1
|
Zhang J, Tang J, Li G, Li N, Wang J, Yao R, Yu T. SINE-VNTR-Alu retrotransposon insertion as a novel mutational event underlying Glanzmann thrombasthenia. J Thromb Haemost 2023; 21:3597-3607. [PMID: 37604334 DOI: 10.1016/j.jtha.2023.08.012] [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: 01/09/2023] [Revised: 08/01/2023] [Accepted: 08/06/2023] [Indexed: 08/23/2023]
Abstract
BACKGROUND Glanzmann thrombasthenia (GT) is an autosomal recessive platelet aggregation disorder caused by mutations in ITGA2B or ITGB3. OBJECTIVES We aimed to assess the phenotype and investigate the genetic etiology of a GT pedigree. METHODS A patient with bleeding manifestations and mild mental retardation was enrolled. Complete blood count, coagulation, and platelet aggregation tests were performed. Causal mutations were identified via whole exome and genome sequencing and subsequently confirmed through polymerase chain reaction and Sanger sequencing. The transcription of ITGB3 was characterized using RNA sequencing and reverse transcription polymerase chain reaction. The αⅡb and β3 biosynthesis was investigated via whole blood flow cytometry and in vitro studies. RESULTS GT was diagnosed in a patient with defective platelet aggregation. Novel compound heterozygous ITGB3 variants were identified, with a maternal nonsense mutation (c.2222G>A, p.Trp741∗) and a paternal SINE-VNTR-Alu (SVA) retrotransposon insertion. The 5' truncated SVA element was inserted in a sense orientation in intron 11 of ITGB3, resulting in aberrant splicing of ITGB3 and significantly reducing β3 protein content. Meanwhile, both the expression and transportation of β3 were damaged by the ITGB3 c.2222G>A. Almost no αⅡb and β3 expressions were detected on the patient's platelets surface. CONCLUSION Novel compound heterozygous ITGB3 mutations were identified in the GT pedigree, resulting in defects of αⅡbβ3 biosynthesis. This is the first report of SVA retrotransposon insertion in the genetic pathogenesis of GT. Our study highlights the importance of combining multiple high-throughput sequencing technologies for the molecular diagnosis of genetic disorders.
Collapse
Affiliation(s)
- Jiasheng Zhang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Tang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guoqiang Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jian Wang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ruen Yao
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Tingting Yu
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|
2
|
Makova KD, Weissensteiner MH. Noncanonical DNA structures are drivers of genome evolution. Trends Genet 2023; 39:109-124. [PMID: 36604282 PMCID: PMC9877202 DOI: 10.1016/j.tig.2022.11.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023]
Abstract
In addition to the canonical right-handed double helix, other DNA structures, termed 'non-B DNA', can form in the genomes across the tree of life. Non-B DNA regulates multiple cellular processes, including replication and transcription, yet its presence is associated with elevated mutagenicity and genome instability. These discordant cellular roles fuel the enormous potential of non-B DNA to drive genomic and phenotypic evolution. Here we discuss recent studies establishing non-B DNA structures as novel functional elements subject to natural selection, affecting evolution of transposable elements (TEs), and specifying centromeres. By highlighting the contributions of non-B DNA to repeated evolution and adaptation to changing environments, we conclude that evolutionary analyses should include a perspective of not only DNA sequence, but also its structure.
Collapse
Affiliation(s)
- Kateryna D Makova
- Department of Biology, Penn State University, 310 Wartik Laboratory, University Park, PA 16802, USA.
| | | |
Collapse
|
3
|
Deng Z, Zhang Y, Gao C, Shen W, Wang S, Ni X, Liu S, Li X. A transposon-introduced G-quadruplex motif is selectively retained and constrained to downregulate CYP321A1. INSECT SCIENCE 2022; 29:1629-1642. [PMID: 35226400 DOI: 10.1111/1744-7917.13021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 01/18/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Insects utilize xenobiotic compounds to up- and downregulate cytochrome P450 monooxygenases (P450s) involved in detoxification of toxic xenobiotics including phytochemicals and pesticides. G-quadruplexes (G4)-forming DNA motifs are enriched in the promoter regions of transcription factors and function as cis-acting elements to regulate these genes. Whether and how P450s gain and keep G4 DNA motifs to regulate their expression still remain unexplored. Here, we show that CYP321A1, a xenobiotic-metabolizing P450 from Helicoverpa zea, a polyphagous insect of economic importance, has acquired and preserved a G4 DNA motif by selectively retaining a transposon known as HzIS1-3 that carries this G4 DNA motif in its promoter region. The HzIS1-3 G4 DNA motif acts as a silencer to suppress the constitutive and induced expression of CYP321A1 by plant allelochemicals flavone and xanthotoxin through folding into an intramolecular parallel or hybrid-1 conformation in the absence or presence of K+ . The G4 ligand N-methylmesoporphyrin IX (NMM) strengthens the silencing effect of HzIS1-3 G4 DNA motif by switching its structure from hybrid-1 to hybrid-2. The enrichment of transposons in P450s and other environment-adaptation genes implies that selective retention of G4 DNA motif-carrying transposons may be the main evolutionary route for these genes to obtain G4 DNA motifs.
Collapse
Affiliation(s)
- Zhongyuan Deng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- Department of Entomology and BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Yuting Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Chao Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Wei Shen
- College of Science, Huazhong Agricultural University, Wuhan, China
| | - Shan Wang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Xinzhi Ni
- USDA-ARS, Crop Genetics and Breeding Research Unit, University of Georgia, Tifton Campus, Tifton, GA, USA
| | - Sisi Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Science, Huazhong Agricultural University, Wuhan, China
| | - Xianchun Li
- Department of Entomology and BIO5 Institute, University of Arizona, Tucson, AZ, USA
| |
Collapse
|
4
|
Dobrovolná M, Bohálová N, Peška V, Wang J, Luo Y, Bartas M, Volná A, Mergny JL, Brázda V. The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation. Int J Mol Sci 2022; 23:8482. [PMID: 35955617 PMCID: PMC9369095 DOI: 10.3390/ijms23158482] [Citation(s) in RCA: 2] [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: 07/06/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/20/2022] Open
Abstract
G-quadruplexes (G4s) have been long considered rare and physiologically unimportant in vitro curiosities, but recent methodological advances have proved their presence and functions in vivo. Moreover, in addition to their functional relevance in bacteria and animals, including humans, their importance has been recently demonstrated in evolutionarily distinct plant species. In this study, we analyzed the genome of Pisum sativum (garden pea, or the so-called green pea), a unique member of the Fabaceae family. Our results showed that this genome contained putative G4 sequences (PQSs). Interestingly, these PQSs were located nonrandomly in the nuclear genome. We also found PQSs in mitochondrial (mt) and chloroplast (cp) DNA, and we experimentally confirmed G4 formation for sequences found in these two organelles. The frequency of PQSs for nuclear DNA was 0.42 PQSs per thousand base pairs (kbp), in the same range as for cpDNA (0.53/kbp), but significantly lower than what was found for mitochondrial DNA (1.58/kbp). In the nuclear genome, PQSs were mainly associated with regulatory regions, including 5'UTRs, and upstream of the rRNA region. In contrast to genomic DNA, PQSs were located around RNA genes in cpDNA and mtDNA. Interestingly, PQSs were also associated with specific transposable elements such as TIR and LTR and around them, pointing to their role in their spreading in nuclear DNA. The nonrandom localization of PQSs uncovered their evolutionary and functional significance in the Pisum sativum genome.
Collapse
Affiliation(s)
- Michaela Dobrovolná
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic
| | - Natália Bohálová
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Department of Experimental Biology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Vratislav Peška
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
| | - Jiawei Wang
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
| | - Yu Luo
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, CEDEX, 91405 Orsay, France
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
| | - Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic
| |
Collapse
|
5
|
Chromosome organization affects genome evolution in Sulfolobus archaea. Nat Microbiol 2022; 7:820-830. [PMID: 35618771 DOI: 10.1038/s41564-022-01127-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 04/21/2022] [Indexed: 12/16/2022]
Abstract
In all organisms, the DNA sequence and the structural organization of chromosomes affect gene expression. The extremely thermophilic crenarchaeon Sulfolobus has one circular chromosome with three origins of replication. We previously revealed that this chromosome has defined A and B compartments that have high and low gene expression, respectively. As well as higher levels of gene expression, the A compartment contains the origins of replication. To evaluate the impact of three-dimensional organization on genome evolution, we characterized the effect of replication origins and compartmentalization on primary sequence evolution in eleven Sulfolobus species. Using single-nucleotide polymorphism analyses, we found that distance from an origin of replication was associated with increased mutation rates in the B but not in the A compartment. The enhanced polymorphisms distal to replication origins suggest that replication termination may have a causal role in their generation. Further mutational analyses revealed that the sequences in the A compartment are less likely to be mutated, and that there is stronger purifying selection than in the B compartment. Finally, we applied the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to show that the B compartment is less accessible than the A compartment. Taken together, our data suggest that compartmentalization of chromosomal DNA can influence chromosome evolution in Sulfolobus. We propose that the A compartment serves as a haven for stable maintenance of gene sequences, while sequences in the B compartment can be diversified.
Collapse
|
6
|
Severov V, Tsvetkov V, Barinov N, Babenko V, Klinov D, Pozmogova G. Spontaneous DNA Synapsis by Forming Noncanonical Intermolecular Structures. Polymers (Basel) 2022; 14:polym14102118. [PMID: 35632001 PMCID: PMC9144187 DOI: 10.3390/polym14102118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/14/2022] [Accepted: 05/20/2022] [Indexed: 01/27/2023] Open
Abstract
We report the spontaneous formation of DNA-DNA junctions in solution in the absence of proteins visualised using atomic force microscopy. The synapsis position fits with potential G-quadruplex (G4) sites. In contrast to the Holliday structure, these conjugates have an affinity for G4 antibodies. Molecular modelling was used to elucidate the possible G4/IM-synaptic complex structures. Our results indicate a new role of the intermolecular noncanonical structures in chromatin architecture and genomic rearrangement.
Collapse
Affiliation(s)
- Viacheslav Severov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119435 Moscow, Russia; (N.B.); (V.B.); (D.K.); (G.P.)
- Correspondence: (V.S.); (V.T.)
| | - Vladimir Tsvetkov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119435 Moscow, Russia; (N.B.); (V.B.); (D.K.); (G.P.)
- Institute of Biodesign and Complex System Modeling, I.M. Sechenov First Moscow State Medical University, Trubetskaya Str. 8-2, 119991 Moscow, Russia
- A.V. Topchiev Institute of Petrochemical Synthesis, Leninsky prospect Str. 29, 119991 Moscow, Russia
- Correspondence: (V.S.); (V.T.)
| | - Nikolay Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119435 Moscow, Russia; (N.B.); (V.B.); (D.K.); (G.P.)
| | - Vladislav Babenko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119435 Moscow, Russia; (N.B.); (V.B.); (D.K.); (G.P.)
| | - Dmitry Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119435 Moscow, Russia; (N.B.); (V.B.); (D.K.); (G.P.)
- Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya str.6, 117198 Moscow, Russia
| | - Galina Pozmogova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119435 Moscow, Russia; (N.B.); (V.B.); (D.K.); (G.P.)
| |
Collapse
|
7
|
Maekawa K, Yamada S, Sharma R, Chaudhuri J, Keeney S. Triple-helix potential of the mouse genome. Proc Natl Acad Sci U S A 2022; 119:e2203967119. [PMID: 35503911 PMCID: PMC9171763 DOI: 10.1073/pnas.2203967119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/30/2022] [Indexed: 01/14/2023] Open
Abstract
Certain DNA sequences, including mirror-symmetric polypyrimidine•polypurine runs, are capable of folding into a triple-helix–containing non–B-form DNA structure called H-DNA. Such H-DNA–forming sequences occur frequently in many eukaryotic genomes, including in mammals, and multiple lines of evidence indicate that these motifs are mutagenic and can impinge on DNA replication, transcription, and other aspects of genome function. In this study, we show that the triplex-forming potential of H-DNA motifs in the mouse genome can be evaluated using S1-sequencing (S1-seq), which uses the single-stranded DNA (ssDNA)–specific nuclease S1 to generate deep-sequencing libraries that report on the position of ssDNA throughout the genome. When S1-seq was applied to genomic DNA isolated from mouse testis cells and splenic B cells, we observed prominent clusters of S1-seq reads that appeared to be independent of endogenous double-strand breaks, that coincided with H-DNA motifs, and that correlated strongly with the triplex-forming potential of the motifs. Fine-scale patterns of S1-seq reads, including a pronounced strand asymmetry in favor of centrally positioned reads on the pyrimidine-containing strand, suggested that this S1-seq signal is specific for one of the four possible isomers of H-DNA (H-y5). By leveraging the abundance and complexity of naturally occurring H-DNA motifs across the mouse genome, we further defined how polypyrimidine repeat length and the presence of repeat-interrupting substitutions modify the structure of H-DNA. This study provides an approach for studying DNA secondary structure genome-wide at high spatial resolution.
Collapse
Affiliation(s)
- Kaku Maekawa
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Shintaro Yamada
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Rahul Sharma
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- HHMI, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| |
Collapse
|
8
|
Vannutelli A, Perreault JP, Ouangraoua A. G-quadruplex occurrence and conservation: more than just a question of guanine–cytosine content. NAR Genom Bioinform 2022; 4:lqac010. [PMID: 35261973 PMCID: PMC8896161 DOI: 10.1093/nargab/lqac010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 12/06/2021] [Accepted: 02/25/2022] [Indexed: 12/14/2022] Open
Abstract
G-quadruplexes are motifs found in DNA and RNA that can fold into tertiary structures. Until now, they have been studied experimentally mainly in humans and a few other species. Recently, predictions have been made with bacterial and archaeal genomes. Nevertheless, a global comparison of predicted G4s (pG4s) across and within the three living kingdoms has not been addressed. In this study, we aimed to predict G4s in genes and transcripts of all kingdoms of living organisms and investigated the differences in their distributions. The relation of the predictions with GC content was studied. It appears that GC content is not the only parameter impacting G4 predictions and abundance. The distribution of pG4 densities varies depending on the class of transcripts and the group of species. Indeed, we have observed that, in coding transcripts, there are more predicted G4s than expected for eukaryotes but not for archaea and bacteria, while in noncoding transcripts, there are as many or fewer predicted G4s in all species groups. We even noticed that some species with the same GC content presented different pG4 profiles. For instance, Leishmania major and Chlamydomonas reinhardtii both have 60% of GC content, but the former has a pG4 density of 0.07 and the latter 1.16.
Collapse
Affiliation(s)
- Anaïs Vannutelli
- Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC, J1K 2R1, Canada
- Department of Biochemistry and Functional Genomics, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, QC J1E 4K8, Canada
| | - Jean-Pierre Perreault
- Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC, J1K 2R1, Canada
| | - Aïda Ouangraoua
- Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC, J1K 2R1, Canada
| |
Collapse
|
9
|
Ma X, Feng Y, Yang Y, Li X, Shi Y, Tao S, Cheng X, Huang J, Wang XE, Chen C, Monchaud D, Zhang W. Genome-wide characterization of i-motifs and their potential roles in the stability and evolution of transposable elements in rice. Nucleic Acids Res 2022; 50:3226-3238. [PMID: 35188565 PMCID: PMC8989525 DOI: 10.1093/nar/gkac121] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/13/2022] [Accepted: 02/07/2022] [Indexed: 12/15/2022] Open
Abstract
I-motifs (iMs) are non-canonical DNA secondary structures that fold from cytosine (C)-rich genomic DNA regions termed putative i-motif forming sequences (PiMFSs). The structure of iMs is stabilized by hemiprotonated C-C base pairs, and their functions are now suspected in key cellular processes in human cells such as genome stability and regulation of gene transcription. In plants, their biological relevance is still largely unknown. Here, we characterized PiMFSs with high potential for i-motif formation in the rice genome by developing and applying a protocol hinging on an iMab antibody-based immunoprecipitation (IP) coupled with high-throughput sequencing (seq), consequently termed iM-IP-seq. We found that PiMFSs had intrinsic subgenomic distributions, cis-regulatory functions and an intricate relationship with DNA methylation. We indeed found that the coordination of PiMFSs with DNA methylation may affect dynamics of transposable elements (TEs) among different cultivated Oryza subpopulations or during evolution of wild rice species. Collectively, our study provides first and unique insights into the biology of iMs in plants, with potential applications in plant biotechnology for improving important agronomic rice traits.
Collapse
Affiliation(s)
- Xing Ma
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Yilong Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Ying Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Xin Li
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan410125, P.R. China
| | - Yining Shi
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Shentong Tao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Jian Huang
- School of Biology & Basic Medical Science, Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Xiu-e Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Caiyan Chen
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan410125, P.R. China
| | - David Monchaud
- Institut de Chimie Moleculaire, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| |
Collapse
|
10
|
Stefos GC, Theodorou G, Politis I. Genomic landscape, polymorphism and possible LINE-associated delivery of G-quadruplex motifs in the bovine genes. Genomics 2022; 114:110272. [PMID: 35092818 DOI: 10.1016/j.ygeno.2022.110272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/12/2022] [Accepted: 01/18/2022] [Indexed: 12/29/2022]
Abstract
G-Quadruplex structures are non-B DNA structures that occur in regions carrying short runs of guanines. They are implicated in several biological processes including transcription, translation, replication and telomere maintenance as well as in several pathological conditions like cancer and thus they have gained the attention of the scientific community. The rise of the -omics era significantly affected the G-quadruplex research and the genome-wide characterization of G-Quadruplexes has been rendered a necessary first step towards applying genomics approaches for their study. While in human and several model organisms there is a considerable number of works studying genome-wide the DNA motifs with potential to form G-quadruplexes (G4-motifs), there is a total absence of any similar studies regarding livestock animals. The objectives of the present study were to provide a detailed characterization of the bovine genic G4-motifs' distribution and properties and to suggest a possible mechanism for the delivery of G4 motifs in the genes. Our data indicate that the distribution of G4-motifs within bovine genes and the annotation of said genes to Gene Ontology terms are similar to what is already shown for other organisms. By investigating their structural characteristics and polymorphism, it is obvious that the overall stability of the putative quadruplex structures is in line with the current notion in the G4 field. Similarly to human, the bovine G4-motifs are overrepresented in specific LINE repeat elements, the L1_BTs in the case of cattle. We highlight the potential role of these elements as vehicles for delivery of G4 motifs in the introns of the bovine genes. Lastly, it seems that a basis exists for connecting traits of agricultural importance to the genetic variation of G4 motifs, thus, the value of cattle as an interesting new model organism for G4-related genetic studies might be worth to be investigated.
Collapse
Affiliation(s)
- Georgios C Stefos
- Agricultural University of Athens, Department of Animal Science, Laboratory of Animal Breeding & Husbandry, 75 Iera Odos, 118 55, Athens, Greece.
| | - Georgios Theodorou
- Agricultural University of Athens, Department of Animal Science, Laboratory of Animal Breeding & Husbandry, 75 Iera Odos, 118 55, Athens, Greece.
| | - Ioannis Politis
- Agricultural University of Athens, Department of Animal Science, Laboratory of Animal Breeding & Husbandry, 75 Iera Odos, 118 55, Athens, Greece
| |
Collapse
|
11
|
Calcino AD, Kenny NJ, Gerdol M. Single individual structural variant detection uncovers widespread hemizygosity in molluscs. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200153. [PMID: 33813894 PMCID: PMC8059565 DOI: 10.1098/rstb.2020.0153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2021] [Indexed: 11/12/2022] Open
Abstract
The advent of complete genomic sequencing has opened a window into genomic phenomena obscured by fragmented assemblies. A good example of these is the existence of hemizygous regions of autosomal chromosomes, which can result in marked differences in gene content between individuals within species. While these hemizygous regions, and presence/absence variation of genes that can result, are well known in plants, firm evidence has only recently emerged for their existence in metazoans. Here, we use recently published, complete genomes from wild-caught molluscs to investigate the prevalence of hemizygosity across a well-known and ecologically important clade. We show that hemizygous regions are widespread in mollusc genomes, not clustered in individual chromosomes, and often contain genes linked to transposition, DNA repair and stress response. With targeted investigations of HSP70-12 and C1qDC, we also show how individual gene families are distributed within pan-genomes. This work suggests that extensive pan-genomes are widespread across the conchiferan Mollusca, and represent useful tools for genomic evolution, allowing the maintenance of additional genetic diversity within the population. As genomic sequencing and re-sequencing becomes more routine, the prevalence of hemizygosity, and its impact on selection and adaptation, are key targets for research across the tree of life. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
Collapse
Affiliation(s)
- Andrew D. Calcino
- Department of Evolutionary Biology, Integrative Zoology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Nathan J. Kenny
- Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| |
Collapse
|
12
|
Evans TA, Erwin JA. Retroelement-derived RNA and its role in the brain. Semin Cell Dev Biol 2020; 114:68-80. [PMID: 33229216 DOI: 10.1016/j.semcdb.2020.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 10/20/2020] [Accepted: 11/04/2020] [Indexed: 12/17/2022]
Abstract
Comprising ~40% of the human genome, retroelements are mobile genetic elements which are transcribed into RNA, then reverse-transcribed into DNA and inserted into a new site in the genome. Retroelements are referred to as "genetic parasites", residing among host genes and relying on host machinery for transcription and evolutionary propagation. The healthy brain has the highest expression of retroelement-derived sequences compared to other somatic tissue, which leads to the question: how does retroelement-derived RNA influence human traits and cellular states? While the functional importance of upregulating retroelement expression in the brain is an active area of research, RNA species derived from retroelements influence both self- and host gene expression by contributing to chromatin remodeling, alternative splicing, somatic mosaicism and translational repression. Here, we review the emerging evidence that the functional importance of RNA derived from retroelements is multifaceted. Retroelements can influence organismal states through the seeding of epigenetic states in chromatin, the production of structured RNA and even catalytically active ribozymes, the generation of cytoplasmic ssDNA and RNA/DNA hybrids, the production of viral-like proteins, and the generation of somatic mutations. Comparative sequencing suggests that retroelements can contribute to intraspecies variation through these mechanisms to alter transcript identity and abundance. In humans, an increasing number of neurodevelopmental and neurodegenerative conditions are associated with dysregulated retroelements, including Aicardi-Goutieres syndrome (AGS), Rett syndrome (RTT), Amyotrophic Lateral Sclerosis (ALS), Alzheimer's disease (AD), multiple sclerosis (MS), schizophrenia (SZ), and aging. Taken together, these concepts suggest a larger functional role for RNA derived from retroelements. This review aims to define retroelement-derived RNA, discuss how it impacts the mammalian genome, as well as summarize data supporting phenotypic consequences of this unique RNA subset in the brain.
Collapse
Affiliation(s)
- Taylor A Evans
- Lieber Institute for Brain Development, Baltimore, MD, USA; Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jennifer Ann Erwin
- Lieber Institute for Brain Development, Baltimore, MD, USA; Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
13
|
Williams JD, Houserova D, Johnson BR, Dyniewski B, Berroyer A, French H, Barchie AA, Bilbrey DD, Demeis JD, Ghee KR, Hughes AG, Kreitz NW, McInnis CH, Pudner SC, Reeves MN, Stahly AN, Turcu A, Watters BC, Daly GT, Langley RJ, Gillespie MN, Prakash A, Larson ED, Kasukurthi MV, Huang J, Jinks-Robertson S, Borchert GM. Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop 'G4 Kissing' interaction. Nucleic Acids Res 2020; 48:5907-5925. [PMID: 32383760 PMCID: PMC7293029 DOI: 10.1093/nar/gkaa357] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 12/27/2022] Open
Abstract
Mammalian antibody switch regions (∼1500 bp) are composed of a series of closely neighboring G4-capable sequences. Whereas numerous structural and genome-wide analyses of roles for minimal G4s in transcriptional regulation have been reported, Long G4-capable regions (LG4s)-like those at antibody switch regions-remain virtually unexplored. Using a novel computational approach we have identified 301 LG4s in the human genome and find LG4s prone to mutation and significantly associated with chromosomal rearrangements in malignancy. Strikingly, 217 LG4s overlap annotated enhancers, and we find the promoters regulated by these enhancers markedly enriched in G4-capable sequences suggesting G4s facilitate promoter-enhancer interactions. Finally, and much to our surprise, we also find single-stranded loops of minimal G4s within individual LG4 loci are frequently highly complementary to one another with 178 LG4 loci averaging >35 internal loop:loop complements of >8 bp. As such, we hypothesized (then experimentally confirmed) that G4 loops within individual LG4 loci directly basepair with one another (similar to characterized stem-loop kissing interactions) forming a hitherto undescribed, higher-order, G4-based secondary structure we term a 'G4 Kiss or G4K'. In conclusion, LG4s adopt novel, higher-order, composite G4 structures directly contributing to the inherent instability, regulatory capacity, and maintenance of these conspicuous genomic regions.
Collapse
Affiliation(s)
- Jonathan D Williams
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Dominika Houserova
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Bradley R Johnson
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Brad Dyniewski
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Alexandra Berroyer
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Hannah French
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Addison A Barchie
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Dakota D Bilbrey
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Jeffrey D Demeis
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Kanesha R Ghee
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Alexandra G Hughes
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Naden W Kreitz
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Cameron H McInnis
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Susanna C Pudner
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Monica N Reeves
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Ashlyn N Stahly
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Ana Turcu
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Brianna C Watters
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Grant T Daly
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Raymond J Langley
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Mark N Gillespie
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Aishwarya Prakash
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mitchell Cancer Institute, Mobile, AL 36688, USA
| | - Erik D Larson
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
- Department of Biomedical Sciences, Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, MI 49007, USA
| | | | - Jingshan Huang
- School of Computing, University of South Alabama, Mobile, AL 36688, USA
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA
| | - Glen M Borchert
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| |
Collapse
|
14
|
Gianfrancesco O, Geary B, Savage AL, Billingsley KJ, Bubb VJ, Quinn JP. The Role of SINE-VNTR-Alu (SVA) Retrotransposons in Shaping the Human Genome. Int J Mol Sci 2019; 20:ijms20235977. [PMID: 31783611 PMCID: PMC6928650 DOI: 10.3390/ijms20235977] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/16/2019] [Accepted: 11/17/2019] [Indexed: 12/29/2022] Open
Abstract
Retrotransposons can alter the regulation of genes both transcriptionally and post-transcriptionally, through mechanisms such as binding transcription factors and alternative splicing of transcripts. SINE-VNTR-Alu (SVA) retrotransposons are the most recently evolved class of retrotransposable elements, found solely in primates, including humans. SVAs are preferentially found at genic, high GC loci, and have been termed "mobile CpG islands". We hypothesise that the ability of SVAs to mobilise, and their non-random distribution across the genome, may result in differential regulation of certain pathways. We analysed SVA distribution patterns across the human reference genome and identified over-representation of SVAs at zinc finger gene clusters. Zinc finger proteins are able to bind to and repress SVA function through transcriptional and epigenetic mechanisms, and the interplay between SVAs and zinc fingers has been proposed as a major feature of genome evolution. We describe observations relating to the clustering patterns of both reference SVAs and polymorphic SVA insertions at zinc finger gene loci, suggesting that the evolution of this network may be ongoing in humans. Further, we propose a mechanism to direct future research and validation efforts, in which the interplay between zinc fingers and their epigenetic modulation of SVAs may regulate a network of zinc finger genes, with the potential for wider transcriptional consequences.
Collapse
Affiliation(s)
- Olympia Gianfrancesco
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Bethany Geary
- Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
| | - Abigail L. Savage
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
| | - Kimberley J. Billingsley
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
| | - Vivien J. Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
| | - John P. Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
- Correspondence:
| |
Collapse
|
15
|
Bacolla A, Ye Z, Ahmed Z, Tainer JA. Cancer mutational burden is shaped by G4 DNA, replication stress and mitochondrial dysfunction. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 147:47-61. [PMID: 30880007 PMCID: PMC6745008 DOI: 10.1016/j.pbiomolbio.2019.03.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 02/01/2023]
Abstract
A hallmark of cancer is genomic instability, which can enable cancer cells to evade therapeutic strategies. Here we employed a computational approach to uncover mechanisms underlying cancer mutational burden by focusing upon relationships between 1) translocation breakpoints and the thousands of G4 DNA-forming sequences within retrotransposons impacting transcription and exemplifying probable non-B DNA structures and 2) transcriptome profiling and cancer mutations. We determined the location and number of G4 DNA-forming sequences in the Genome Reference Consortium Human Build 38 and found a total of 358,605 covering ∼13.4 million bases. By analyzing >97,000 unique translocation breakpoints from the Catalogue Of Somatic Mutations In Cancer (COSMIC), we found that breakpoints are overrepresented at G4 DNA-forming sequences within hominid-specific SVA retrotransposons, and generally occur in tumors with mutations in tumor suppressor genes, such as TP53. Furthermore, correlation analyses between mRNA levels and exome mutational loads from The Cancer Genome Atlas (TCGA) encompassing >450,000 gene-mutation regressions revealed strong positive and negative associations, which depended upon tissue of origin. The strongest positive correlations originated from genes not listed as cancer genes in COSMIC; yet, these show strong predictive power for survival in most tumor types by Kaplan-Meier estimation. Thus, correlation analyses of DNA structure and gene expression with mutation loads complement and extend more traditional approaches to elucidate processes shaping genomic instability in cancer. The combined results point to G4 DNA, activation of cell cycle/DNA repair pathways, and mitochondrial dysfunction as three major factors driving the accumulation of somatic mutations in cancer cells.
Collapse
Affiliation(s)
- Albino Bacolla
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
| | - Zu Ye
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
| | - Zamal Ahmed
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
| | - John A Tainer
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
| |
Collapse
|
16
|
Orozco-Arias S, Isaza G, Guyot R. Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning. Int J Mol Sci 2019; 20:E3837. [PMID: 31390781 PMCID: PMC6696364 DOI: 10.3390/ijms20153837] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 01/26/2023] Open
Abstract
Transposable elements (TEs) are genomic units able to move within the genome of virtually all organisms. Due to their natural repetitive numbers and their high structural diversity, the identification and classification of TEs remain a challenge in sequenced genomes. Although TEs were initially regarded as "junk DNA", it has been demonstrated that they play key roles in chromosome structures, gene expression, and regulation, as well as adaptation and evolution. A highly reliable annotation of these elements is, therefore, crucial to better understand genome functions and their evolution. To date, much bioinformatics software has been developed to address TE detection and classification processes, but many problematic aspects remain, such as the reliability, precision, and speed of the analyses. Machine learning and deep learning are algorithms that can make automatic predictions and decisions in a wide variety of scientific applications. They have been tested in bioinformatics and, more specifically for TEs, classification with encouraging results. In this review, we will discuss important aspects of TEs, such as their structure, importance in the evolution and architecture of the host, and their current classifications and nomenclatures. We will also address current methods and their limitations in identifying and classifying TEs.
Collapse
Affiliation(s)
- Simon Orozco-Arias
- Department of Computer Science, Universidad Autónoma de Manizales, Manizales 170001, Colombia
- Department of Systems and Informatics, Universidad de Caldas, Manizales 170001, Colombia
| | - Gustavo Isaza
- Department of Systems and Informatics, Universidad de Caldas, Manizales 170001, Colombia
| | - Romain Guyot
- Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales 170001, Colombia.
- Institut de Recherche pour le Développement, CIRAD, University Montpellier, 34000 Montpellier, France.
| |
Collapse
|
17
|
Lightfoot HL, Hagen T, Tatum NJ, Hall J. The diverse structural landscape of quadruplexes. FEBS Lett 2019; 593:2083-2102. [PMID: 31325371 DOI: 10.1002/1873-3468.13547] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 07/09/2019] [Accepted: 07/15/2019] [Indexed: 12/15/2022]
Abstract
G-quadruplexes are secondary structures formed in G-rich sequences in DNA and RNA. Considerable research over the past three decades has led to in-depth insight into these unusual structures in DNA. Since the more recent exploration into RNA G-quadruplexes, such structures have demonstrated their in cellulo existence, function and roles in pathology. In comparison to Watson-Crick-based secondary structures, most G-quadruplexes display highly redundant structural characteristics. However, numerous reports of G-quadruplex motifs/structures with unique features (e.g. bulges, long loops, vacancy) have recently surfaced, expanding the repertoire of G-quadruplex scaffolds. This review addresses G-quadruplex formation and structure, including recent reports of non-canonical G-quadruplex structures. Improved methods of detection will likely further expand this collection of novel structures and ultimately change the face of quadruplex-RNA targeting as a therapeutic strategy.
Collapse
Affiliation(s)
- Helen L Lightfoot
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
| | - Timo Hagen
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
| | - Natalie J Tatum
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
| |
Collapse
|
18
|
Ruggiero E, Tassinari M, Perrone R, Nadai M, Richter SN. Stable and Conserved G-Quadruplexes in the Long Terminal Repeat Promoter of Retroviruses. ACS Infect Dis 2019; 5:1150-1159. [PMID: 31081611 PMCID: PMC6630527 DOI: 10.1021/acsinfecdis.9b00011] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Retroviruses
infect almost all vertebrates, from humans to domestic and farm animals,
from primates to wild animals, where they cause severe diseases, including
immunodeficiencies, neurological disorders, and cancer. Nonhuman retroviruses
have also been recently associated with human diseases. To date, no
effective treatments are available; therefore, finding retrovirus-specific
therapeutic targets is becoming an impelling issue. G-Quadruplexes
are four-stranded nucleic acid structures that form in guanine-rich
regions. Highly conserved G-quadruplexes located in the long-terminal-repeat
(LTR) promoter of HIV-1 were shown to modulate the virus transcription
machinery; moreover, the astonishingly high degree of conservation
of G-quadruplex sequences in all primate lentiviruses corroborates
the idea that these noncanonical nucleic acid structures are crucial
elements in the lentiviral biology and thus have been selected for
during evolution. In this work, we aimed at investigating the presence
and conservation of G-quadruplexes in the Retroviridae family. Genomewide
bioinformatics analysis showed that, despite their documented high
genetic variability, most retroviruses contain highly conserved putative
G-quadruplex-forming sequences in their promoter regions. Biophysical
and biomolecular assays proved that these sequences actually fold
into G-quadruplexes in physiological concentrations of relevant cations
and that they are further stabilized by ligands. These results validate
the relevance of G-quadruplexes in retroviruses and endorse the employment
of G-quadruplex ligands as innovative antiretroviral drugs. This study
indicates new possible pathways in the management of retroviral infections
in humans and animal species. Moreover, it may shed light on the mechanism
and functions of retrovirus genomes and derived transposable elements
in the human genome.
Collapse
Affiliation(s)
- Emanuela Ruggiero
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
| | - Martina Tassinari
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
| | - Rosalba Perrone
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, California 94945, United States
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
| | - Sara N. Richter
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
| |
Collapse
|
19
|
Escudeiro A, Adega F, Robinson TJ, Heslop-Harrison JS, Chaves R. Conservation, Divergence, and Functions of Centromeric Satellite DNA Families in the Bovidae. Genome Biol Evol 2019; 11:1152-1165. [PMID: 30888421 PMCID: PMC6475130 DOI: 10.1093/gbe/evz061] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2019] [Indexed: 12/18/2022] Open
Abstract
Repetitive satellite DNA (satDNA) sequences are abundant in eukaryote genomes, with a structural and functional role in centromeric function. We analyzed the nucleotide sequence and chromosomal location of the five known cattle (Bos taurus) satDNA families in seven species from the tribe Tragelaphini (Bovinae subfamily). One of the families (SAT1.723) was present at the chromosomes’ centromeres of the Tragelaphini species, as well in two more distantly related bovid species, Ovis aries and Capra hircus. Analysis of the interaction of SAT1.723 with centromeric proteins revealed that this satDNA sequence is involved in the centromeric activity in all the species analyzed and that it is preserved for at least 15–20 Myr across Bovidae species. The satDNA sequence similarity among the analyzed species reflected different stages of homogeneity/heterogeneity, revealing the evolutionary history of each satDNA family. The SAT1.723 monomer-flanking regions showed the presence of transposable elements, explaining the extensive shuffling of this satDNA between different genomic regions.
Collapse
Affiliation(s)
- Ana Escudeiro
- Department of Genetics and Biotechnology, CAG - Laboratory of Cytogenomics and Animal Genomics, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
| | - Filomena Adega
- Department of Genetics and Biotechnology, CAG - Laboratory of Cytogenomics and Animal Genomics, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
| | | | | | - Raquel Chaves
- Department of Genetics and Biotechnology, CAG - Laboratory of Cytogenomics and Animal Genomics, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
| |
Collapse
|
20
|
Prislan I, Sajko S, Ulrih NP, Fürst L. Proof of concept web application for understanding the energetic basis of oligonucleotide unfolding. RSC Adv 2019; 9:41453-41461. [PMID: 35541576 PMCID: PMC9076490 DOI: 10.1039/c9ra09800c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/27/2019] [Indexed: 11/21/2022] Open
Abstract
Measuring and quantifying thermodynamic parameters that determine both the stability of and interactions between biological macromolecules are an essential and necessary complement to structural studies. Although basic thermodynamic parameters for an observed process can be readily obtained, the data interpretation is often slow and analysis quality can be extremely variable. We have started to develop a web application that will help users to perform thermodynamic characterizations of oligonucleotide unfolding. The application can perform global fitting of calorimetric and spectroscopic data, and uses a three-state equilibrium model to obtain thermodynamic parameters for each transition step – namely, the Gibbs energy, the enthalpy, and the heat capacity. In addition, the application can define the number of K+ ions and the number of water molecules being released or taken up during unfolding. To test our application, we used UV spectroscopy, circular dichroism, and differential scanning calorimetry to monitor folding and unfolding of a model 22-nucleotide-long sequence of a human 3′-telomeric overhang, known as Tel22. The obtained data were uploaded to the web application and the global fit revealed that unfolding of Tel22 involves at least one intermediate state, and that K+ ions are released during the unfolding, whereas water molecules are taken up. A novel web application: performing global fitting of oligonucleotide unfolding experimental data in style.![]()
Collapse
Affiliation(s)
- Iztok Prislan
- Biotechnical Faculty
- University of Ljubljana
- Ljubljana
- Slovenia
| | - Sara Sajko
- Max Perutz Labs Vienna
- Medical University of Vienna
- 1030 Vienna
- Austria
| | | | - Luka Fürst
- Faculty of Computer and Information Science
- University of Ljubljana
- Ljubljana
- Slovenia
| |
Collapse
|
21
|
Disease onset in X-linked dystonia-parkinsonism correlates with expansion of a hexameric repeat within an SVA retrotransposon in TAF1. Proc Natl Acad Sci U S A 2017; 114:E11020-E11028. [PMID: 29229810 PMCID: PMC5754783 DOI: 10.1073/pnas.1712526114] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The genetic basis of X-Linked dystonia-parkinsonism (XDP) has been difficult to unravel, in part because all patients inherit the same haplotype of seven sequence variants, none of which has ever been identified in control individuals. This study revealed that one of the haplotype markers, a retrotransposon insertion within an intron of TAF1, has a variable number of hexameric repeats among affected individuals with an increase in repeat number strongly correlated with earlier age at disease onset. These data support a contributing role for this sequence in disease pathogenesis while further suggesting that XDP may be part of a growing list of neurodegenerative disorders associated with unstable repeat expansions. X-linked dystonia-parkinsonism (XDP) is a neurodegenerative disease associated with an antisense insertion of a SINE-VNTR-Alu (SVA)-type retrotransposon within an intron of TAF1. This unique insertion coincides with six additional noncoding sequence changes in TAF1, the gene that encodes TATA-binding protein–associated factor-1, which appear to be inherited together as an identical haplotype in all reported cases. Here we examined the sequence of this SVA in XDP patients (n = 140) and detected polymorphic variation in the length of a hexanucleotide repeat domain, (CCCTCT)n. The number of repeats in these cases ranged from 35 to 52 and showed a highly significant inverse correlation with age at disease onset. Because other SVAs exhibit intrinsic promoter activity that depends in part on the hexameric domain, we assayed the transcriptional regulatory effects of varying hexameric lengths found in the unique XDP SVA retrotransposon using luciferase reporter constructs. When inserted sense or antisense to the luciferase reading frame, the XDP variants repressed or enhanced transcription, respectively, to an extent that appeared to vary with length of the hexamer. Further in silico analysis of this SVA sequence revealed multiple motifs predicted to form G-quadruplexes, with the greatest potential detected for the hexameric repeat domain. These data directly link sequence variation within the XDP-specific SVA sequence to phenotypic variability in clinical disease manifestation and provide insight into potential mechanisms by which this intronic retroelement may induce transcriptional interference in TAF1 expression.
Collapse
|
22
|
Creamer KM, Lawrence JB. XIST RNA: a window into the broader role of RNA in nuclear chromosome architecture. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160360. [PMID: 28947659 PMCID: PMC5627162 DOI: 10.1098/rstb.2016.0360] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2017] [Indexed: 12/31/2022] Open
Abstract
XIST RNA triggers the transformation of an active X chromosome into a condensed, inactive Barr body and therefore provides a unique window into transitions of higher-order chromosome architecture. Despite recent progress, how XIST RNA localizes and interacts with the X chromosome remains poorly understood. Genetic engineering of XIST into a trisomic autosome demonstrates remarkable capacity of XIST RNA to localize and comprehensively silence that autosome. Thus, XIST does not require X chromosome-specific sequences but operates on mechanisms available genome-wide. Prior results suggested XIST localization is controlled by attachment to the insoluble nuclear scaffold. Our recent work affirms that scaffold attachment factor A (SAF-A) is involved in anchoring XIST, but argues against the view that SAF-A provides a unimolecular bridge between RNA and the chromosome. Rather, we suggest that a complex meshwork of architectural proteins interact with XIST RNA. Parallel work studying the territory of actively transcribed chromosomes suggests that repeat-rich RNA 'coats' euchromatin and may impact chromosome architecture in a manner opposite of XIST A model is discussed whereby RNA may not just recruit histone modifications, but more directly impact higher-order chromatin condensation via interaction with architectural proteins of the nucleus.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'.
Collapse
Affiliation(s)
- K M Creamer
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - J B Lawrence
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655, USA
| |
Collapse
|
23
|
Vergara Z, Sequeira-Mendes J, Morata J, Peiró R, Hénaff E, Costas C, Casacuberta JM, Gutierrez C. Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin. Nucleic Acids Res 2017; 45:8358-8368. [PMID: 28605523 PMCID: PMC5737333 DOI: 10.1093/nar/gkx524] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 06/05/2017] [Indexed: 12/28/2022] Open
Abstract
Genomic stability depends on faithful genome replication. This is achieved by the concerted activity of thousands of DNA replication origins (ORIs) scattered throughout the genome. The DNA and chromatin features determining ORI specification are not presently known. We have generated a high-resolution genome-wide map of 3230 ORIs in cultured Arabidopsis thaliana cells. Here, we focused on defining the features associated with ORIs in heterochromatin. In pericentromeric gene-poor domains ORIs associate almost exclusively with the retrotransposon class of transposable elements (TEs), in particular of the Gypsy family. ORI activity in retrotransposons occurs independently of TE expression and while maintaining high levels of H3K9me2 and H3K27me1, typical marks of repressed heterochromatin. ORI-TEs largely colocalize with chromatin signatures defining GC-rich heterochromatin. Importantly, TEs with active ORIs contain a local GC content higher than the TEs lacking them. Our results lead us to conclude that ORI colocalization with retrotransposons is determined by their transposition mechanism based on transcription, and a specific chromatin landscape. Our detailed analysis of ORIs responsible for heterochromatin replication has implications on the mechanisms of ORI specification in other multicellular organisms in which retrotransposons are major components of heterochromatin and of the entire genome.
Collapse
Affiliation(s)
- Zaida Vergara
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Joana Sequeira-Mendes
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Jordi Morata
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus Universitat Autónoma de Barcelona, Bellaterra, Cerdanyola del Valles, 08193 Barcelona, Spain
| | - Ramón Peiró
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Elizabeth Hénaff
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus Universitat Autónoma de Barcelona, Bellaterra, Cerdanyola del Valles, 08193 Barcelona, Spain
| | - Celina Costas
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Josep M Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus Universitat Autónoma de Barcelona, Bellaterra, Cerdanyola del Valles, 08193 Barcelona, Spain
| | - Crisanto Gutierrez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
24
|
Auboeuf D. Genome evolution is driven by gene expression-generated biophysical constraints through RNA-directed genetic variation: A hypothesis. Bioessays 2017; 39. [DOI: 10.1002/bies.201700069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Didier Auboeuf
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210; Laboratory of Biology and Modelling of the Cell; Site Jacques Monod; Lyon France
| |
Collapse
|
25
|
Gianfrancesco O, Bubb VJ, Quinn JP. SVA retrotransposons as potential modulators of neuropeptide gene expression. Neuropeptides 2017; 64:3-7. [PMID: 27743609 PMCID: PMC5529292 DOI: 10.1016/j.npep.2016.09.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 09/06/2016] [Accepted: 09/06/2016] [Indexed: 12/21/2022]
Abstract
Many facets of human behaviour are likely to have developed in part due to evolutionary changes in the regulation of neuropeptide and other brain-related genes. This has allowed species-specific expression patterns and unique epigenetic modulation in response to our environment, regulating response not only at the molecular level, but also contributing to differences in behaviour between individuals. As such, genetic variants or epigenetic changes that may alter neuropeptide gene expression are predicted to play a role in behavioural conditions and psychiatric illness. It is therefore of interest to identify regulatory elements that have the potential to drive differential gene expression. Retrotransposons are mobile genetic elements that are known to be drivers of genomic diversity, with the ability to alter expression of nearby genes. In particular, the SINE-VNTR-Alu (SVA) class of retrotransposons is specific to hominids, and its appearance and expansion across the genome has been associated with the evolution of numerous behavioural traits, presumably through their ability to confer unique regulatory properties at the site of their insertion. We review the evidence for SVAs as regulatory elements, exploring how polymorphic variation within these repetitive sequences can drive allele specific gene expression, which would be associated with changes in behaviour and disease risk through the alteration of molecular pathways that are central to healthy brain function.
Collapse
Affiliation(s)
- Olympia Gianfrancesco
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool, L69 3BX, UK
| | - Vivien J Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool, L69 3BX, UK
| | - John P Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool, L69 3BX, UK.
| |
Collapse
|
26
|
Yadav V, Hemansi, Kim N, Tuteja N, Yadav P. G Quadruplex in Plants: A Ubiquitous Regulatory Element and Its Biological Relevance. FRONTIERS IN PLANT SCIENCE 2017; 8:1163. [PMID: 28725233 PMCID: PMC5495829 DOI: 10.3389/fpls.2017.01163] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/16/2017] [Indexed: 10/31/2023]
Abstract
G quadruplexes (G4) are higher-order DNA and RNA secondary structures formed by G-rich sequences that are built around tetrads of hydrogen-bonded guanine bases. Potential G4 quadruplex sequences have been identified in G-rich eukaryotic non-telomeric and telomeric genomic regions. Upon function, G4 formation is known to involve in chromatin remodeling, gene regulation and has been associated with genomic instability, genetic diseases and cancer progression. The natural role and biological validation of G4 structures is starting to be explored, and is of particular interest for the therapeutic interventions for human diseases. However, the existence and physiological role of G4 DNA and G4 RNA in plants species have not been much investigated yet and therefore, is of great interest for the development of improved crop varieties for sustainable agriculture. In this context, several recent studies suggests that these highly diverse G4 structures in plants can be employed to regulate expression of genes involved in several pathophysiological conditions including stress response to biotic and abiotic stresses as well as DNA damage. In the current review, we summarize the recent findings regarding the emerging functional significance of G4 structures in plants and discuss their potential value in the development of improved crop varieties.
Collapse
Affiliation(s)
- Vikas Yadav
- Department of Biochemistry, Central University of HaryanaMahendergarh, India
| | - Hemansi
- Department of Microbiology, Central University of HaryanaMahendergarh, India
| | - Nayun Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, HoustonTX, United States
- The University of Texas Graduate School of Biomedical Sciences, HoustonTX, United States
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB)New Delhi, India
| | - Puja Yadav
- Department of Microbiology, Central University of HaryanaMahendergarh, India
| |
Collapse
|
27
|
Li Z, Chen F, Huang C, Zheng W, Yu C, Cheng H, Zhou R. Genome-wide mapping and characterization of microsatellites in the swamp eel genome. Sci Rep 2017; 7:3157. [PMID: 28600492 PMCID: PMC5466649 DOI: 10.1038/s41598-017-03330-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/26/2017] [Indexed: 11/09/2022] Open
Abstract
We described genome-wide screening and characterization of microsatellites in the swamp eel genome. A total of 99,293 microsatellite loci were identified in the genome with an overall density of 179 microsatellites per megabase of genomic sequences. The dinucleotide microsatellites were the most abundant type representing 71% of the total microsatellite loci and the AC-rich motifs were the most recurrent in all repeat types. Microsatellite frequency decreased as numbers of repeat units increased, which was more obvious in long than short microsatellite motifs. Most of microsatellites were located in non-coding regions, whereas only approximately 1% of the microsatellites were detected in coding regions. Trinucleotide repeats were most abundant microsatellites in the coding regions, which represented amino acid repeats in proteins. There was a chromosome-biased distribution of microsatellites in non-coding regions, with the highest density of 203.95/Mb on chromosome 8 and the least on chromosome 7 (164.06/Mb). The most abundant dinucleotides (AC)n was mainly located on chromosome 8. Notably, genomic mapping showed that there was a chromosome-biased association of genomic distributions between microsatellites and transposon elements. Thus, the novel dataset of microsatellites in swamp eel provides a valuable resource for further studies on QTL-based selection breeding, genetic resource conservation and evolutionary genetics.
Collapse
Affiliation(s)
- Zhigang Li
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Feng Chen
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Chunhua Huang
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Weixin Zheng
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Chunlai Yu
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Hanhua Cheng
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China.
| | - Rongjia Zhou
- Hubei Key Laboratory of Cell Homeostasis, Laboratory of Molecular and Developmental Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, P. R. China.
| |
Collapse
|
28
|
Sekridova AV, Varizhuk AM, Tatarinova ON, Severov VV, Barinov NA, Smirnov IP, Lazarev VN, Klinov DV, Pozmogova GE. Conformational polymorphysm of G-rich fragments of DNA Alu-repeats. I. Noncanonical structures. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2017. [DOI: 10.1134/s1990750817010097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
29
|
Sekridova AV, Varizhuk AM, Tatarinova ON, Severov VV, Barinov NA, Smirnov IP, Lazarev VN, Klinov DV, Pozmogova GE. [Conformational polymorphysm of G-rich fragments of DNA ALU-repeats. I. Potential noncanonical structures]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2017; 62:535-543. [PMID: 27797328 DOI: 10.18097/pbmc20166205535] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this paper, we report results of systematic studies of conformational polymorphism of G-rich DNA fragments from Alu repeats. Alu retrotransposones are primate-specific short interspersed elements. Using the Alu sequence from the prooncogen bcl2 intron and the consensus AluSx sequence as representative examples, we determined characteristic Alu sites that are capable of adopting G-quadruplex (GQ) conformations (i.e., potential quadruplex sites - PQSAlu), and demonstrated by bioinformatics methods that those sites are Alu-specific in the human genome. Genomic frequencies of PQSAlu were assessed (~1/10000 b.p.). The sites were found to be characteristic of young (active) Alu families (Alu-Y). A recombinant DNA sequence bearing the Alu element from the human bcl2 gene (304 b.p.) and its PQS-mutant (Alu-PQS) were constructed. The formation of noncanonical structures in Alubcl2 dsDNA and the absence of such structures in the case of Alu-PQS were shown using DMS-footprinting and AFM microscopy. Expression vectors bearing wild-type and mutant Alu insertions in the promoter regions were obtained, and the effects of these insertions on the expression of the reporter gene in НЕК293 and HeLa cell lines were compared. Our findings on the spatial organization of Alu repeats may provide insight into the mechanisms of genomic rearrangements which underlie many oncological and neurodegenerative diseases.
Collapse
Affiliation(s)
- A V Sekridova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - A M Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - O N Tatarinova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - V V Severov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - N A Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - I P Smirnov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - V N Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - D V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - G E Pozmogova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| |
Collapse
|
30
|
Sahakyan AB, Murat P, Mayer C, Balasubramanian S. G-quadruplex structures within the 3' UTR of LINE-1 elements stimulate retrotransposition. Nat Struct Mol Biol 2017; 24:243-247. [PMID: 28134931 DOI: 10.1038/nsmb.3367] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/22/2016] [Indexed: 12/28/2022]
Abstract
Long interspersed nuclear elements (LINEs) are ubiquitous transposable elements in higher eukaryotes that have a significant role in shaping genomes, owing to their abundance. Here we report that guanine-rich sequences in the 3' untranslated regions (UTRs) of hominoid-specific LINE-1 elements are coupled with retrotransposon speciation and contribute to retrotransposition through the formation of G-quadruplex (G4) structures. We demonstrate that stabilization of the G4 motif of a human-specific LINE-1 element by small-molecule ligands stimulates retrotransposition.
Collapse
Affiliation(s)
- Aleksandr B Sahakyan
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Pierre Murat
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Clemens Mayer
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| |
Collapse
|
31
|
Moriyama K, Lai MS, Masai H. Interaction of Rif1 Protein with G-Quadruplex in Control of Chromosome Transactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:287-310. [PMID: 29357064 DOI: 10.1007/978-981-10-6955-0_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recent studies on G-quadruplex (G4) revealed crucial and conserved functions of G4 in various biological systems. We recently showed that Rif1, a conserved nuclear factor, binds to G4 present in the intergenic regions and plays a major role in spatiotemporal regulation of DNA replication. Rif1 may tether chromatin fibers through binding to G4, generating specific chromatin domains that dictate the replication timing. G4 and its various binding partners are now implicated in many other chromosome regulations, including transcription, replication initiation, recombination, gene rearrangement, and transposition.
Collapse
Affiliation(s)
- Kenji Moriyama
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Mong Sing Lai
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Hisao Masai
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
| |
Collapse
|
32
|
Biswas B, Kandpal M, Jauhari UK, Vivekanandan P. Genome-wide analysis of G-quadruplexes in herpesvirus genomes. BMC Genomics 2016; 17:949. [PMID: 27871228 PMCID: PMC5117502 DOI: 10.1186/s12864-016-3282-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/09/2016] [Indexed: 11/10/2022] Open
Abstract
Background G-quadruplexes are increasingly recognized as regulatory elements in human, animal, bacterial and plant genomes. The presence and function of G-quadruplexes are not well studied among herpesviruses; in particular, there are no systematic genome-wide analysis of these important secondary structures in herpesvirus genomes. Results We performed genome-wide analysis of putative quadruplex sequences (PQS) in human herpesviruses. We found unusually high PQS densities among human herpesviruses. PQS are enriched in the repeat regions and regulatory regions of human herpesviruses. Interestingly, PQS densities are higher in regulatory regions of immediate early genes compared to early and late genes in most herpesviruses. In addition, the majority of genes functionally conserved across human herpesviruses contain one or more PQS within the regulatory regions. We also describe the existence of unique intramolecular PQS repeats or repetitive G-quadruplex motifs in herpesviruses. Functional studies confirm a role for G-quadruplexes in regulating the gene expression of human herpesviruses. Conclusion The pervasiveness of PQS, their enrichment and conservation at specific genomic locations suggest that these structural entities may represent a novel class of functional elements in herpesviruses. Our findings provide the necessary framework for studies on the biological role of G-quadruplexes in herpesviruses. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3282-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Banhi Biswas
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Manish Kandpal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Utkarsh Kumar Jauhari
- Department of Civil Engineering, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India.
| |
Collapse
|
33
|
Abstract
Repetitive DNA--sequence motifs repeated hundreds or thousands of times in the genome--makes up the major proportion of all the nuclear DNA in most eukaryotic genomes. However, the significance of repetitive DNA in the genome is not completely understood, and it has been considered to have both structural and functional roles, or perhaps even no essential role. High-throughput DNA sequencing reveals huge numbers of repetitive sequences. Most bioinformatic studies focus on low-copy DNA including genes, and hence, the analyses collapse repeats in assemblies presenting only one or a few copies, often masking out and ignoring them in both DNA and RNA read data. Chromosomal studies are proving vital to examine the distribution and evolution of sequences because of the challenges of analysis of sequence data. Many questions are open about the origin, evolutionary mode and functions that repetitive sequences might have in the genome. Some, the satellite DNAs, are present in long arrays of similar motifs at a small number of sites, while others, particularly the transposable elements (DNA transposons and retrotranposons), are dispersed over regions of the genome; in both cases, sequence motifs may be located at relatively specific chromosome domains such as centromeres or subtelomeric regions. Here, we overview a range of works involving detailed characterization of the nature of all types of repetitive sequences, in particular their organization, abundance, chromosome localization, variation in sequence within and between chromosomes, and, importantly, the investigation of their transcription or expression activity. Comparison of the nature and locations of sequences between more, and less, related species is providing extensive information about their evolution and amplification. Some repetitive sequences are extremely well conserved between species, while others are among the most variable, defining differences between even closely relative species. These data suggest contrasting modes of evolution of repetitive DNA of different types, including selfish sequences that propagate themselves and may even be transferred horizontally between species rather than by descent, through to sequences that have a tendency to amplification because of their sequence motifs, to those that have structural significance because of their bulk rather than precise sequence. Functional consequences of repeats include generation of variability by movement and insertion in the genome (giving useful genetic markers), the definition of centromeres, expression under stress conditions and regulation of gene expression via RNA moieties. Molecular cytogenetics and bioinformatic studies in a comparative context are now enabling understanding of the nature and behaviour of this major genomic component.
Collapse
Affiliation(s)
- Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, 60131, Italy
| | - Ettore Olmo
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, 60131, Italy
| | | |
Collapse
|
34
|
Hall LL, Lawrence JB. RNA as a fundamental component of interphase chromosomes: could repeats prove key? Curr Opin Genet Dev 2016; 37:137-147. [PMID: 27218204 DOI: 10.1016/j.gde.2016.04.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 04/01/2016] [Accepted: 04/06/2016] [Indexed: 11/29/2022]
Abstract
Beginning with the precedent of XIST RNA as a 'chromosomal RNA' (cRNA), there is growing interest in the possibility that a diversity of non-coding RNAs may function in chromatin. We review findings which lead us to suggest that RNA is essentially a widespread component of interphase chromosomes. Further, RNA likely contributes to architecture and regulation, with repeat-rich 'junk' RNA in euchromatin (ecRNA) promoting a more open chromatin state. Thousands of low-abundance nuclear RNAs have been reported, however it remains a challenge to determine which of these may function in chromatin. Recent findings indicate that repetitive sequences are enriched in chromosome-associated non-coding RNAs, and repeat-rich RNA shows unusual properties, including localization and stability, with similarities to XIST RNA. We suggest two frontiers in genome biology are emerging and may intersect: the broad contribution of RNA to interphase chromosomes and the distinctive properties of repeat-rich intronic or intergenic junk sequences that may play a role in chromosome structure and regulation.
Collapse
Affiliation(s)
- Lisa L Hall
- Department of Cell & Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Jeanne B Lawrence
- Department of Cell & Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
| |
Collapse
|