoint shared between two idic(X)(p11) lines and two Xp translocations that shared breakpoints with idic(X)(p11) lines. Four of the breakpoint regions included large inverted repeats composed of repetitive gene clusters and segmental duplications, which corresponded to regions of copy-number variation. These data indicate that the rearrangement sites on Xp11.2 that lead to isodicentric chromosome formation and translocations are probably not random and suggest that the complex repetitive architecture of this region predisposes it to rearrangements, some of which are recurrent.
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Affiliation(s)
| | | | | | | | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York 10029, USA
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Strawbridge EM, Benson G, Gelfand Y, Benham CJ. The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome. Curr Genet 2010; 56:321-40. [PMID: 20446088 PMCID: PMC2908449 DOI: 10.1007/s00294-010-0302-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 04/05/2010] [Accepted: 04/08/2010] [Indexed: 02/06/2023]
Abstract
Although a variety of possible functions have been proposed for inverted repeat sequences (IRs), it is not known which of them might occur in vivo. We investigate this question by assessing the distributions and properties of IRs in the Saccharomyces cerevisiae (SC) genome. Using the IRFinder algorithm we detect 100,514 IRs having copy length greater than 6 bp and spacer length less than 77 bp. To assess statistical significance we also determine the IR distributions in two types of randomization of the S. cerevisiae genome. We find that the S. cerevisiae genome is significantly enriched in IRs relative to random. The S. cerevisiae IRs are significantly longer and contain fewer imperfections than those from the randomized genomes, suggesting that processes to lengthen and/or correct errors in IRs may be operative in vivo. The S. cerevisiae IRs are highly clustered in intergenic regions, while their occurrence in coding sequences is consistent with random. Clustering is stronger in the 3' flanks of genes than in their 5' flanks. However, the S. cerevisiae genome is not enriched in those IRs that would extrude cruciforms, suggesting that this is not a common event. Various explanations for these results are considered.
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Affiliation(s)
| | - Gary Benson
- Laboratory for Biocomputing and Informatics, Boston University, Boston, MA USA
| | - Yevgeniy Gelfand
- Laboratory for Biocomputing and Informatics, Boston University, Boston, MA USA
| | - Craig J. Benham
- Department of Mathematics, University of California, Davis, CA 95616 USA
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42
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Loot C, Bikard D, Rachlin A, Mazel D. Cellular pathways controlling integron cassette site folding. EMBO J 2010; 29:2623-34. [PMID: 20628355 DOI: 10.1038/emboj.2010.151] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 06/11/2010] [Indexed: 11/09/2022] Open
Abstract
By mobilizing small DNA units, integrons have a major function in the dissemination of antibiotic resistance among bacteria. The acquisition of gene cassettes occurs by recombination between the attI and attC sites catalysed by the IntI1 integron integrase. These recombination reactions use an unconventional mechanism involving a folded single-stranded attC site. We show that cellular bacterial processes delivering ssDNA, such as conjugation and replication, favour proper folding of the attC site. By developing a very sensitive in vivo assay, we also provide evidence that attC sites can recombine as cruciform structures by extrusion from double-stranded DNA. Moreover, we show an influence of DNA superhelicity on attC site extrusion in vitro and in vivo. We show that the proper folding of the attC site depends on both the propensity to form non-recombinogenic structures and the length of their variable terminal structures. These results draw the network of cell processes that regulate integron recombination.
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Affiliation(s)
- Céline Loot
- Institut Pasteur, Unité Plasticité du Génome Bactérien, Paris, France
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43
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Losch FO, Bredenbeck A, Hollstein VM, Walden P, Wrede P. Evidence for a large double-cruciform DNA structure on the X chromosome of human and chimpanzee. Hum Genet 2007; 122:337-43. [PMID: 17638018 DOI: 10.1007/s00439-007-0405-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Accepted: 07/09/2007] [Indexed: 01/05/2023]
Abstract
The human X chromosome consists of a high number of large inverted repeat (IR) DNA sequences which fulfill all requirements for formation of cruciform DNA structures. Such alternative DNA structures are suggested to have a great impact in altering the chromatin architecture and function. Our comprehensive analysis of the corresponding orthologous nucleotide sequences of an IR sequence from Homo sapiens and Pan troglodytes revealed that most of the nucleotide differences between the two species are symmetrical to the apex of the IR, and that the spacer region of the orthologous IRs are in reverse orientation. We provide evidence that this IR forms a large non-B DNA structure containing two Holliday junctions, allowing intrastrand nucleotide pairing of the arms and interstrand pairing of the spacer region of the IR. This structure would extrude into a large double-cruciform DNA structure providing the molecular basis of translocation events and regulation of gene expression.
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MESH Headings
- Animals
- Antigens, Neoplasm/genetics
- Base Sequence
- Chromosomes, Human, X/chemistry
- Chromosomes, Human, X/genetics
- DNA/chemistry
- DNA/genetics
- DNA, Cruciform/chemistry
- DNA, Cruciform/genetics
- Humans
- Models, Molecular
- Nucleic Acid Conformation
- Pan troglodytes/genetics
- Phylogeny
- Repetitive Sequences, Nucleic Acid
- Sequence Homology, Nucleic Acid
- Species Specificity
- X Chromosome/chemistry
- X Chromosome/genetics
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Affiliation(s)
- Florian O Losch
- Clinical Research Group Tumor Immunology, Department of Dermatology, Charité - Universitätsmedizin Berlin, 10098 Berlin, Germany.
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Deletion of the cruciform binding domain in CBP/14-3-3 displays reduced origin binding and initiation of DNA replication in budding yeast. BMC Mol Biol 2007; 8:27. [PMID: 17430600 PMCID: PMC1865385 DOI: 10.1186/1471-2199-8-27] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Accepted: 04/12/2007] [Indexed: 11/17/2022] Open
Abstract
Background Initiation of eukaryotic DNA replication involves many protein-protein and protein-DNA interactions. We have previously shown that 14-3-3 proteins bind cruciform DNA and associate with mammalian and yeast replication origins in a cell cycle dependent manner. Results By expressing the human 14-3-3ε, as the sole member of 14-3-3 proteins family in Saccharomyces cerevisiae, we show that 14-3-3ε complements the S. cerevisiae Bmh1/Bmh2 double knockout, conserves its cruciform binding activity, and associates in vivo with the yeast replication origins ARS307. Deletion of the α5-helix, the potential cruciform binding domain of 14-3-3, decreased the cruciform binding activity of the protein as well as its association with the yeast replication origins ARS307 and ARS1. Furthermore, the mutant cells had a reduced ability to stably maintain plasmids bearing one or multiple origins. Conclusion 14-3-3, a cruciform DNA binding protein, associates with yeast origins of replication and functions as an initiator of DNA replication, presumably through binding to cruciform DNA forming at yeast replicators.
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Arunkumar KP, Nagaraju J. Unusually long palindromes are abundant in mitochondrial control regions of insects and nematodes. PLoS One 2006; 1:e110. [PMID: 17205114 PMCID: PMC1762429 DOI: 10.1371/journal.pone.0000110] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2006] [Accepted: 11/26/2006] [Indexed: 11/29/2022] Open
Abstract
Background Palindromes are known to be involved in a variety of biological processes. In the present investigation we carried out a comprehensive analysis of palindromes in the mitochondrial control regions (CRs) of several animal groups to study their frequency, distribution and architecture to gain insights into the origin of replication of mtDNA. Methodology/Principal Findings Many species of Arthropoda, Nematoda, Mollusca and Annelida harbor palindromes and inverted repeats (IRs) in their CRs. Lower animals like cnidarians and higher animal groups like chordates are almost devoid of palindromes and IRs. The study revealed that palindrome occurrence is positively correlated with the AT content of CRs, and that IRs are likely to give rise to longer palindromes. Conclusions/Significance The present study attempts to explain possible reasons and gives in silico evidence for absence of palindromes and IRs from CR of vertebrate mtDNA and acquisition and retention of the same in insects. Study of CRs of different animal phyla uncovered unique architecture of this locus, be it high abundance of long palindromes and IRs in CRs of Insecta and Nematoda, or short IRs of 10–20 nucleotides with a spacer region of 12–14 bases in subphylum Chelicerata, or nearly complete of absence of any long palindromes and IRs in Vertebrata, Cnidaria and Echinodermata.
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Nakano SI, Kirihata T, Fujii S, Sakai H, Kuwahara M, Sawai H, Sugimoto N. Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides. Nucleic Acids Res 2006; 35:486-94. [PMID: 17169988 PMCID: PMC1802612 DOI: 10.1093/nar/gkl1073] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
A self-complementary nucleotide sequence can form both a unimolecular hairpin and a bimolecular duplex. In this study, the secondary structures of the self-complementary DNA and RNA oligonucleotides with different sequences and lengths were investigated under various solution conditions by gel electrophoresis, circular dichroism (CD) and electron paramagnetic resonance (EPR) spectroscopy and a ultraviolet (UV) melting analysis. The DNA sequences tended to adopt a hairpin conformation at low cation concentrations, but a bimolecular duplex was preferentially formed at an elevated cationic strength. On the other hand, fully matched RNA sequences adopted a bimolecular duplex regardless of the cation concentration. The thermal melting experiments indicated a greater change in the melting temperature of the bimolecular duplexes (by approximately 20 degrees C) than that of the hairpin (by approximately 10 degrees C) by increasing the NaCl concentration from 10 mM to 1 M. Hairpin formations were also observed for the palindrome DNA sequences derived from Escherichia coli, but association of the complementary palindrome sequences was observed when spermine, one of the major cationic molecules in a cell, existed at the physiological concentration. The results indicate the role of cations for shifting the structural equilibrium toward a nucleotide assembly and implicate nucleotide structures in cells.
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Affiliation(s)
- Shu-ichi Nakano
- Frontier Institute for Biomolecular Engineering Research (FIBER)8–9–1 Okamoto, Higashinada–ku, Kobe 658–8501, Japan
| | - Toshimasa Kirihata
- Department of Chemistry, Faculty of Science and Engineering, Konan University8–9–1 Okamoto, Higashinada–ku, Kobe 658–8501, Japan
| | - Satoshi Fujii
- Frontier Institute for Biomolecular Engineering Research (FIBER)8–9–1 Okamoto, Higashinada–ku, Kobe 658–8501, Japan
- Department of Chemistry, Faculty of Science and Engineering, Konan University8–9–1 Okamoto, Higashinada–ku, Kobe 658–8501, Japan
| | - Hiroshi Sakai
- Department of Chemistry, Faculty of Science and Engineering, Konan University8–9–1 Okamoto, Higashinada–ku, Kobe 658–8501, Japan
| | - Masayasu Kuwahara
- Faculty of Engineering, Gunma University1-5-1 Tenjin-chou, Kiryu, Gunma 376-8515, Japan
- PRESTO, Japan Science and Technology Agency (JST)Saitama 332-0012, Japan
| | - Hiroaki Sawai
- Faculty of Engineering, Gunma University1-5-1 Tenjin-chou, Kiryu, Gunma 376-8515, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER)8–9–1 Okamoto, Higashinada–ku, Kobe 658–8501, Japan
- Department of Chemistry, Faculty of Science and Engineering, Konan University8–9–1 Okamoto, Higashinada–ku, Kobe 658–8501, Japan
- To whom correspondence should be addressed. Tel: +81 78 435 2497; Fax: +81 78 435 2539;
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Uzbekova S, Roy-Sabau M, Dalbiès-Tran R, Perreau C, Papillier P, Mompart F, Thelie A, Pennetier S, Cognie J, Cadoret V, Royere D, Monget P, Mermillod P. Zygote arrest 1 gene in pig, cattle and human: evidence of different transcript variants in male and female germ cells. Reprod Biol Endocrinol 2006; 4:12. [PMID: 16551357 PMCID: PMC1435755 DOI: 10.1186/1477-7827-4-12] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Accepted: 03/21/2006] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Zygote arrest 1 (ZAR1) is one of the few known oocyte-specific maternal-effect genes essential for the beginning of embryo development discovered in mice. This gene is evolutionary conserved in vertebrates and ZAR1 protein is characterized by the presence of atypical plant homeobox zing finger domain, suggesting its role in transcription regulation. This work was aimed at the study of this gene, which could be one of the key regulators of successful preimplantation development of domestic animals, in pig and cattle, as compared with human. METHODS Screenings of somatic cell hybrid panels and in silico research were performed to characterize ZAR1 chromosome localization and sequences. Rapid amplification of cDNA ends was used to obtain full-length cDNAs. Spatio-temporal mRNA expression patterns were studied using Northern blot, reverse transcription coupled to polymerase chain reaction and in situ hybridization. RESULTS We demonstrated that ZAR1 is a single copy gene, positioned on chromosome 8 in pig and 6 in cattle, and several variants of correspondent cDNA were cloned from oocytes. Sequence analysis of ZAR1 cDNAs evidenced numerous short inverted repeats within the coding sequences and putative Pumilio-binding and embryo-deadenylation elements within the 3'-untranslated regions, indicating the potential regulation ways. We showed that ZAR1 expressed exclusively in oocytes in pig ovary, persisted during first cleavages in embryos developed in vivo and declined sharply in morulae and blastocysts. ZAR1 mRNA was also detected in testis, and, at lower level, in hypothalamus and pituitary in both species. For the first time, ZAR1 was localized in testicular germ cells, notably in round spermatids. In addition, in pig, cattle and human only shorter ZAR1 transcript variants resulting from alternative splicing were found in testis as compared to oocyte. CONCLUSION Our data suggest that in addition to its role in early embryo development highlighted by expression pattern of full-length transcript in oocytes and early embryos, ZAR1 could also be implicated in the regulation of meiosis and post meiotic differentiation of male and female germ cells through expression of shorter splicing variants. Species conservation of ZAR1 expression and regulation underlines the central role of this gene in early reproductive processes.
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Affiliation(s)
- Svetlana Uzbekova
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Monica Roy-Sabau
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Rozenn Dalbiès-Tran
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Christine Perreau
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Pascal Papillier
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Florence Mompart
- Laboratoire de Génétique Cellulaire, INRA, Chemin de Borde-Rouge – Auzeville, BP 52627 31326 Castanet-Tolosan Cedex, France
| | - Aurore Thelie
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Sophie Pennetier
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Juliette Cognie
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Veronique Cadoret
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
- Service de Médecine et Biologie de la Reproduction, UMR 6175, Centre Hospitalier Universitaire Bretonneau, 37044 Tours, France
| | - Dominique Royere
- Service de Médecine et Biologie de la Reproduction, UMR 6175, Centre Hospitalier Universitaire Bretonneau, 37044 Tours, France
| | - Philippe Monget
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Pascal Mermillod
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
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48
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Warburton PE, Giordano J, Cheung F, Gelfand Y, Benson G. Inverted repeat structure of the human genome: the X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes. Genome Res 2004; 14:1861-9. [PMID: 15466286 PMCID: PMC524409 DOI: 10.1101/gr.2542904] [Citation(s) in RCA: 193] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We have performed the first genome-wide analysis of the Inverted Repeat (IR) structure in the human genome, using a novel and efficient software package called Inverted Repeats Finder (IRF). After masking of known repetitive elements, IRF detected 22,624 human IRs characterized by arm size from 25 bp to >100 kb with at least 75% identity, and spacer length up to 100 kb. This analysis required 6 h on a desktop PC. In all, 166 IRs had arm lengths >8 kb. From this set, IRs were excluded if they were in unfinished/unassembled regions of the genome, or clustered with other closely related IRs, yielding a set of 96 large IRs. Of these, 24 (25%) occurred on the X-chromosome, although it represents only approximately 5% of the genome. Of the X-chromosome IRs, 83.3% were >/=99% identical, compared with 28.8% of autosomal IRs. Eleven IRs from Chromosome X, one from Chromosome 11, and seven already described from Chromosome Y contain genes predominantly expressed in testis. PCR analysis of eight of these IRs correctly amplified the corresponding region in the human genome, and six were also confirmed in gorilla or chimpanzee genomes. Similarity dot-plots revealed that 22 IRs contained further secondary homologous structures partially categorized into three distinct patterns. The prevalence of large highly homologous IRs containing testes genes on the X- and Y-chromosomes suggests a possible role in male germ-line gene expression and/or maintaining sequence integrity by gene conversion.
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Affiliation(s)
- Peter E Warburton
- Department of Human Genetics, Mount Sinai School of Medicine, New York, New York 10029, USA.
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Wang L, Lin CM, Brooks S, Cimbora D, Groudine M, Aladjem MI. The human beta-globin replication initiation region consists of two modular independent replicators. Mol Cell Biol 2004; 24:3373-86. [PMID: 15060158 PMCID: PMC381644 DOI: 10.1128/mcb.24.8.3373-3386.2004] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous studies have shown that mammalian cells contain replicator sequences, which can determine where DNA replication initiates. However, the specific sequences that confer replicator activity were not identified. Here we report a detailed analysis of replicator sequences that dictate initiation of DNA replication from the human beta-globin locus. This analysis suggests that the beta-globin replication initiation region contains two adjacent, redundant replicators. Each replicator was capable of initiating DNA replication independently at ectopic sites. Within each of these two replicators, we identified short, discrete, nonredundant sequences, which cooperatively determine replicator activity. Experiments with somatic cell hybrids further demonstrated that the requirements for initiation at ectopic sites were similar to the requirements for initiation within native human chromosomes. The replicator clustering and redundancy exemplified in the human beta-globin locus may account for the extreme difficulty in identifying replicator sequences in mammalian cells and suggest that mammalian replication initiation sites may be determined by cooperative sequence modules.
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Affiliation(s)
- Lixin Wang
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
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50
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Pakleza C, Cognet JAH. Biopolymer Chain Elasticity: A novel concept and a least deformation energy principle predicts backbone and overall folding of DNA TTT hairpins in agreement with NMR distances. Nucleic Acids Res 2003; 31:1075-85. [PMID: 12560506 PMCID: PMC149214 DOI: 10.1093/nar/gkg194] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A new molecular modelling methodology is presented and shown to apply to all published solution structures of DNA hairpins with TTT in the loop. It is based on the theory of elasticity of thin rods and on the assumption that single-stranded B-DNA behaves as a continuous, unshearable, unstretchable and flexible thin rod. It requires four construction steps: (i) computation of the tri-dimensional trajectory of the elastic line, (ii) global deformation of single-stranded helical DNA onto the elastic line, (iii) optimisation of the nucleoside rotations about the elastic line, (iv) energy minimisation to restore backbone bond lengths and bond angles. This theoretical approach called 'Biopolymer Chain Elasticity' (BCE) is capable of reproducing the tri-dimensional course of the sugar-phosphate chain and, using NMR-derived distances, of reproducing models close to published solution structures. This is shown by computing three different types of distance criteria. The natural description provided by the elastic line and by the new parameter, Omega, which corresponds to the rotation angles of nucleosides about the elastic line, offers a considerable simplification of molecular modelling of hairpin loops. They can be varied independently from each other, since the global shape of the hairpin loop is preserved in all cases.
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Affiliation(s)
- Christophe Pakleza
- Laboratoire de Physico-chimie Biomoléculaire et Cellulaire, UMR 7033 CNRS, T22-12, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris cedex 05, France
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