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Yan H, Mendieta JP, Zhang X, Marand AP, Liang Y, Luo Z, Minow MAA, Roulé T, Wagner D, Tu X, Wang Y, Zhong S, Wessler SR, Schmitz RJ. Evolution of plant cell-type-specific cis -regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574753. [PMID: 38260561 PMCID: PMC10802394 DOI: 10.1101/2024.01.08.574753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Cis -regulatory elements (CREs) are critical in regulating gene expression, and yet our understanding of CRE evolution remains a challenge. Here, we constructed a comprehensive single-cell atlas of chromatin accessibility in Oryza sativa , integrating data from 104,029 nuclei representing 128 discrete cell states across nine distinct organs. We used comparative genomics to compare cell-type resolved chromatin accessibility between O. sativa and 57,552 nuclei from four additional grass species ( Zea mays, Sorghum bicolor, Panicum miliaceum , and Urochloa fusca ). Accessible chromatin regions (ACRs) had different levels of conservation depending on the degree of cell-type specificity. We found a complex relationship between ACRs with conserved noncoding sequences, cell-type specificity, conservation, and tissue-specific switching. Additionally, we found that epidermal ACRs were less conserved compared to other cell types, potentially indicating that more rapid regulatory evolution has occurred in the L1 epidermal layer of these species. Finally, we identified and characterized a conserved subset of ACRs that overlapped the repressive histone modification H3K27me3, implicating them as potentially critical silencer CREs maintained by evolution. Collectively, this comparative genomics approach highlights the dynamics of cell-type-specific CRE evolution in plants.
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Mills A, Jaganatha V, Cortez A, Guzman M, Burnette JM, Collin M, Lopez-Lopez B, Wessler SR, Van Norman JM, Nelson DC, Rasmussen CG. A Course-Based Undergraduate Research Experience in CRISPR-Cas9 Experimental Design to Support Reverse Genetic Studies in Arabidopsis thaliana. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2021; 22:e00155-21. [PMID: 34594454 PMCID: PMC8442021 DOI: 10.1128/jmbe.00155-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
Gene-editing tools such as CRISPR-Cas9 have created unprecedented opportunities for genetic studies in plants and animals. We designed a course-based undergraduate research experience (CURE) to train introductory biology students in the concepts and implementation of gene-editing technology as well as develop their soft skills in data management and scientific communication. We present two versions of the course that can be implemented with twice-weekly meetings over a 5-week period. In the remote-learning version, students performed homology searches, designed guide RNAs (gRNAs) and primers, and learned the principles of molecular cloning. This version is appropriate when access to laboratory equipment or in-person instruction is limited, such as during closures that have occurred in response to the COVID-19 pandemic. In person, students designed gRNAs, cloned CRISPR-Cas9 constructs, and performed genetic transformation of Arabidopsis thaliana. Students learned how to design effective gRNA pairs targeting their assigned gene with an 86% success rate. Final exams tested students' ability to apply knowledge of an unfamiliar genome database to characterize gene structure and to properly design gRNAs. Average final exam scores of ∼73% and ∼84% for in-person and remote-learning CUREs, respectively, indicated that students met learning outcomes. The highly parallel nature of the CURE makes it possible to target dozens to hundreds of genes, depending on the number of sections. Applying this approach in a sensitized mutant background enables focused reverse genetic screens for genetic suppressors or enhancers. The course can be adapted readily to other organisms or projects that employ gene editing.
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Liu K, Wessler SR. Transposition of Mutator-like transposable elements (MULEs) resembles hAT and Transib elements and V(D)J recombination. Nucleic Acids Res 2017; 45:6644-6655. [PMID: 28482040 PMCID: PMC5499845 DOI: 10.1093/nar/gkx357] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/13/2017] [Accepted: 04/20/2017] [Indexed: 12/11/2022] Open
Abstract
Mutator-like transposable elements (MULEs) are widespread across fungal, plant and animal species. Despite their abundance and importance as genetic tools in plants, the transposition mechanism of the MULE superfamily was previously unknown. Discovery of the Muta1 element from Aedes aegypti and its successful transposition in yeast facilitated the characterization of key steps in Muta1 transposition. Here we show that purified transposase binds specifically to the Muta1 ends and catalyzes excision through double strand breaks (DSB) and the joining of newly excised transposon ends with target DNA. In the process, the DSB forms hairpin intermediates on the flanking DNA side. Analysis of transposase proteins containing site-directed mutations revealed the importance of the conserved DDE motif and a W residue. The transposition pathway resembles that of the V(D)J recombination reaction and the mechanism of hAT and Transib transposases including the importance of the conserved W residue in both MULEs and hATs. In addition, yeast transposition and in vitro assays demonstrated that the terminal motif and subterminal repeats of the Muta1 terminal inverted repeat also influence Muta1 transposition. Collectively, our data provides new insights to understand the evolutionary relationships between MULE, hAT and Transib elements and the V(D)J recombinase.
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Chen J, Wrightsman TR, Wessler SR, Stajich JE. RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing. PeerJ 2017; 5:e2942. [PMID: 28149701 PMCID: PMC5274521 DOI: 10.7717/peerj.2942] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/26/2016] [Indexed: 12/26/2022] Open
Abstract
Background Transposable element (TE) polymorphisms are important components of population genetic variation. The functional impacts of TEs in gene regulation and generating genetic diversity have been observed in multiple species, but the frequency and magnitude of TE variation is under appreciated. Inexpensive and deep sequencing technology has made it affordable to apply population genetic methods to whole genomes with methods that identify single nucleotide and insertion/deletion polymorphisms. However, identifying TE polymorphisms, particularly transposition events or non-reference insertion sites can be challenging due to the repetitive nature of these sequences, which hamper both the sensitivity and specificity of analysis tools. Methods We have developed the tool RelocaTE2 for identification of TE insertion sites at high sensitivity and specificity. RelocaTE2 searches for known TE sequences in whole genome sequencing reads from second generation sequencing platforms such as Illumina. These sequence reads are used as seeds to pinpoint chromosome locations where TEs have transposed. RelocaTE2 detects target site duplication (TSD) of TE insertions allowing it to report TE polymorphism loci with single base pair precision. Results and Discussion The performance of RelocaTE2 is evaluated using both simulated and real sequence data. RelocaTE2 demonstrate high level of sensitivity and specificity, particularly when the sequence coverage is not shallow. In comparison to other tools tested, RelocaTE2 achieves the best balance between sensitivity and specificity. In particular, RelocaTE2 performs best in prediction of TSDs for TE insertions. Even in highly repetitive regions, such as those tested on rice chromosome 4, RelocaTE2 is able to report up to 95% of simulated TE insertions with less than 0.1% false positive rate using 10-fold genome coverage resequencing data. RelocaTE2 provides a robust solution to identify TE insertion sites and can be incorporated into analysis workflows in support of describing the complete genotype from light coverage genome sequencing.
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Liu K, Wessler SR. Functional characterization of the active Mutator-like transposable element, Muta1 from the mosquito Aedes aegypti. Mob DNA 2017; 8:1. [PMID: 28096902 PMCID: PMC5225508 DOI: 10.1186/s13100-016-0084-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/19/2016] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Mutator-like transposable elements (MULEs) are widespread with members in fungi, plants, and animals. Most of the research on the MULE superfamily has focused on plant MULEs where they were discovered and where some are extremely active and have significant impact on genome structure. The maize MuDR element has been widely used as a tool for both forward and reverse genetic studies because of its high transposition rate and preference for targeting genic regions. However, despite being widespread, only a few active MULEs have been identified, and only one, the rice Os3378, has demonstrated activity in a non-host organism. RESULTS Here we report the identification of potentially active MULEs in the mosquito Aedes aegypti. We demonstrate that one of these, Muta1, is capable of excision and reinsertion in a yeast transposition assay. Element reinsertion generated either 8 bp or 9 bp target site duplications (TSDs) with no apparent sequence preference. Mutagenesis analysis of donor site TSDs in the yeast assay indicates that their presence is important for precise excision and enhanced transposition. Site directed mutagenesis of the putative DDE catalytic motif and other conserved residues in the transposase protein abolished transposition activity. CONCLUSIONS Collectively, our data indicates that the Muta1 transposase of Ae. aegypti can efficiently catalyze both excision and reinsertion reactions in yeast. Mutagenesis analysis reveals that several conserved amino acids, including the DDE triad, play important roles in transposase function. In addition, donor site TSD also impacts the transposition of Muta1.
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Elgin SCR, Bangera G, Decatur SM, Dolan EL, Guertin L, Newstetter WC, San Juan EF, Smith MA, Weaver GC, Wessler SR, Brenner KA, Labov JB. Insights from a Convocation: Integrating Discovery-Based Research into the Undergraduate Curriculum. CBE LIFE SCIENCES EDUCATION 2016; 15:15/2/fe2. [PMID: 27146158 PMCID: PMC4909350 DOI: 10.1187/cbe.16-03-0118] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The National Academies of Sciences, Engineering, and Medicine organized a convocation in 2015 to explore and elucidate opportunities, barriers, and realities of course-based undergraduate research experiences, known as CUREs, as a potentially integral component of undergraduate science, technology, engineering, and mathematics education. This paper summarizes the convocation and resulting report.
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Hancock CN, Zhang F, Floyd K, Richardson AO, Lafayette P, Tucker D, Wessler SR, Parrott WA. The rice miniature inverted repeat transposable element mPing is an effective insertional mutagen in soybean. PLANT PHYSIOLOGY 2011; 157:552-62. [PMID: 21844309 PMCID: PMC3192579 DOI: 10.1104/pp.111.181206] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 08/04/2011] [Indexed: 05/18/2023]
Abstract
Insertional mutagenesis of legume genomes such as soybean (Glycine max) should aid in identifying genes responsible for key traits such as nitrogen fixation and seed quality. The relatively low throughput of soybean transformation necessitates the use of a transposon-tagging strategy where a single transformation event will produce many mutations over a number of generations. However, existing transposon-tagging tools being used in legumes are of limited utility because of restricted transposition (Ac/Ds: soybean) or the requirement for tissue culture activation (Tnt1: Medicago truncatula). A recently discovered transposable element from rice (Oryza sativa), mPing, and the genes required for its mobilization, were transferred to soybean to determine if it will be an improvement over the other available transposon-tagging tools. Stable transformation events in soybean were tested for mPing transposition. Analysis of mPing excision at early and late embryo developmental stages revealed increased excision during late development in most transgenic lines, suggesting that transposition is developmentally regulated. Transgenic lines that produced heritable mPing insertions were identified, with the plants from the highest activity line producing at least one new insertion per generation. Analysis of the mPing insertion sites in the soybean genome revealed that features displayed in rice were retained including transposition to unlinked sites and a preference for insertion within 2.5 kb of a gene. Taken together these findings indicate that mPing has the characteristics necessary for an effective transposon-tagging resource.
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Han Y, Wessler SR. MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Nucleic Acids Res 2010; 38:e199. [PMID: 20880995 PMCID: PMC3001096 DOI: 10.1093/nar/gkq862] [Citation(s) in RCA: 364] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) are a special type of Class 2 non-autonomous transposable element (TE) that are abundant in the non-coding regions of the genes of many plant and animal species. The accurate identification of MITEs has been a challenge for existing programs because they lack coding sequences and, as such, evolve very rapidly. Because of their importance to gene and genome evolution, we developed MITE-Hunter, a program pipeline that can identify MITEs as well as other small Class 2 non-autonomous TEs from genomic DNA data sets. The output of MITE-Hunter is composed of consensus TE sequences grouped into families that can be used as a library file for homology-based TE detection programs such as RepeatMasker. MITE-Hunter was evaluated by searching the rice genomic database and comparing the output with known rice TEs. It discovered most of the previously reported rice MITEs (97.6%), and found sixteen new elements. MITE-Hunter was also compared with two other MITE discovery programs, FINDMITE and MUST. Unlike MITE-Hunter, neither of these programs can search large genomic data sets including whole genome sequences. More importantly, MITE-Hunter is significantly more accurate than either FINDMITE or MUST as the vast majority of their outputs are false-positives.
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Ludwig SR, Bowen B, Beach L, Wessler SR. A regulatory gene as a novel visible marker for maize transformation. Science 2010; 247:449-50. [PMID: 17788612 DOI: 10.1126/science.247.4941.449] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The temporal and spatial patterns of anthocyanin pigmentation in the maize plant are determined by the presence or absence of the R protein product, a presumed transcriptional activator. At least 50 unique patterns of pigmentation, conditioned by members of the R gene family, have been described. In this study, microprojectiles were used to introduce into maize cells a vector containing the transcription unit from one of these genes (Lc) fused to a constitutive promoter. This chimeric gene induces cell autonomous pigmentation in tissues that are not normally pigmented by the Lc gene. As a reporter for gene expression studies in maize, R is unique because it can be quantified in living tissue simply by counting the number of pigmented cells following bombardment. R may also be useful as a visible marker for selecting stably transformed cell lineages that can give rise to transgenic plants.
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Gleick PH, Adams RM, Amasino RM, Anders E, Anderson DJ, Anderson WW, Anselin LE, Arroyo MK, Asfaw B, Ayala FJ, Bax A, Bebbington AJ, Bell G, Bennett MVL, Bennetzen JL, Berenbaum MR, Berlin OB, Bjorkman PJ, Blackburn E, Blamont JE, Botchan MR, Boyer JS, Boyle EA, Branton D, Briggs SP, Briggs WR, Brill WJ, Britten RJ, Broecker WS, Brown JH, Brown PO, Brunger AT, Cairns J, Canfield DE, Carpenter SR, Carrington JC, Cashmore AR, Castilla JC, Cazenave A, Chapin FS, Ciechanover AJ, Clapham DE, Clark WC, Clayton RN, Coe MD, Conwell EM, Cowling EB, Cowling RM, Cox CS, Croteau RB, Crothers DM, Crutzen PJ, Daily GC, Dalrymple GB, Dangl JL, Darst SA, Davies DR, Davis MB, De Camilli PV, Dean C, DeFries RS, Deisenhofer J, Delmer DP, DeLong EF, DeRosier DJ, Diener TO, Dirzo R, Dixon JE, Donoghue MJ, Doolittle RF, Dunne T, Ehrlich PR, Eisenstadt SN, Eisner T, Emanuel KA, Englander SW, Ernst WG, Falkowski PG, Feher G, Ferejohn JA, Fersht A, Fischer EH, Fischer R, Flannery KV, Frank J, Frey PA, Fridovich I, Frieden C, Futuyma DJ, Gardner WR, Garrett CJR, Gilbert W, Goldberg RB, Goodenough WH, Goodman CS, Goodman M, Greengard P, Hake S, Hammel G, Hanson S, Harrison SC, Hart SR, Hartl DL, Haselkorn R, Hawkes K, Hayes JM, Hille B, Hökfelt T, House JS, Hout M, Hunten DM, Izquierdo IA, Jagendorf AT, Janzen DH, Jeanloz R, Jencks CS, Jury WA, Kaback HR, Kailath T, Kay P, Kay SA, Kennedy D, Kerr A, Kessler RC, Khush GS, Kieffer SW, Kirch PV, Kirk K, Kivelson MG, Klinman JP, Klug A, Knopoff L, Kornberg H, Kutzbach JE, Lagarias JC, Lambeck K, Landy A, Langmuir CH, Larkins BA, Le Pichon XT, Lenski RE, Leopold EB, Levin SA, Levitt M, Likens GE, Lippincott-Schwartz J, Lorand L, Lovejoy CO, Lynch M, Mabogunje AL, Malone TF, Manabe S, Marcus J, Massey DS, McWilliams JC, Medina E, Melosh HJ, Meltzer DJ, Michener CD, Miles EL, Mooney HA, Moore PB, Morel FMM, Mosley-Thompson ES, Moss B, Munk WH, Myers N, Nair GB, Nathans J, Nester EW, Nicoll RA, Novick RP, O'Connell JF, Olsen PE, Opdyke ND, Oster GF, Ostrom E, Pace NR, Paine RT, Palmiter RD, Pedlosky J, Petsko GA, Pettengill GH, Philander SG, Piperno DR, Pollard TD, Price PB, Reichard PA, Reskin BF, Ricklefs RE, Rivest RL, Roberts JD, Romney AK, Rossmann MG, Russell DW, Rutter WJ, Sabloff JA, Sagdeev RZ, Sahlins MD, Salmond A, Sanes JR, Schekman R, Schellnhuber J, Schindler DW, Schmitt J, Schneider SH, Schramm VL, Sederoff RR, Shatz CJ, Sherman F, Sidman RL, Sieh K, Simons EL, Singer BH, Singer MF, Skyrms B, Sleep NH, Smith BD, Snyder SH, Sokal RR, Spencer CS, Steitz TA, Strier KB, Südhof TC, Taylor SS, Terborgh J, Thomas DH, Thompson LG, Tjian RT, Turner MG, Uyeda S, Valentine JW, Valentine JS, Van Etten JL, van Holde KE, Vaughan M, Verba S, von Hippel PH, Wake DB, Walker A, Walker JE, Watson EB, Watson PJ, Weigel D, Wessler SR, West-Eberhard MJ, White TD, Wilson WJ, Wolfenden RV, Wood JA, Woodwell GM, Wright HE, Wu C, Wunsch C, Zoback ML. Climate change and the integrity of science. Science 2010; 328:689-90. [PMID: 20448167 DOI: 10.1126/science.328.5979.689] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Hancock CN, Zhang F, Wessler SR. Transposition of the Tourist-MITE mPing in yeast: an assay that retains key features of catalysis by the class 2 PIF/Harbinger superfamily. Mob DNA 2010; 1:5. [PMID: 20226077 PMCID: PMC2836001 DOI: 10.1186/1759-8753-1-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Accepted: 02/01/2010] [Indexed: 12/25/2022] Open
Abstract
Background PIF/Harbinger is the most recently discovered DNA transposon superfamily and is now known to populate genomes from fungi to plants to animals. Mobilization of superfamily members requires two separate element-encoded proteins (ORF1 and TPase). Members of this superfamily also mobilize Tourist-like miniature inverted repeat transposable elements (MITEs), which are the most abundant transposable elements associated with the genes of plants, especially the cereal grasses. The phylogenetic analysis of many plant genomes indicates that MITEs can amplify rapidly from one or a few elements to hundreds or thousands. The most active DNA transposon identified to date in plants or animals is mPing, a rice Tourist-like MITE that is a deletion derivative of the autonomous Ping element. Ping and the closely related Pong are the only known naturally active PIF/Harbinger elements. Some rice strains accumulate ~40 new mPing insertions per plant per generation. In this study we report the development of a yeast transposition assay as a first step in deciphering the mechanism underlying the amplification of Tourist-MITEs. Results The ORF1 and TPase proteins encoded by Ping and Pong have been shown to mobilize mPing in rice and in transgenic Arabidopsis. Initial tests of the native proteins in a yeast assay resulted in very low transposition. Significantly higher activities were obtained by mutation of a putative nuclear export signal (NES) in the TPase that increased the amount of TPase in the nucleus. When introduced into Arabidopsis, the NES mutant protein also catalyzed higher frequencies of mPing excision from the gfp reporter gene. Our yeast assay retains key features of excision and insertion of mPing including precise excision, extended insertion sequence preference, and a requirement for two proteins that can come from either Ping or Pong or both elements. Conclusions The yeast transposition assay provides a robust platform for analysis of the mechanism underlying transposition catalyzed by the two proteins of PIF/Harbinger elements. It recapitulates all of the features of excision and reinsertion of mPing as seen in plant systems. Furthermore, a mutation of a putative NES in the TPase increased transposition both in yeast and plants.
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Naito K, Zhang F, Tsukiyama T, Saito H, Hancock CN, Richardson AO, Okumoto Y, Tanisaka T, Wessler SR. Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 2009; 461:1130-4. [PMID: 19847266 DOI: 10.1038/nature08479] [Citation(s) in RCA: 319] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 09/02/2009] [Indexed: 12/15/2022]
Abstract
High-copy-number transposable elements comprise the majority of eukaryotic genomes where they are major contributors to gene and genome evolution. However, it remains unclear how a host genome can survive a rapid burst of hundreds or thousands of insertions because such bursts are exceedingly rare in nature and therefore difficult to observe in real time. In a previous study we reported that in a few rice strains the DNA transposon mPing was increasing its copy number by approximately 40 per plant per generation. Here we exploit the completely sequenced rice genome to determine 1,664 insertion sites using high-throughput sequencing of 24 individual rice plants and assess the impact of insertion on the expression of 710 genes by comparative microarray analysis. We find that the vast majority of transposable element insertions either upregulate or have no detectable effect on gene transcription. This modest impact reflects a surprising avoidance of exon insertions by mPing and a preference for insertion into 5' flanking sequences of genes. Furthermore, we document the generation of new regulatory networks by a subset of mPing insertions that render adjacent genes stress inducible. As such, this study provides evidence for models first proposed previously for the involvement of transposable elements and other repetitive sequences in genome restructuring and gene regulation.
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Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK. The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science 2009; 326:1112-5. [PMID: 19965430 DOI: 10.1126/science.1178534] [Citation(s) in RCA: 2482] [Impact Index Per Article: 165.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Wei F, Stein JC, Liang C, Zhang J, Fulton RS, Baucom RS, De Paoli E, Zhou S, Yang L, Han Y, Pasternak S, Narechania A, Zhang L, Yeh CT, Ying K, Nagel DH, Collura K, Kudrna D, Currie J, Lin J, Kim H, Angelova A, Scara G, Wissotski M, Golser W, Courtney L, Kruchowski S, Graves TA, Rock SM, Adams S, Fulton LA, Fronick C, Courtney W, Kramer M, Spiegel L, Nascimento L, Kalyanaraman A, Chaparro C, Deragon JM, Miguel PS, Jiang N, Wessler SR, Green PJ, Yu Y, Schwartz DC, Meyers BC, Bennetzen JL, Martienssen RA, McCombie WR, Aluru S, Clifton SW, Schnable PS, Ware D, Wilson RK, Wing RA. Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genet 2009; 5:e1000728. [PMID: 19936048 PMCID: PMC2773423 DOI: 10.1371/journal.pgen.1000728] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 10/16/2009] [Indexed: 12/20/2022] Open
Abstract
Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on approximately 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses.
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Yang G, Nagel DH, Feschotte C, Hancock CN, Wessler SR. Tuned for transposition: molecular determinants underlying the hyperactivity of a Stowaway MITE. Science 2009; 325:1391-4. [PMID: 19745152 DOI: 10.1126/science.1175688] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Miniature inverted repeat transposable elements (MITEs) are widespread in eukaryotic genomes, where they can attain high copy numbers despite a lack of coding capacity. However, little is known about how they originate and amplify. We performed a genome-wide screen of functional interactions between Stowaway MITEs and potential transposases in the rice genome and identified a transpositionally active MITE that possesses key properties that enhance transposition. Although not directly related to its autonomous element, the MITE has less affinity for the transposase than does the autonomous element but lacks a motif repressing transposition in the autonomous element. The MITE contains internal sequences that enhance transposition. These findings suggest that MITEs achieve high transposition activity by scavenging transposases encoded by distantly related and self-restrained autonomous elements.
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Han Y, Burnette JM, Wessler SR. TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences. Nucleic Acids Res 2009; 37:e78. [PMID: 19429695 PMCID: PMC2699529 DOI: 10.1093/nar/gkp295] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2009] [Revised: 04/15/2009] [Accepted: 04/15/2009] [Indexed: 11/23/2022] Open
Abstract
Gene families compose a large proportion of eukaryotic genomes. The rapidly expanding genomic sequence database provides a good opportunity to study gene family evolution and function. However, most gene family identification programs are restricted to searching protein databases where data are often lagging behind the genomic sequence data. Here, we report a user-friendly web-based pipeline, named TARGeT (Tree Analysis of Related Genes and Transposons), which uses either a DNA or amino acid 'seed' query to: (i) automatically identify and retrieve gene family homologs from a genomic database, (ii) characterize gene structure and (iii) perform phylogenetic analysis. Due to its high speed, TARGeT is also able to characterize very large gene families, including transposable elements (TEs). We evaluated TARGeT using well-annotated datasets, including the ascorbate peroxidase gene family of rice, maize and sorghum and several TE families in rice. In all cases, TARGeT rapidly recapitulated the known homologs and predicted new ones. We also demonstrated that TARGeT outperforms similar pipelines and has functionality that is not offered elsewhere.
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Monden Y, Naito K, Okumoto Y, Saito H, Oki N, Tsukiyama T, Ideta O, Nakazaki T, Wessler SR, Tanisaka T. High potential of a transposon mPing as a marker system in japonica x japonica cross in rice. DNA Res 2009; 16:131-40. [PMID: 19270311 PMCID: PMC2671205 DOI: 10.1093/dnares/dsp004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although quantitative traits loci (QTL) analysis has been widely performed to isolate agronomically important genes, it has been difficult to obtain molecular markers between individuals with similar phenotypes (assortative mating). Recently, the miniature inverted-repeat transposable element mPing was shown to be active in the japonica strain Gimbozu EG4 where it had accumulated more than 1000 copies. In contrast, most other japonicas, including Nipponbare, have 50 or fewer mPing insertions in their genome. In this study we have exploited the polymorphism of mPing insertion sites to generate 150 PCR markers in a cross between the closely related japonicas, Nipponbare × Gimbozu (EG4). These new markers were distributed in genic regions of the whole genome and showed significantly higher polymorphism (150 of 183) than all other molecular markers tested including short sequence repeat markers (46 of 661). In addition, we performed QTL analysis with these markers using recombinant inbred lines derived from Nipponbare × Gimbozu EG4, and successfully mapped a locus involved in heading date on the short arm of chromosome 6. Moreover, we could easily map two novel loci involved in the culm length on the short arms of chromosomes 3 and 10.
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Abstract
The formation of hybrid zones between nascent species is a widespread phenomenon. The evolutionary consequences of hybridization are influenced by numerous factors, including the action of natural selection on quantitative trait variation. Here we examine how the genetic basis of floral traits of two species of Louisiana Irises affects the extent of quantitative trait variation in their hybrids. Quantitative trait locus (QTL) mapping was used to assess the size (magnitude) of phenotypic effects of individual QTL, the degree to which QTL for different floral traits are colocalized, and the occurrence of mixed QTL effects. These aspects of quantitative genetic variation would be expected to influence (1) the number of genetic steps (in terms of QTL substitutions) separating the parental species phenotypes; (2) trait correlations; and (3) the potential for transgressive segregation in hybrid populations. Results indicate that some Louisiana Iris floral trait QTL have large effects and QTL for different traits tend to colocalize. Transgressive variation was observed for six of nine traits, despite the fact that mixed QTL effects influence few traits. Overall, our QTL results imply that the genetic basis of floral morphology and color traits might facilitate the maintenance of phenotypic divergence between Iris fulva and Iris brevicaulis, although a great deal of phenotypic variation was observed among hybrids.
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Kwon SJ, Kim DH, Lim MH, Long Y, Meng JL, Lim KB, Kim JA, Kim JS, Jin M, Kim HI, Ahn SN, Wessler SR, Yang TJ, Park BS. Terminal repeat retrotransposon in miniature (TRIM) as DNA markers in Brassica relatives. Mol Genet Genomics 2007; 278:361-70. [PMID: 17690909 DOI: 10.1007/s00438-007-0249-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Accepted: 05/11/2007] [Indexed: 11/24/2022]
Abstract
We have developed a display system using a unique sequence of terminal repeat retrotransposon in miniature (TRIM) elements, which were recently identified from gene-rich regions of Brassica rapa. The technique, named TRIM display, is based on modification of the AFLP technique using an adapter primer for the restriction fragments of BfaI and a primer derived from conserved terminal repeat sequences of TRIM elements, Br1 and Br2. TRIM display using genomic DNA produced 50-70 bands ranging from 100 to 700 bp in all the species of the family Brassicaceae. TRIM display using B. rapa cDNA produced about 20 bands. Sequences of 11 randomly selected bands, 7 from genomic DNA and 4 from cDNA, begin with about 104 bp of the terminal repeat sequences of TRIM elements Br1 or Br2 and end with unique sequences indicating that all bands are derived from unique insertion sites of TRIM elements. Furthermore, 7 of the 11 unique sequences showed significant similarity with expressed gene. Most of the TRIM display bands were polymorphic between genera and about 55% (132 of 239 bands) are polymorphic among 19 commercial F1 hybrid cultivars. Analysis of phylogenetic relationships shows clear-cut lineage among the 19 cultivars. Furthermore, a combination of 11 polymorphic bands derived from only one primer combination can clearly distinguish one cultivar from the others. TRIM display bands were reproducible and inheritable through successive generations that is revealed by genetic mapping of 6 out of 27 polymorphic TRIM markers on the genetic map of Brassica napus. Collective data provide evidence that TRIM display can provide useful DNA markers in Brassica relatives because these markers are distributed in gene-rich regions, and are sometimes involved in the restructuring of genes.
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Yang G, Zhang F, Hancock CN, Wessler SR. Transposition of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2007; 104:10962-7. [PMID: 17578919 PMCID: PMC1904124 DOI: 10.1073/pnas.0702080104] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An active miniature inverted repeat transposable element (MITE), mPing, was discovered by computer-assisted analysis of rice genome sequence. The mPing element is mobile in rice cell culture and in a few rice strains where it has been amplified to >1,000 copies during recent domestication. However, determination of the transposase source and characterization of the mechanism of transposition have been hampered by the high copy number of mPing and the presence of several candidate autonomous elements in the rice genome. Here, we report that mPing is active in Arabidopsis thaliana, where its transposition is catalyzed by three sources of transposase from rice: the autonomous Ping and Pong elements and by a cDNA derived from a Ping transcript. In addition to transposase, the product of a second element-encoded ORF of unknown function is also required for mPing transposition. Excision of mPing in A. thaliana is usually precise, and transposed copies usually insert into unlinked sites in the genome that are preferentially in or near genes. As such, this will be a valuable assay system for the dissection of MITE transposition and a potentially powerful tagging system for gene discovery in eukaryotes.
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Holligan D, Zhang X, Jiang N, Pritham EJ, Wessler SR. The transposable element landscape of the model legume Lotus japonicus. Genetics 2006; 174:2215-28. [PMID: 17028332 PMCID: PMC1698628 DOI: 10.1534/genetics.106.062752] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Accepted: 09/18/2006] [Indexed: 11/18/2022] Open
Abstract
The largest component of plant and animal genomes characterized to date is transposable elements (TEs). The availability of a significant amount of Lotus japonicus genome sequence has permitted for the first time a comprehensive study of the TE landscape in a legume species. Here we report the results of a combined computer-assisted and experimental analysis of the TEs in the 32.4 Mb of finished TAC clones. While computer-assisted analysis facilitated a determination of TE abundance and diversity, the availability of complete TAC sequences permitted identification of full-length TEs, which facilitated the design of tools for genomewide experimental analysis. In addition to containing all TE types found in previously characterized plant genomes, the TE component of L. japonicus contained several surprises. First, it is the second species (after Oryza sativa) found to be rich in Pack-MULEs, with >1000 elements that have captured and amplified gene fragments. In addition, we have identified what appears to be a legume-specific MULE family that was previously identified only in fungal species. Finally, the L. japonicus genome contains many hundreds, perhaps thousands of Sireviruses: Ty1/copia-like elements with an extra ORF. Significantly, several of the L. japonicus Sireviruses have recently amplified and may still be actively transposing.
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Naito K, Cho E, Yang G, Campbell MA, Yano K, Okumoto Y, Tanisaka T, Wessler SR. Dramatic amplification of a rice transposable element during recent domestication. Proc Natl Acad Sci U S A 2006; 103:17620-5. [PMID: 17101970 PMCID: PMC1693796 DOI: 10.1073/pnas.0605421103] [Citation(s) in RCA: 164] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Indexed: 11/18/2022] Open
Abstract
Despite the prevalence of transposable elements in the genomes of higher eukaryotes, what is virtually unknown is how they amplify to very high copy numbers without killing their host. Here, we report the discovery of rice strains where a miniature inverted-repeat transposable element (mPing) has amplified from approximately 50 to approximately 1,000 copies in four rice strains. We characterized 280 of the insertions and found that 70% were within 5 kb of coding regions but that insertions into exons and introns were significantly underrepresented. Further analyses of gene expression and transposable-element activity demonstrate that the ability of mPing to attain high copy numbers is because of three factors: (i) the rapid selection against detrimental insertions, (ii) the neutral or minimal effect of the remaining insertions on gene transcription, and (iii) the continued mobility of mPingelements in strains that already have > 1,000 copies. The rapid increase in mPing copy number documented in this study represents a potentially valuable source of population diversity in self-fertilizing plants like rice.
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Yang G, Weil CF, Wessler SR. A rice Tc1/mariner-like element transposes in yeast. THE PLANT CELL 2006; 18:2469-78. [PMID: 17041148 PMCID: PMC1626630 DOI: 10.1105/tpc.106.045906] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The Tc1/mariner transposable element superfamily is widely distributed in animal and plant genomes. However, no active plant element has been previously identified. Nearly identical copies of a rice (Oryza sativa) Tc1/mariner element called Osmar5 in the genome suggested potential activity. Previous studies revealed that Osmar5 encoded a protein that bound specifically to its own ends. In this report, we show that Osmar5 is an active transposable element by demonstrating that expression of its coding sequence in yeast promotes the excision of a nonautonomous Osmar5 element located in a reporter construct. Element excision produces transposon footprints, whereas element reinsertion occurs at TA dinucleotides that were either tightly linked or unlinked to the excision site. Several site-directed mutations in the transposase abolished activity, whereas mutations in the transposase binding site prevented transposition of the nonautonomous element from the reporter construct. This report of an active plant Tc1/mariner in yeast will provide a foundation for future comparative analyses of animal and plant elements in addition to making a new wide host range transposable element available for plant gene tagging.
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Bouck A, Peeler R, Arnold ML, Wessler SR. Genetic mapping of species boundaries in Louisiana irises using IRRE retrotransposon display markers. Genetics 2005; 171:1289-303. [PMID: 16079236 PMCID: PMC1456832 DOI: 10.1534/genetics.105.044552] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2005] [Accepted: 07/20/2005] [Indexed: 01/25/2023] Open
Abstract
Genetic mapping studies provide insight into the pattern and extent of genetic incompatibilities affecting hybridization between closely related species. Genetic maps of two species of Louisiana Irises, Iris fulva and I. brevicaulis, were constructed from transposon-based molecular markers segregating in reciprocal backcross (BC1) interspecific hybrids and used to investigate genomic patterns of species barriers inhibiting introgression. Linkage mapping analyses indicated very little genetic incompatibility between I. fulva and I. brevicaulis in the form of map regions exhibiting transmission ratio distortion, and this was confirmed using a Bayesian multipoint mapping analysis. These results demonstrate the utility of transposon-based marker systems for genetic mapping studies of wild plant species and indicate that the genomes of I. fulva and I. brevicaulis are highly permeable to gene flow and introgression from one another via backcrossing.
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