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Characterization of contiguous gene deletions in COL4A6 and COL4A5 in Alport syndrome-diffuse leiomyomatosis. J Hum Genet 2017; 62:733-735. [PMID: 28275241 DOI: 10.1038/jhg.2017.28] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 01/31/2017] [Accepted: 01/31/2017] [Indexed: 11/08/2022]
Abstract
Alport syndrome-diffuse leiomyomatosis (AS-DL, OMIM: 308940) is a rare variant of the X-linked Alport syndrome that shows overgrowth of visceral smooth muscles in the gastrointestinal, respiratory and female reproductive tracts in addition to renal symptoms. AS-DL results from deletions that encompass the 5' ends of the COL4A5 and COL4A6 genes, but deletion breakpoints between COL4A5 and COL4A6 have been determined in only four cases. Here, we characterize deletion breakpoints in five AS-DL patients and show a contiguous COL4A6/COL4A5 deletion in each case. We also demonstrate that eight out of nine deletion alleles involved sequences homologous between COL4A5 and COL4A6. Most breakpoints took place in recognizable transposed elements, including long and short interspersed repeats, DNA transposons and long-terminal repeat retrotransposons. Because deletions involved the bidirectional promoter region in each case, we suggest that the occurrence of leiomyomatosis in AS-DL requires inactivation of both genes. Altogether, our study highlights the importance of homologous recombination involving multiple transposed elements for the development of this continuous gene syndrome and other atypical loss-of-function phenotypes.
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Contribution of Syncytins and Other Endogenous Retroviral Envelopes to Human Placenta Pathologies. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 145:111-162. [DOI: 10.1016/bs.pmbts.2016.12.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Sonnenberg ASM, Gao W, Lavrijssen B, Hendrickx P, Sedaghat-Tellgerd N, Foulongne-Oriol M, Kong WS, Schijlen EGWM, Baars JJP, Visser RGF. A detailed analysis of the recombination landscape of the button mushroom Agaricus bisporus var. bisporus. Fungal Genet Biol 2016; 93:35-45. [PMID: 27288752 DOI: 10.1016/j.fgb.2016.06.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 05/13/2016] [Accepted: 06/01/2016] [Indexed: 11/28/2022]
Abstract
The button mushroom (Agaricus bisporus) is one of the world's most cultivated mushroom species, but in spite of its economic importance generation of new cultivars by outbreeding is exceptional. Previous genetic analyses of the white bisporus variety, including all cultivars and most wild isolates revealed that crossing over frequencies are low, which might explain the lack of introducing novel traits into existing cultivars. By generating two high quality whole genome sequence assemblies (one de novo and the other by improving the existing reference genome) of the first commercial white hybrid Horst U1, a detailed study of the crossover (CO) landscape was initiated. Using a set of 626 SNPs in a haploid offspring of 139 single spore isolates and whole genome sequencing on a limited number of homo- and heterokaryotic single spore isolates, we precisely mapped all COs showing that they are almost exclusively restricted to regions of about 100kb at the chromosome ends. Most basidia of A. bisporus var. bisporus produce two spores and pair preferentially via non-sister nuclei. Combined with the COs restricted to the chromosome ends, these spores retain most of the heterozygosity of the parent thus explaining how present-day white cultivars are genetically so close to the first hybrid marketed in 1980. To our knowledge this is the first example of an organism which displays such specific CO landscape.
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Affiliation(s)
- Anton S M Sonnenberg
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, 6708 PB Wageningen, The Netherlands.
| | - Wei Gao
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, 6708 PB Wageningen, The Netherlands
| | - Brian Lavrijssen
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, 6708 PB Wageningen, The Netherlands
| | - Patrick Hendrickx
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, 6708 PB Wageningen, The Netherlands
| | - Narges Sedaghat-Tellgerd
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, 6708 PB Wageningen, The Netherlands
| | - Marie Foulongne-Oriol
- INRA, UR1264 MycSA, Mycologie et Sécurité des Aliments, F-33883 Villenave d'Ornon, France
| | - Won-Sik Kong
- Mushroom Research Division, National Institute of Horticultural and Herbal Science, RDA, Eumseong 27709, Republic of Korea
| | - Elio G W M Schijlen
- PRI Bioscience, Wageningen University & Research Centre, 6708 PB Wageningen, The Netherlands
| | - Johan J P Baars
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, 6708 PB Wageningen, The Netherlands
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, 6708 PB Wageningen, The Netherlands
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Ye C, Ji G, Liang C. detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes. Sci Rep 2016; 6:19688. [PMID: 26795595 PMCID: PMC4726161 DOI: 10.1038/srep19688] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 12/14/2015] [Indexed: 12/27/2022] Open
Abstract
Miniature inverted repeat transposable elements (MITEs) are prevalent in eukaryotic genomes, including plants and animals. Classified as a type of non-autonomous DNA transposable elements, they play important roles in genome organization and evolution. Comprehensive and accurate genome-wide detection of MITEs in various eukaryotic genomes can improve our understanding of their origins, transposition processes, regulatory mechanisms, and biological relevance with regard to gene structures, expression, and regulation. In this paper, we present a new MATLAB-based program called detectMITE that employs a novel numeric calculation algorithm to replace conventional string matching algorithms in MITE detection, adopts the Lempel-Ziv complexity algorithm to filter out MITE candidates with low complexity, and utilizes the powerful clustering program CD-HIT to cluster similar MITEs into MITE families. Using the rice genome as test data, we found that detectMITE can more accurately, comprehensively, and efficiently detect MITEs on a genome-wide scale than other popular MITE detection tools. Through comparison with the potential MITEs annotated in Repbase, the widely used eukaryotic repeat database, detectMITE has been shown to find known and novel MITEs with a complete structure and full-length copies in the genome. detectMITE is an open source tool (https://sourceforge.net/projects/detectmite).
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Affiliation(s)
- Congting Ye
- Department of Automation, Xiamen University, Xiamen, Fujian 361005, China.,Department of Biology, Miami University, Oxford, Ohio 45056, USA
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, Fujian 361005, China.,Innovation Center for Cell Biology, Xiamen University, Xiamen, Fujian 361102, China
| | - Chun Liang
- Department of Biology, Miami University, Oxford, Ohio 45056, USA
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5
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Tempel S, Talla E. VisualTE: a graphical interface for transposable element analysis at the genomic scale. BMC Genomics 2015; 16:139. [PMID: 25881276 PMCID: PMC4367877 DOI: 10.1186/s12864-015-1351-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Accepted: 02/18/2015] [Indexed: 12/01/2022] Open
Abstract
Background Transposable elements are mobile DNA repeat sequences, known to have high impact on genes, genome structure and evolution. This has stimulated broad interest in the detailed biological studies of transposable elements. Hence, we have developed an easy-to-use tool for the comparative analysis of the structural organization and functional relationships of transposable elements, to help understand their functional role in genomes. Results We named our new software VisualTE and describe it here. VisualTE is a JAVA stand-alone graphical interface that allows users to visualize and analyze all occurrences of transposable element families in annotated genomes. VisualTE reads and extracts transposable elements and genomic information from annotation and repeat data. Result analyses are displayed in several graphical panels that include location and distribution on the chromosome, the occurrence of transposable elements in the genome, their size distribution, and neighboring genes’ features and ontologies. With these hallmarks, VisualTE provides a convenient tool for studying transposable element copies and their functional relationships with genes, at the whole-genome scale, and in diverse organisms. Conclusions VisualTE graphical interface makes possible comparative analyses of transposable elements in any annotated sequence as well as structural organization and functional relationships between transposable elements and other genetic object. This tool is freely available at: http://lcb.cnrs-mrs.fr/spip.php?article867. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1351-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sébastien Tempel
- Aix Marseille Université, CNRS, LCB UMR 7283, Marseille, 13402, France.
| | - Emmanuel Talla
- Aix Marseille Université, CNRS, LCB UMR 7283, Marseille, 13402, France.
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7
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Borchert GM, Holton NW, Williams JD, Hernan WL, Bishop IP, Dembosky JA, Elste JE, Gregoire NS, Kim JA, Koehler WW, Lengerich JC, Medema AA, Nguyen MA, Ower GD, Rarick MA, Strong BN, Tardi NJ, Tasker NM, Wozniak DJ, Gatto C, Larson ED. Comprehensive analysis of microRNA genomic loci identifies pervasive repetitive-element origins. Mob Genet Elements 2014; 1:8-17. [PMID: 22016841 DOI: 10.4161/mge.1.1.15766] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 04/06/2011] [Accepted: 04/06/2011] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRs) are small non-coding RNAs that generally function as negative regulators of target messenger RNAs (mRNAs) at the posttranscriptional level. MiRs bind to the 3'UTR of target mRNAs through complementary base pairing, resulting in target mRNA cleavage or translation repression. To date, over 15,000 distinct miRs have been identified in organisms ranging from viruses to man and interest in miR research continues to intensify. Of note, the most enlightening aspect of miR function-the mRNAs they target-continues to be elusive. Descriptions of the molecular origins of independent miR molecules currently support the hypothesis that miR hairpin generation is based on the adjacent insertion of two related transposable elements (TEs) at one genomic locus. Thus transcription across such TE interfaces establishes many, if not the majority of functional miRs. The implications of these findings are substantial for understanding how TEs confer increased genomic fitness, describing miR transcriptional regulations and making accurate miR target predictions. In this work, we have performed a comprehensive analysis of the genomic events responsible for the formation of all currently annotated miR loci. We find that the connection between miRs and transposable elements is more significant than previously appreciated, and more broadly, supports an important role for repetitive elements in miR origin, expression and regulatory network formation. Further, we demonstrate the utility of these findings in miR target prediction. Our results greatly expand the existing repertoire of defined miR origins, detailing the formation of 2,392 of 15,176 currently recognized miR genomic loci and supporting a mobile genetic element model for the genomic establishment of functional miRs.
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Affiliation(s)
- Glen M Borchert
- School of Biological Sciences; Illinois State University; Normal, IL USA
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Roberts JT, Cooper EA, Favreau CJ, Howell JS, Lane LG, Mills JE, Newman DC, Perry TJ, Russell ME, Wallace BM, Borchert GM. Continuing analysis of microRNA origins: Formation from transposable element insertions and noncoding RNA mutations. Mob Genet Elements 2014; 3:e27755. [PMID: 24475369 DOI: 10.4161/mge.27755] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 01/03/2014] [Accepted: 01/07/2014] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRs) are small noncoding RNAs that typically act as regulators of gene expression by base pairing with the 3' UTR of messenger RNAs (mRNAs) and either repressing their translation or initiating degradation. As of this writing over 24,500 distinct miRs have been identified, but the functions of the vast majority of these remain undescribed. This paper represents a summary of our in depth analysis of the genomic origins of miR loci, detailing the formation of 1,213 of the 7,321 recently identified miRs and thereby bringing the total number of miR loci with defined molecular origin to 3,605. Interestingly, our analyses also identify evidence for a second, novel mechanism of miR locus generation through describing the formation of 273 miR loci from mutations to other forms of noncoding RNAs. Importantly, several independent investigations of the genomic origins of miR loci have now supported the hypothesis that miR hairpins are formed by the adjacent genomic insertion of two complementary transposable elements (TEs) into opposing strands. While our results agree that subsequent transcription over such TE interfaces leads to the formation of the majority of functional miR loci, we now also find evidence suggesting that a subset of miR loci were actually formed by an alternative mechanism-point mutations in other structurally complex, noncoding RNAs (e.g., tRNAs and snoRNAs).
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Affiliation(s)
- Justin T Roberts
- Department of Biological Sciences, University of South Alabama; Mobile, AL USA
| | - Elvera A Cooper
- Department of Biological Sciences, University of South Alabama; Mobile, AL USA
| | - Connor J Favreau
- Department of Biological Sciences, University of South Alabama; Mobile, AL USA
| | - Jacob S Howell
- Department of Biological Sciences, University of South Alabama; Mobile, AL USA
| | - Lee G Lane
- Department of Biological Sciences, University of South Alabama; Mobile, AL USA
| | - James E Mills
- Department of Biological Sciences, University of South Alabama; Mobile, AL USA
| | - Derrick C Newman
- Department of Biological Sciences, University of South Alabama; Mobile, AL USA
| | - Tabitha J Perry
- Department of Biological Sciences, University of South Alabama; Mobile, AL USA
| | - Meaghan E Russell
- Department of Biological Sciences, University of South Alabama; Mobile, AL USA
| | - Brittany M Wallace
- Department of Biological Sciences, University of South Alabama; Mobile, AL USA
| | - Glen M Borchert
- Department of Biological Sciences, University of South Alabama; Mobile, AL USA
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REViewer: a tool for linear visualization of repetitive elements within a sequence query. Genomics 2013; 102:209-14. [PMID: 23891933 DOI: 10.1016/j.ygeno.2013.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 05/28/2013] [Accepted: 07/16/2013] [Indexed: 01/20/2023]
Abstract
A species-specific population of arrangements of repetitive elements (REs), called RE arrays, exists in the human and mouse genomes. We developed an RE analytical tool, named REViewer, for visualizing RE occurrences within RE arrays and other genomic regions as an interactive line map. REViewer utilizes an RE reference library which is established with two RE types: 1) REMiner-generated undefined REs and 2) RepeatMasker-derived defined REs. RE occurrences within queries are visualized as a line map using these two RE types. The REViewer's controller provides analytical options, such as zoom, customization of axis unit, and RE type selection. The functionality of REViewer was evaluated using the human chromosome Y sequence. The REViewer is determined to be an efficient tool that facilitates visualization of up to 6000 REs in RE arrays and other genomic regions. The maximum query size is linked to the RE mining tools (e.g., REMiner, RepeatMasker), not to REViewer.
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Yang G. MITE Digger, an efficient and accurate algorithm for genome wide discovery of miniature inverted repeat transposable elements. BMC Bioinformatics 2013; 14:186. [PMID: 23758809 PMCID: PMC3680318 DOI: 10.1186/1471-2105-14-186] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 06/02/2013] [Indexed: 11/25/2022] Open
Abstract
Background Miniature inverted repeat transposable elements (MITEs) are abundant non-autonomous elements, playing important roles in shaping gene and genome evolution. Their characteristic structural features are suitable for automated identification by computational approaches, however, de novo MITE discovery at genomic levels is still resource expensive. Efficient and accurate computational tools are desirable. Existing algorithms process every member of a MITE family, therefore a major portion of the computing task is redundant. Results In this study, redundant computing steps were analyzed and a novel algorithm emphasizing on the reduction of such redundant computing was implemented in MITE Digger. It completed processing the whole rice genome sequence database in ~15 hours and produced 332 MITE candidates with low false positive (1.8%) and false negative (0.9%) rates. MITE Digger was also tested for genome wide MITE discovery with four other genomes. Conclusions MITE Digger is efficient and accurate for genome wide retrieval of MITEs. Its user friendly interface further facilitates genome wide analyses of MITEs on a routine basis. The MITE Digger program is available at: http://labs.csb.utoronto.ca/yang/MITEDigger.
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Affiliation(s)
- Guojun Yang
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada.
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11
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Steinbiss S, Kastens S, Kurtz S. LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons. Mob DNA 2012; 3:18. [PMID: 23131050 PMCID: PMC3582472 DOI: 10.1186/1759-8753-3-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 08/31/2012] [Indexed: 11/30/2022] Open
Abstract
Background Long terminal repeat (LTR) retrotransposons are a class of eukaryotic mobile elements characterized by a distinctive sequence similarity-based structure. Hence they are well suited for computational identification. Current software allows for a comprehensive genome-wide de novo detection of such elements. The obvious next step is the classification of newly detected candidates resulting in (super-)families. Such a de novo classification approach based on sequence-based clustering of transposon features has been proposed before, resulting in a preliminary assignment of candidates to families as a basis for subsequent manual refinement. However, such a classification workflow is typically split across a heterogeneous set of glue scripts and generic software (for example, spreadsheets), making it tedious for a human expert to inspect, curate and export the putative families produced by the workflow. Results We have developed LTRsift, an interactive graphical software tool for semi-automatic postprocessing of de novo predicted LTR retrotransposon annotations. Its user-friendly interface offers customizable filtering and classification functionality, displaying the putative candidate groups, their members and their internal structure in a hierarchical fashion. To ease manual work, it also supports graphical user interface-driven reassignment, splitting and further annotation of candidates. Export of grouped candidate sets in standard formats is possible. In two case studies, we demonstrate how LTRsift can be employed in the context of a genome-wide LTR retrotransposon survey effort. Conclusions LTRsift is a useful and convenient tool for semi-automated classification of newly detected LTR retrotransposons based on their internal features. Its efficient implementation allows for convenient and seamless filtering and classification in an integrated environment. Developed for life scientists, it is helpful in postprocessing and refining the output of software for predicting LTR retrotransposons up to the stage of preparing full-length reference sequence libraries. The LTRsift software is freely available at
http://www.zbh.uni-hamburg.de/LTRsift under an open-source license.
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Affiliation(s)
- Sascha Steinbiss
- Center for Bioinformatics, University of Hamburg, 20146 Hamburg, Bundesstrasse 43, Germany.
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Janicki M, Rooke R, Yang G. Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes. Chromosome Res 2012; 19:787-808. [PMID: 21850457 DOI: 10.1007/s10577-011-9230-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A major portion of most eukaryotic genomes are transposable elements (TEs). During evolution, TEs have introduced profound changes to genome size, structure, and function. As integral parts of genomes, the dynamic presence of TEs will continue to be a major force in reshaping genomes. Early computational analyses of TEs in genome sequences focused on filtering out "junk" sequences to facilitate gene annotation. When the high abundance and diversity of TEs in eukaryotic genomes were recognized, these early efforts transformed into the systematic genome-wide categorization and classification of TEs. The availability of genomic sequence data reversed the classical genetic approaches to discovering new TE families and superfamilies. Curated TE databases and their accurate annotation of genome sequences in turn facilitated the studies on TEs in a number of frontiers including: (1) TE-mediated changes of genome size and structure, (2) the influence of TEs on genome and gene functions, (3) TE regulation by host, (4) the evolution of TEs and their population dynamics, and (5) genomic scale studies of TE activity. Bioinformatics and genomic approaches have become an integral part of large-scale studies on TEs to extract information with pure in silico analyses or to assist wet lab experimental studies. The current revolution in genome sequencing technology facilitates further progress in the existing frontiers of research and emergence of new initiatives. The rapid generation of large-sequence datasets at record low costs on a routine basis is challenging the computing industry on storage capacity and manipulation speed and the bioinformatics community for improvement in algorithms and their implementations.
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Affiliation(s)
- Mateusz Janicki
- Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, Mississauga, ON L5L1C6, Canada
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