1
|
Sahu P, Barik S, Ghosh K, Subramanian H. High Nucleotide Skew Palindromic DNA Sequences Function as Potential Replication Origins due to their Unzipping Propensity. J Mol Evol 2024:10.1007/s00239-024-10202-y. [PMID: 39313579 DOI: 10.1007/s00239-024-10202-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Accepted: 08/27/2024] [Indexed: 09/25/2024]
Abstract
Locations of DNA replication initiation in prokaryotes, called "origins of replication", are well-characterized. However, a mechanistic understanding of the sequence dependence of the local unzipping of double-stranded DNA, the first step towards replication initiation, is lacking. Here, utilizing a Markov chain model that was created to address the directional nature of DNA unzipping and replication, we model the sequence dependence of local melting of double-stranded linear DNA segments. We show that generalized palindromic sequences with high nucleotide skews have a low kinetic barrier for local melting near melting temperatures. This allows for such sequences to function as potential replication origins. We support our claim with evidence for high-skew palindromic sequences within the replication origins of mitochondrial DNA, bacteria, archaea and plasmids.
Collapse
Affiliation(s)
- Parthasarathi Sahu
- Department of Physics, National Institute of Technology, Durgapur, India
| | - Sashikanta Barik
- Department of Physics, National Institute of Technology, Durgapur, India
| | - Koushik Ghosh
- Department of Physics, National Institute of Technology, Durgapur, India
| | | |
Collapse
|
2
|
Banazadeh M, Abiri A, Poortaheri MM, Asnaashari L, Langarizadeh MA, Forootanfar H. Unexplored power of CRISPR-Cas9 in neuroscience, a multi-OMICs review. Int J Biol Macromol 2024; 263:130413. [PMID: 38408576 DOI: 10.1016/j.ijbiomac.2024.130413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/27/2023] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
The neuroscience and neurobiology of gene editing to enhance learning and memory is of paramount interest to the scientific community. The advancements of CRISPR system have created avenues to treat neurological disorders by means of versatile modalities varying from expression to suppression of genes and proteins. Neurodegenerative disorders have also been attributed to non-canonical DNA secondary structures by affecting neuron activity through controlling gene expression, nucleosome shape, transcription, translation, replication, and recombination. Changing DNA regulatory elements which could contribute to the fate and function of neurons are thoroughly discussed in this review. This study presents the ability of CRISPR system to boost learning power and memory, treat or cure genetically-based neurological disorders, and alleviate psychiatric diseases by altering the activity and the irritability of the neurons at the synaptic cleft through DNA manipulation, and also, epigenetic modifications using Cas9. We explore and examine how each different OMIC techniques can come useful when altering DNA sequences. Such insight into the underlying relationship between OMICs and cellular behaviors leads us to better neurological and psychiatric therapeutics by intelligently designing and utilizing the CRISPR/Cas9 technology.
Collapse
Affiliation(s)
- Mohammad Banazadeh
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Ardavan Abiri
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520, USA
| | | | - Lida Asnaashari
- Student Research Committee, Kerman Universiy of Medical Sciences, Kerman, Iran
| | - Mohammad Amin Langarizadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Hamid Forootanfar
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran.
| |
Collapse
|
3
|
Smirnov E, Molínová P, Chmúrčiaková N, Vacík T, Cmarko D. Non-canonical DNA structures in the human ribosomal DNA. Histochem Cell Biol 2023; 160:499-515. [PMID: 37750997 DOI: 10.1007/s00418-023-02233-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 09/27/2023]
Abstract
Non-canonical structures (NCS) refer to the various forms of DNA that differ from the B-conformation described by Watson and Crick. It has been found that these structures are usual components of the genome, actively participating in its essential functions. The present review is focused on the nine kinds of NCS appearing or likely to appear in human ribosomal DNA (rDNA): supercoiling structures, R-loops, G-quadruplexes, i-motifs, DNA triplexes, cruciform structures, DNA bubbles, and A and Z DNA conformations. We discuss the conditions of their generation, including their sequence specificity, distribution within the locus, dynamics, and beneficial and detrimental role in the cell.
Collapse
Affiliation(s)
- Evgeny Smirnov
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic.
| | - Pavla Molínová
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Nikola Chmúrčiaková
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Tomáš Vacík
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Dušan Cmarko
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| |
Collapse
|
4
|
Nickoloff JA, Jaiswal AS, Sharma N, Williamson EA, Tran MT, Arris D, Yang M, Hromas R. Cellular Responses to Widespread DNA Replication Stress. Int J Mol Sci 2023; 24:16903. [PMID: 38069223 PMCID: PMC10707325 DOI: 10.3390/ijms242316903] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Replicative DNA polymerases are blocked by nearly all types of DNA damage. The resulting DNA replication stress threatens genome stability. DNA replication stress is also caused by depletion of nucleotide pools, DNA polymerase inhibitors, and DNA sequences or structures that are difficult to replicate. Replication stress triggers complex cellular responses that include cell cycle arrest, replication fork collapse to one-ended DNA double-strand breaks, induction of DNA repair, and programmed cell death after excessive damage. Replication stress caused by specific structures (e.g., G-rich sequences that form G-quadruplexes) is localized but occurs during the S phase of every cell division. This review focuses on cellular responses to widespread stress such as that caused by random DNA damage, DNA polymerase inhibition/nucleotide pool depletion, and R-loops. Another form of global replication stress is seen in cancer cells and is termed oncogenic stress, reflecting dysregulated replication origin firing and/or replication fork progression. Replication stress responses are often dysregulated in cancer cells, and this too contributes to ongoing genome instability that can drive cancer progression. Nucleases play critical roles in replication stress responses, including MUS81, EEPD1, Metnase, CtIP, MRE11, EXO1, DNA2-BLM, SLX1-SLX4, XPF-ERCC1-SLX4, Artemis, XPG, FEN1, and TATDN2. Several of these nucleases cleave branched DNA structures at stressed replication forks to promote repair and restart of these forks. We recently defined roles for EEPD1 in restarting stressed replication forks after oxidative DNA damage, and for TATDN2 in mitigating replication stress caused by R-loop accumulation in BRCA1-defective cells. We also discuss how insights into biological responses to genome-wide replication stress can inform novel cancer treatment strategies that exploit synthetic lethal relationships among replication stress response factors.
Collapse
Affiliation(s)
- Jac A. Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO 80523, USA
| | - Aruna S. Jaiswal
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO 80523, USA
| | - Elizabeth A. Williamson
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Manh T. Tran
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Dominic Arris
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Ming Yang
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Robert Hromas
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| |
Collapse
|
5
|
Gall-Duncan T, Luo J, Jurkovic CM, Fischer LA, Fujita K, Deshmukh AL, Harding RJ, Tran S, Mehkary M, Li V, Leib DE, Chen R, Tanaka H, Mason AG, Lévesque D, Khan M, Razzaghi M, Prasolava T, Lanni S, Sato N, Caron MC, Panigrahi GB, Wang P, Lau R, Castel AL, Masson JY, Tippett L, Turner C, Spies M, La Spada AR, Campos EI, Curtis MA, Boisvert FM, Faull RLM, Davidson BL, Nakamori M, Okazawa H, Wold MS, Pearson CE. Antagonistic roles of canonical and Alternative-RPA in disease-associated tandem CAG repeat instability. Cell 2023; 186:4898-4919.e25. [PMID: 37827155 PMCID: PMC11209935 DOI: 10.1016/j.cell.2023.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 06/30/2023] [Accepted: 09/09/2023] [Indexed: 10/14/2023]
Abstract
Expansions of repeat DNA tracts cause >70 diseases, and ongoing expansions in brains exacerbate disease. During expansion mutations, single-stranded DNAs (ssDNAs) form slipped-DNAs. We find the ssDNA-binding complexes canonical replication protein A (RPA1, RPA2, and RPA3) and Alternative-RPA (RPA1, RPA3, and primate-specific RPA4) are upregulated in Huntington disease and spinocerebellar ataxia type 1 (SCA1) patient brains. Protein interactomes of RPA and Alt-RPA reveal unique and shared partners, including modifiers of CAG instability and disease presentation. RPA enhances in vitro melting, FAN1 excision, and repair of slipped-CAGs and protects against CAG expansions in human cells. RPA overexpression in SCA1 mouse brains ablates expansions, coincident with decreased ATXN1 aggregation, reduced brain DNA damage, improved neuron morphology, and rescued motor phenotypes. In contrast, Alt-RPA inhibits melting, FAN1 excision, and repair of slipped-CAGs and promotes CAG expansions. These findings suggest a functional interplay between the two RPAs where Alt-RPA may antagonistically offset RPA's suppression of disease-associated repeat expansions, which may extend to other DNA processes.
Collapse
Affiliation(s)
- Terence Gall-Duncan
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jennifer Luo
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Laura A Fischer
- Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kyota Fujita
- Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Amit L Deshmukh
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rachel J Harding
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Stephanie Tran
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mustafa Mehkary
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Vanessa Li
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - David E Leib
- Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Ran Chen
- Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hikari Tanaka
- Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Amanda G Mason
- Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Dominique Lévesque
- Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Mahreen Khan
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mortezaali Razzaghi
- Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Tanya Prasolava
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stella Lanni
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Nozomu Sato
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Marie-Christine Caron
- CHU de Québec-Université Laval, Oncology Division, Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec, QC, Canada
| | - Gagan B Panigrahi
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Peixiang Wang
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rachel Lau
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Jean-Yves Masson
- CHU de Québec-Université Laval, Oncology Division, Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec, QC, Canada
| | - Lynette Tippett
- School of Psychology, University of Auckland, Auckland, New Zealand; University Research Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Clinton Turner
- Anatomical Pathology, LabPlus, Auckland City Hospital, Auckland, New Zealand
| | - Maria Spies
- Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Albert R La Spada
- Pathology & Laboratory Medicine, Neurology, and Biological Chemistry, University of California, Irvine School of Medicine, Irvine, CA, USA; Neurobiology & Behavior, University of California, Irvine, Irvine, CA, USA; Center for Neurotherapeutics, University of California, Irvine, Irvine, CA 92697, USA
| | - Eric I Campos
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Maurice A Curtis
- University Research Centre for Brain Research, University of Auckland, Auckland, New Zealand; Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | | | - Richard L M Faull
- University Research Centre for Brain Research, University of Auckland, Auckland, New Zealand; Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | - Beverly L Davidson
- Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Masayuki Nakamori
- Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hitoshi Okazawa
- Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Marc S Wold
- Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Christopher E Pearson
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.
| |
Collapse
|
6
|
Nitipan S, Saithong P. Characterization and sequencing analysis of pLP2.5-11 and pLP3.0-4 novel cryptic plasmids from Lactiplantibacillus plantarum WP72/27. 3 Biotech 2023; 13:263. [PMID: 37408733 PMCID: PMC10317920 DOI: 10.1007/s13205-023-03684-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/25/2023] [Indexed: 07/07/2023] Open
Abstract
We sequenced and described two cryptic plasmids from Lactiplantibacillus plantarum strain WP72/27, termed pLP2.5-11 (OP831909) and pLP3.0-4 (OP831910). Nucleotide sequencing gave the sizes of pLP2.5-11 and pLP3.0-4 as 2754 and 3197 base pairs, with G + C contents 38.89% and 40.88% and predicted two and eight putative open reading frames, respectively. The RepA protein of pLP2.5-11 shared a 99% identity with pC30il, pLP1 and pC30il, whereas the RepB protein of pLP3.0-4 shared a 98% identity with pXY3, a member of the rolling-circle replication (RCR) pC194 family. The origin of plasmid replication was predicted to consist of inverted and directed repeat sequences upstream of the Rep genes. Sequence analysis predicted that both pLP2.5-11 and pLP3.0-4 plasmids replicate via a rolling-circle process. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03684-y.
Collapse
Affiliation(s)
- Supachai Nitipan
- Department of Biology, Faculty of Science, Thaksin University, Phattalung Campus, Phattalung, 93210 Thailand
- Microbial Technology for Agriculture, Food and Environment Research Center, Thaksin University, Phatthalung Campus, Phatthalung, 93210 Thailand
| | - Pramuan Saithong
- Department of Applied Microbiology, Institute of Food Research and Product Development, Kasetsart University, Bangkok, 10900 Thailand
| |
Collapse
|
7
|
Getz LJ, Brown JM, Sobot L, Chow A, Mahendrarajah J, Thomas N. Attenuation of a DNA cruciform by a conserved regulator directs T3SS1 mediated virulence in Vibrio parahaemolyticus. Nucleic Acids Res 2023; 51:6156-6171. [PMID: 37158250 PMCID: PMC10325908 DOI: 10.1093/nar/gkad370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/23/2023] [Accepted: 04/27/2023] [Indexed: 05/10/2023] Open
Abstract
Pathogenic Vibrio species account for 3-5 million annual life-threatening human infections. Virulence is driven by bacterial hemolysin and toxin gene expression often positively regulated by the winged helix-turn-helix (wHTH) HlyU transcriptional regulator family and silenced by histone-like nucleoid structural protein (H-NS). In the case of Vibrio parahaemolyticus, HlyU is required for virulence gene expression associated with type 3 Secretion System-1 (T3SS1) although its mechanism of action is not understood. Here, we provide evidence for DNA cruciform attenuation mediated by HlyU binding to support concomitant virulence gene expression. Genetic and biochemical experiments revealed that upon HlyU mediated DNA cruciform attenuation, an intergenic cryptic promoter became accessible allowing for exsA mRNA expression and initiation of an ExsA autoactivation feedback loop at a separate ExsA-dependent promoter. Using a heterologous E. coli expression system, we reconstituted the dual promoter elements which revealed that HlyU binding and DNA cruciform attenuation were strictly required to initiate the ExsA autoactivation loop. The data indicate that HlyU acts to attenuate a transcriptional repressive DNA cruciform to support T3SS1 virulence gene expression and reveals a non-canonical extricating gene regulation mechanism in pathogenic Vibrio species.
Collapse
Affiliation(s)
- Landon J Getz
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
| | - Justin M Brown
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
| | - Lauren Sobot
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
| | - Alexandra Chow
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
| | - Jastina Mahendrarajah
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
| | - Nikhil A Thomas
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
- Department of Medicine, Faculty of Medicine, Dalhousie University. Halifax, NS, Canada
| |
Collapse
|
8
|
Himmelstrand K, Brandström Durling M, Karlsson M, Stenlid J, Olson Å. Multiple rearrangements and low inter- and intra-species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex. Front Microbiol 2023; 14:1159811. [PMID: 37275157 PMCID: PMC10234125 DOI: 10.3389/fmicb.2023.1159811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/16/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Mitochondria are essential organelles in the eukaryotic cells and responsible for the energy production but are also involved in many other functions including virulence of some fungal species. Although the evolution of fungal mitogenomes have been studied at some taxonomic levels there are still many things to be learned from studies of closely related species. Methods In this study, we have analyzed 60 mitogenomes in the five species of the Heterobasidion annosum sensu lato complex that all are necrotrophic pathogens on conifers. Results and Discussion Compared to other fungal genera the genomic and genetic variation between and within species in the complex was low except for multiple rearrangements. Several translocations of large blocks with core genes have occurred between the five species and rearrangements were frequent in intergenic areas. Mitogenome lengths ranged between 108 878 to 116 176 bp, mostly as a result of intron variation. There was a high degree of homology of introns, homing endonuclease genes, and intergenic ORFs among the five Heterobasidion species. Three intergenic ORFs with unknown function (uORF6, uORF8 and uORF9) were found in all five species and was located in conserved synteny blocks. A 13 bp long GC-containing self-complementary palindrome was discovered in many places in the five species that were optional in presence/absence. The within species variation is very low, among 48 H. parviporum mitogenomes, there was only one single intron exchange, and SNP frequency was 0.28% and indel frequency 0.043%. The overall low variation in the Heterobasidion annosum sensu lato complex suggests a slow evolution of the mitogenome.
Collapse
Affiliation(s)
| | | | | | | | - Åke Olson
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| |
Collapse
|
9
|
Wang G, Vasquez KM. Dynamic alternative DNA structures in biology and disease. Nat Rev Genet 2023; 24:211-234. [PMID: 36316397 DOI: 10.1038/s41576-022-00539-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Repetitive elements in the human genome, once considered 'junk DNA', are now known to adopt more than a dozen alternative (that is, non-B) DNA structures, such as self-annealed hairpins, left-handed Z-DNA, three-stranded triplexes (H-DNA) or four-stranded guanine quadruplex structures (G4 DNA). These dynamic conformations can act as functional genomic elements involved in DNA replication and transcription, chromatin organization and genome stability. In addition, recent studies have revealed a role for these alternative structures in triggering error-generating DNA repair processes, thereby actively enabling genome plasticity. As a driving force for genetic variation, non-B DNA structures thus contribute to both disease aetiology and evolution.
Collapse
Affiliation(s)
- Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA.
| |
Collapse
|
10
|
Genomic Analysis of Non-B Nucleic Acids Structures in SARS-CoV-2: Potential Key Roles for These Structures in Mutability, Translation, and Replication? Genes (Basel) 2023; 14:genes14010157. [PMID: 36672896 PMCID: PMC9859294 DOI: 10.3390/genes14010157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/01/2023] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Non-B nucleic acids structures have arisen as key contributors to genetic variation in SARS-CoV-2. Herein, we investigated the presence of defining spike protein mutations falling within inverted repeats (IRs) for 18 SARS-CoV-2 variants, discussed the potential roles of G-quadruplexes (G4s) in SARS-CoV-2 biology, and identified potential pseudoknots within the SARS-CoV-2 genome. Surprisingly, there was a large variation in the number of defining spike protein mutations arising within IRs between variants and these were more likely to occur in the stem region of the predicted hairpin stem-loop secondary structure. Notably, mutations implicated in ACE2 binding and propagation (e.g., ΔH69/V70, N501Y, and D614G) were likely to occur within IRs, whilst mutations involved in antibody neutralization and reduced vaccine efficacy (e.g., T19R, ΔE156, ΔF157, R158G, and G446S) were rarely found within IRs. We also predicted that RNA pseudoknots could predominantly be found within, or next to, 29 mutations found in the SARS-CoV-2 spike protein. Finally, the Omicron variants BA.2, BA.4, BA.5, BA.2.12.1, and BA.2.75 appear to have lost two of the predicted G4-forming sequences found in other variants. These were found in nsp2 and the sequence complementary to the conserved stem-loop II-like motif (S2M) in the 3' untranslated region (UTR). Taken together, non-B nucleic acids structures likely play an integral role in SARS-CoV-2 evolution and genetic diversity.
Collapse
|
11
|
Mak CH. Nucleic acid folding simulations using a physics-based atomistic free energy model. J Chem Phys 2022; 156:174114. [PMID: 35525642 DOI: 10.1063/5.0086304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Performing full-resolution atomistic simulations of nucleic acid folding has remained a challenge for biomolecular modeling. Understanding how nucleic acids fold and how they transition between different folded structures as they unfold and refold has important implications for biology. This paper reports a theoretical model and computer simulation of the ab initio folding of DNA inverted repeat sequences. The formulation is based on an all-atom conformational model of the sugar-phosphate backbone via chain closure, and it incorporates three major molecular-level driving forces-base stacking, counterion-induced backbone self-interactions, and base pairing-via separate analytical theories designed to capture and reproduce the effects of the solvent without requiring explicit water and ions in the simulation. To accelerate computational throughput, a mixed numerical/analytical algorithm for the calculation of the backbone conformational volume is incorporated into the Monte Carlo simulation, and special stochastic sampling techniques were employed to achieve the computational efficiency needed to fold nucleic acids from scratch. This paper describes implementation details, benchmark results, and the advantages and technical challenges with this approach.
Collapse
Affiliation(s)
- Chi H Mak
- Departments of Chemistry and Quantitative and Computational Biology, and Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, California 90089, USA
| |
Collapse
|
12
|
Ou-Yang H, Yang SH, Chen W, Yang SH, Cidem A, Sung LY, Chen CM. Cruciform DNA Structures Act as Legible Templates for Accelerating Homologous Recombination in Transgenic Animals. Int J Mol Sci 2022; 23:3973. [PMID: 35409332 PMCID: PMC9000021 DOI: 10.3390/ijms23073973] [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: 02/26/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 11/16/2022] Open
Abstract
Inverted repeat (IR) DNA sequences compose cruciform structures. Some genetic disorders are the result of genome inversion or translocation by cruciform DNA structures. The present study examined whether exogenous DNA integration into the chromosomes of transgenic animals was related to cruciform DNA structures. Large imperfect cruciform structures were frequently predicted around predestinated transgene integration sites in host genomes of microinjection-based transgenic (Tg) animals (αLA-LPH Tg goat, Akr1A1eGFP/eGFP Tg mouse, and NFκB-Luc Tg mouse) or CRISPR/Cas9 gene-editing (GE) animals (αLA-AP1 GE mouse). Transgene cassettes were imperfectly matched with their predestinated sequences. According to the analyzed data, we proposed a putative model in which the flexible cruciform DNA structures acted as a legible template for DNA integration into linear DNAs or double-strand break (DSB) alleles. To demonstrate this model, artificial inverted repeat knock-in (KI) reporter plasmids were created to analyze the KI rate using the CRISPR/Cas9 system in NIH3T3 cells. Notably, the KI rate of the 5′ homologous arm inverted repeat donor plasmid (5′IR) with the ROSA gRNA group (31.5%) was significantly higher than the knock-in reporter donor plasmid (KIR) with the ROSA gRNA group (21.3%, p < 0.05). However, the KI rate of the 3′ inverted terminal repeat/inverted repeat donor plasmid (3′ITRIR) group was not different from the KIR group (23.0% vs. 22.0%). These results demonstrated that the legibility of the sequence with the cruciform DNA existing in the transgene promoted homologous recombination (HR) with a higher KI rate. Our findings suggest that flexible cruciform DNAs folded by IR sequences improve the legibility and accelerate DNA 3′-overhang integration into the host genome via homologous recombination machinery.
Collapse
Affiliation(s)
- Huan Ou-Yang
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei 106, Taiwan
| | - Shiao-Hsuan Yang
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Reproductive Medicine Center, Department of Gynecology, Changhua Christian Hospital, Changhua 515, Taiwan
| | - Wei Chen
- Division of Pulmonary and Critical Care Medicine, Chia-Yi Christian Hospital, Chiayi 600, Taiwan;
| | - Shang-Hsun Yang
- Department of Physiology, National Cheng Kung University, Tainan 701, Taiwan;
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Abdulkadir Cidem
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- Department of Molecular Biology and Genetics, Erzurum Technical University, Erzurum 25250, Turkey
| | - Li-Ying Sung
- Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei 106, Taiwan
| | - Chuan-Mu Chen
- Program in Translational Medicine, Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; (H.O.-Y.); (S.-H.Y.); (A.C.)
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
- Rong-Hsing Translational Medicine Research Center, Taichung Veterans General Hospital, Taichung 407, Taiwan
| |
Collapse
|
13
|
Structural switching/polymorphism by sequential base substitution at quasi-palindromic SNP site (G → A) in LCR of human β-globin gene cluster. Int J Biol Macromol 2021; 201:216-225. [PMID: 34973267 DOI: 10.1016/j.ijbiomac.2021.12.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 11/20/2022]
Abstract
The human β-globin gene Locus Control Region (LCR), a dominant regulator of globin gene expression contains five tissue-specific DNase I-hypersensitive sites (HSs). A single nucleotide polymorphism (SNP) (A → G) present in HS4 region of locus control region (LCR), have shown a notable association between the G allele and the occurrence of β-thalassemia. This SNP site exhibiting a hairpin - duplex equilibrium manifested in A → B like DNA transition has previously been reported from this laboratory. Since, DNA is a dynamic and adaptable molecule, so any change of a single base within a primary DNA sequence can produce major biological consequences commonly manifested in genetic disorders such as sickle cell anemia and β-thalassemia. Herein, the differential behavior of sequential single base substitutions G → A on the quasi-palindromic sequence (d-TGGGGGCCCCA; HPG11) has been explored. A combination of native gel electrophoresis, circular dichroism (CD), and UV-thermal denaturation (Tm) techniques have been used to investigate the structural polymorphism associated with various variants of HPG11 i.e. HPG11A2 to HPG11A5. The CD spectra confirmed that all the HPG11 variants exhibit a hairpin - duplex equilibrium. Oligomer concentration dependence on CD spectra has been correlated with A → B DNA conformational transition. However, as revealed in gel electrophoresis, HPG11A2 → A5 exhibit the formation of a tetramolecular structure (four-way junction) at higher oligomer concentration. UV-melting studies also supported the melting of hairpin, duplex and four-way junction structure. This polymorphism pattern may possibly be significant for DNA-protein recognition, in the process of regulation of LCR in the β-globin gene.
Collapse
|
14
|
Yin C, Yau SST. Inverted repeats in coronavirus SARS-CoV-2 genome manifest the evolution events. J Theor Biol 2021; 530:110885. [PMID: 34478743 PMCID: PMC8406619 DOI: 10.1016/j.jtbi.2021.110885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/13/2021] [Accepted: 08/25/2021] [Indexed: 11/24/2022]
Abstract
The world faces a great unforeseen challenge through the COVID-19 pandemic caused by coronavirus SARS-CoV-2. The virus genome structure and evolution are positioned front and center for further understanding insights on vaccine development, monitoring of transmission trajectories, and prevention of zoonotic infections of new coronaviruses. Of particular interest are genomic elements Inverse Repeats (IRs), which maintain genome stability, regulate gene expressions, and are the targets of mutations. However, little research attention is given to the IR content analysis in the SARS-CoV-2 genome. In this study, we propose a geometric analysis method and using the method to investigate the distributions of IRs in SARS-CoV-2 and its related coronavirus genomes. The method represents each genomic IR sequence pair as a single point and constructs the geometric shape of the genome using the IRs. Thus, the IR shape can be considered as the signature of the genome. The genomes of different coronaviruses are then compared using the constructed IR shapes. The results demonstrate that SARS-CoV-2 genome, specifically, has an abundance of IRs, and the IRs in coronavirus genomes show an increase during evolution events.
Collapse
Affiliation(s)
- Changchuan Yin
- Department of Mathematics, Statistics, and Computer Science, The University of Illinois at Chicago, Chicago, IL 60607-7045, USA.
| | - Stephen S-T Yau
- Department of Mathematical Sciences, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
15
|
The minicircular and extremely heteroplasmic mitogenome of the holoparasitic plant Rhopalocnemis phalloides. Curr Biol 2021; 32:470-479.e5. [PMID: 34906352 DOI: 10.1016/j.cub.2021.11.053] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/25/2021] [Accepted: 11/22/2021] [Indexed: 12/14/2022]
Abstract
The plastid and nuclear genomes of parasitic plants exhibit deeply altered architectures,1-13 whereas the few examined mitogenomes range from deeply altered to conventional.14-20 To provide further insight on mitogenome evolution in parasitic plants, we report the highly modified mitogenome of Rhopalocnemis phalloides, a holoparasite in Balanophoraceae. Its mitogenome is uniquely arranged in 21 minicircular chromosomes that vary in size from 4,949 to 7,861 bp, with a total length of only 130,713 bp. All chromosomes share an identical 896 bp conserved region, with a large stem-loop that acts as the origin of replication, flanked on each side by hypervariable and semi-conserved regions. Similar minicircular structures with shared and unique regions have been observed in parasitic animals and free-living protists,21-24 suggesting convergent structural evolution. Southern blots confirm both the minicircular structure and the replication origin of the mitochondrial chromosomes. PacBio reads provide evidence for chromosome recombination and rolling-circle replication for the R. phalloides mitogenome. Despite its small size, the mitogenome harbors a typical set of genes and introns within the unique regions of each chromosome, yet introns are the smallest among seed plants and ferns. The mitogenome also exhibits extreme heteroplasmy, predominantly involving short indels and more complex variants, many of which cause potential loss-of-function mutations for some gene copies. All heteroplasmic variants are transcribed, and functional and nonfunctional protein-coding variants are spliced and RNA edited. Our findings offer a unique perspective into how mitogenomes of parasitic plants can be deeply altered and shed light on plant mitogenome replication.
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Pandya N, Bhagwat SR, Kumar A. Regulatory role of Non-canonical DNA Polymorphisms in human genome and their relevance in Cancer. Biochim Biophys Acta Rev Cancer 2021; 1876:188594. [PMID: 34303788 DOI: 10.1016/j.bbcan.2021.188594] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 12/17/2022]
Abstract
DNA has the ability to form polymorphic structures like canonical duplex DNA and non-canonical triplex DNA, Cruciform, Z-DNA, G-quadruplex (G4), i-motifs, and hairpin structures. The alteration in the form of DNA polymorphism in the response to environmental changes influences the gene expression. Non-canonical structures are engaged in various biological functions, including chromatin epigenetic and gene expression regulation via transcription and translation, as well as DNA repair and recombination. The presence of non-canonical structures in the regulatory region of the gene alters the gene expression and affects the cellular machinery. Formation of non-canonical structure in the regulatory site of cancer-related genes either inhibits or dysregulate the gene function and promote tumour formation. In the current article, we review the influence of non-canonical structure on the regulatory mechanisms in human genome. Moreover, we have also discussed the relevance of non-canonical structures in cancer and provided information on the drugs used for their treatment by targeting these structures.
Collapse
Affiliation(s)
- Nirali Pandya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Sonali R Bhagwat
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India.
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Goswami P, Bartas M, Lexa M, Bohálová N, Volná A, Červeň J, Červeňová V, Pečinka P, Špunda V, Fojta M, Brázda V. SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci. Brief Bioinform 2021; 22:1338-1345. [PMID: 33341900 PMCID: PMC7799342 DOI: 10.1093/bib/bbaa385] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/16/2020] [Accepted: 11/27/2020] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 is an intensively investigated virus from the order Nidovirales (Coronaviridae family) that causes COVID-19 disease in humans. Through enormous scientific effort, thousands of viral strains have been sequenced to date, thereby creating a strong background for deep bioinformatics studies of the SARS-CoV-2 genome. In this study, we inspected high-frequency mutations of SARS-CoV-2 and carried out systematic analyses of their overlay with inverted repeat (IR) loci and CpG islands. The main conclusion of our study is that SARS-CoV-2 hot-spot mutations are significantly enriched within both IRs and CpG island loci. This points to their role in genomic instability and may predict further mutational drive of the SARS-CoV-2 genome. Moreover, CpG islands are strongly enriched upstream from viral ORFs and thus could play important roles in transcription and the viral life cycle. We hypothesize that hypermethylation of these loci will decrease the transcription of viral ORFs and could therefore limit the progression of the disease.
Collapse
Affiliation(s)
- Pratik Goswami
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Matej Lexa
- Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Natália Bohálová
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.,Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jiří Červeň
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Veronika Červeňová
- Department of Mathematics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Vladimír Špunda
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.,Global Change Research Institute of the Czech Academy of Sciences, Brno, Czech Republic
| | - Miroslav Fojta
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Václav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| |
Collapse
|
20
|
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.
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Alternative DNA Structures In Vivo: Molecular Evidence and Remaining Questions. Microbiol Mol Biol Rev 2020; 85:85/1/e00110-20. [PMID: 33361270 DOI: 10.1128/mmbr.00110-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Duplex DNA naturally folds into a right-handed double helix in physiological conditions. Some sequences of unusual base composition may nevertheless form alternative structures, as was shown for many repeated sequences in vitro However, evidence for the formation of noncanonical structures in living cells is difficult to gather. It mainly relies on genetic assays demonstrating their function in vivo or through genetic instability reflecting particular properties of such structures. Efforts were made to reveal their existence directly in a living cell, mainly by generating antibodies specific to secondary structures or using chemical ligands selected for their affinity to these structures. Among secondary structure-forming DNAs are G-quadruplexes, human fragile sites containing minisatellites, AT-rich regions, inverted repeats able to form cruciform structures, hairpin-forming CAG/CTG triplet repeats, and triple helices formed by homopurine-homopyrimidine GAA/TTC trinucleotide repeats. Many of these alternative structures are involved in human pathologies, such as neurological or developmental disorders, as in the case of trinucleotide repeats, or cancers triggered by translocations linked to fragile sites. This review will discuss and highlight evidence supporting the formation of alternative DNA structures in vivo and will emphasize the role of the mismatch repair machinery in binding mispaired DNA duplexes, triggering genetic instability.
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Kumar M, Kaushik M, Kukreti S. Interaction of a photosensitizer methylene blue with various structural forms (cruciform, bulge duplex and hairpin) of designed DNA sequences. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 242:118716. [PMID: 32731146 DOI: 10.1016/j.saa.2020.118716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
Functionally important, local structural transitions in DNA generate various alternative conformations. Cruciform is one of such alternative DNA structures, usually targeted in genomes by various proteins. Symmetry elements in sequence as inverted repeats are the key factor for cruciform formation, facilitated by the presence of the AT-rich regions. Here, we used biophysical and biochemical techniques such as Gel electrophoresis, Circular dichroism (CD), and UV-thermal melting analysis to explore the structural status of the designed DNA sequences, which had potential to form cruciform structures under physiological conditions. The gel electrophoresis analysis revealed that the designed 53-mer DNA oligonucleotide sequence CR forms an intermolecular bulge duplex with flanking ends, while another sequence CRC adopts an intramolecular hairpin structure with flanking ends. Their equimolar complex (CRCRC) bestowed much-retarded migration due to the formation of a quite intriguing cruciform structure. CD studies confirmed that all the alternative structures (cruciform, bulge duplex, and hairpin with flanking ends) exhibit characteristics of B-DNA type conformation. A triphasic UV-thermal melting curve displayed by the complex formed by the equimolar ratio (CRCRC) is also suggestive of the formation of the cruciform structure. The interaction studies of CR, CRC, and their equimolar complex (1:1) with a photosensitizer methylene blue (MB) indicated that MB could not stabilize the discrete structures formed by CR and CRC sequences, however, the cruciform structure showed a quite significant increment in the melting temperature. Such studies facilitate our understanding of various secondary structures possibly present inside the cell and their interactions with drug/dye molecules.
Collapse
Affiliation(s)
- Mohan Kumar
- Department of Chemistry, University of Delhi, Delhi, India; Department of Chemistry, Shri Varshney College, Aligarh, Uttar Pradesh, India
| | - Mahima Kaushik
- Nano-bioconjugate Chemistry Lab, Cluster Innovation Centre, University of Delhi, Delhi, India
| | | |
Collapse
|
25
|
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.
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
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.
Collapse
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.)
| |
Collapse
|
30
|
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.
Collapse
|
31
|
Hogan RI, Hopkins K, Wheeler AJ, Allcock AL, Yesson C. Novel diversity in mitochondrial genomes of deep-sea Pennatulacea (Cnidaria: Anthozoa: Octocorallia). Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:764-777. [PMID: 31317811 DOI: 10.1080/24701394.2019.1634699] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We present the first documented complete mitogenomes of deep-sea Pennatulacea, representing nine genera and eight families. These include one species each of the deep-sea genera Funiculina, Halipteris, Protoptilum and Distichoptilum, four species each of Umbellula and Pennatula, three species of Kophobelemnon and two species of Anthoptilum, as well as one species of the epi- and mesobenthic genus Virgularia. Seventeen circular genomes ranged from 18,513 bp (Halipteris cf. finmarchica) to 19,171 bp (Distichoptilum gracile) and contained all genes standard to octocoral mitochondrial genomes (14 protein-coding genes, two ribosomal RNA genes and one transfer RNA). We found at least three different gene orders in Pennatulacea: the ancestral gene order, the gene order found in bamboo corals (Family Isididae), and a novel gene order. The mitogenome of one species of Umbellula has a bipartite genome (∼13 kbp and ∼5 kbp), with good evidence that both parts are circular.
Collapse
Affiliation(s)
- Raissa I Hogan
- Department of Zoology, Ryan Institute, National University of Ireland , Galway , Ireland
| | - Kevin Hopkins
- Institute of Zoology, Zoological Society of London, Regent's Park , London , UK
| | - Andrew J Wheeler
- School of Biological, Earth and Environmental Sciences/iCRAG/ERI, University College Cork , Cork , Ireland
| | - A Louise Allcock
- Department of Zoology, Ryan Institute, National University of Ireland , Galway , Ireland
| | - Chris Yesson
- Institute of Zoology, Zoological Society of London, Regent's Park , London , UK
| |
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
Bartas M, Bažantová P, Brázda V, Liao JC, Červeň J, Pečinka P. Identification of Distinct Amino Acid Composition of Human Cruciform Binding Proteins. Mol Biol 2019. [DOI: 10.1134/s0026893319010023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
34
|
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.
Collapse
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.
| |
Collapse
|
35
|
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.
Collapse
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.
| |
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
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.
Collapse
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.
| |
Collapse
|
38
|
Carr CE, Marky LA. Effect of GCAA stabilizing loops on three- and four-way intramolecular junctions. Phys Chem Chem Phys 2018; 20:5046-5056. [PMID: 29388988 DOI: 10.1039/c7cp08329g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Tetraloops are a common way of changing the melting behavior of a DNA or RNA structure without changing the sequence of the stem. Because of the ubiquitous nature of tetraloops, our goal is to understand the effect a GCAA tetraloop, which belongs to the GNRA family of tetraloops, has on the unfolding thermodynamics of intramolecular junctions. Specifically, we have described the melting behavior of intramolecular three-way and four-way junctions where a T5 loop has been replaced with a GCAA tetraloops in different positions. Their thermodynamic profiles, including ΔnNa+ and ΔnW, were analyzed based on the position of the tetraloop. We obtained between -16.7 and -27.5 kcal mol-1 for all junctions studied. The experimental data indicates the influence of the GCAA tetraloop is primarily dictated by the native unfolding of the junction; if the tetraloop is placed on a stem that unfolds as a single domain when the tetraloop is not present, it will unfold as a single domain when the tetraloop is present but with a higher thermal stability. Conversely, if the tetraloop is placed on a stem which unfolds cooperatively with other stems when the tetraloop is not present, the tetraloop will increase the thermal stability of all the stems in the melting domain. The oligonucleotide structure and not the tetraloop itself affects ion uptake; three-way junctions do not gain an increase in ion uptake, but four-way junctions do. This is not the case for water immobilization, where the position of the tetraloop dictates the amount of water immobilized.
Collapse
Affiliation(s)
- Carolyn E Carr
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA.
| | | |
Collapse
|
39
|
Carr CE, Marky LA. Melting Behavior of a DNA Four-Way Junction Using Spectroscopic and Calorimetric Techniques. J Am Chem Soc 2017; 139:14443-14455. [DOI: 10.1021/jacs.7b06429] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Carolyn E. Carr
- Department of Pharmaceutical
Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
| | - Luis A. Marky
- Department of Pharmaceutical
Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
| |
Collapse
|
40
|
Nagy YI, Hussein MMM, Ragab YM, Attia AS. Isogenic mutations in the Moraxella catarrhalis CydDC system display pleiotropic phenotypes and reveal the role of a palindrome sequence in its transcriptional regulation. Microbiol Res 2017. [PMID: 28647125 DOI: 10.1016/j.micres.2017.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Moraxella catarrhalis is becoming an important human respiratory tract pathogen affecting significant proportions from the population. However, still little is known about its physiology and molecular regulation. To this end, the CydDC, which is a heterodimeric ATP binding cassette transporter that has been shown to contribute to the maintenance of the redox homeostasis across the periplasm in other Gram-negative bacteria, is studied here. Amino acids multiple sequence alignments indicated that M. catarrhalis CydC is different from the CydC proteins of the bacterial species in which this system has been previously studied. These findings prompted further interest in studying this system in M. catarrhalis. Isogenic mutant in the CydDC system showed suppression in growth rate, hypersensitivity to oxidative and reductive stress and increased accumulation of intracellular cysteine levels. In addition, the growth of cydC- mutant exhibited hypersensitivity to exogenous cysteine; however, it did not display a significant difference from its wild-type counterpart in the murine pulmonary clearance model. Moreover, a palindrome was detected 94bp upstream of the cydD ORF suggesting it might act as a potential regulatory element. Real-time reverse transcription-PCR analysis showed that deletion/change in the palindrome resulted into alterations in the transcription levels of cydC. A better understanding of such system and its regulation helps in developing better ways to combat M. catarrhalis infections.
Collapse
Affiliation(s)
- Yosra I Nagy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Manal M M Hussein
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Yasser M Ragab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Ahmed S Attia
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt.
| |
Collapse
|
41
|
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.
Collapse
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
| |
Collapse
|
42
|
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.
Collapse
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:
| |
Collapse
|
43
|
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.
Collapse
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.
| |
Collapse
|
44
|
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.
Collapse
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.
| |
Collapse
|
45
|
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.
Collapse
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.
| |
Collapse
|
46
|
Brázda V, Kolomazník J, Lýsek J, Hároníková L, Coufal J, Št'astný J. Palindrome analyser - A new web-based server for predicting and evaluating inverted repeats in nucleotide sequences. Biochem Biophys Res Commun 2016; 478:1739-45. [PMID: 27603574 DOI: 10.1016/j.bbrc.2016.09.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/02/2016] [Indexed: 10/21/2022]
Abstract
DNA cruciform structures play an important role in the regulation of natural processes including gene replication and expression, as well as nucleosome structure and recombination. They have also been implicated in the evolution and development of diseases such as cancer and neurodegenerative disorders. Cruciform structures are formed by inverted repeats, and their stability is enhanced by DNA supercoiling and protein binding. They have received broad attention because of their important roles in biology. Computational approaches to study inverted repeats have allowed detailed analysis of genomes. However, currently there are no easily accessible and user-friendly tools that can analyse inverted repeats, especially among long nucleotide sequences. We have developed a web-based server, Palindrome analyser, which is a user-friendly application for analysing inverted repeats in various DNA (or RNA) sequences including genome sequences and oligonucleotides. It allows users to search and retrieve desired gene/nucleotide sequence entries from the NCBI databases, and provides data on length, sequence, locations and energy required for cruciform formation. Palindrome analyser also features an interactive graphical data representation of the distribution of the inverted repeats, with options for sorting according to the length of inverted repeat, length of loop, and number of mismatches. Palindrome analyser can be accessed at http://bioinformatics.ibp.cz.
Collapse
Affiliation(s)
- Václav Brázda
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic.
| | - Jan Kolomazník
- Mendel University in Brno, Zemědělská 1, 613 00, Brno, Czech Republic
| | - Jiří Lýsek
- Mendel University in Brno, Zemědělská 1, 613 00, Brno, Czech Republic
| | - Lucia Hároníková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic
| | - Jan Coufal
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic
| | - Jiří Št'astný
- Mendel University in Brno, Zemědělská 1, 613 00, Brno, Czech Republic
| |
Collapse
|
47
|
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.
Collapse
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
| | | |
Collapse
|
48
|
Abstract
The integron is a powerful system which, by capturing, stockpiling, and rearranging new functions carried by gene encoding cassettes, confers upon bacteria a rapid adaptation capability in changing environments. Chromosomally located integrons (CI) have been identified in a large number of environmental Gram-negative bacteria. Integron evolutionary history suggests that these sedentary CIs acquired mobility among bacterial species through their association with transposable elements and conjugative plasmids. As a result of massive antibiotic use, these so-called mobile integrons are now widespread in clinically relevant bacteria and are considered to be the principal agent in the emergence and rise of antibiotic multiresistance in Gram-negative bacteria. Cassette rearrangements are catalyzed by the integron integrase, a site-specific tyrosine recombinase. Central to these reactions is the single-stranded DNA nature of one of the recombination partners, the attC site. This makes the integron a unique recombination system. This review describes the current knowledge on this atypical recombination mechanism, its implications in the reactions involving the different types of sites, attC and attI, and focuses on the tight regulation exerted by the host on integron activity through the control of attC site folding. Furthermore, cassette and integrase expression are also highly controlled by host regulatory networks and the bacterial stress (SOS) response. These intimate connections to the host make the integron a genetically stable and efficient system, granting the bacteria a low cost, highly adaptive evolution potential "on demand".
Collapse
|
49
|
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.
Collapse
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
| |
Collapse
|
50
|
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.
Collapse
|