TRACER: a resource to study the regulatory architecture of the mouse genome
© Chen et al.; licensee BioMed Central Ltd. 2013
Received: 31 October 2012
Accepted: 22 March 2013
Published: 2 April 2013
Mammalian genes are regulated through the action of multiple regulatory elements, often distributed across large regions. The mechanisms that control the integration of these diverse inputs into specific gene expression patterns are still poorly understood. New approaches enabling the dissection of these mechanisms in vivo are needed.
Here, we describe TRACER (http://tracerdatabase.embl.de), a resource that centralizes information from a large on-going functional exploration of the mouse genome with different transposon-associated regulatory sensors. Hundreds of insertions have been mapped to specific genomic positions, and their corresponding regulatory potential has been documented by analysis of the expression of the reporter sensor gene in mouse embryos. The data can be easily accessed and provides information on the regulatory activities present in a large number of genomic regions, notably in gene-poor intervals that have been associated with human diseases.
TRACER data enables comparisons with the expression pattern of neighbouring genes, activity of surrounding regulatory elements or with other genomic features, revealing the underlying regulatory architecture of these loci. TRACER mouse lines can also be requested for in vivo transposition and chromosomal engineering, to analyse further regions of interest.
KeywordsGene regulation and expression Genome organisation Regulatory landscapes Chromosomal engineering Mouse models of human structural variation
Recent progress in whole genome chromatin profiling has led to the identification of chromatin features that are strongly correlated with gene regulatory elements [21–26], opening ways to obtain a comprehensive catalogue of these elements, and a better annotation of the regulatory genome . Databases that document the in vivo activities of experimentally validated regulatory elements – mostly enhancers – further complement these approaches . Such datasets on regulatory activity can be compared to gene expression data in developing mouse embryos [29–35]. However one cannot reduce gene expression to a catalogue of the many potential regulatory elements present in the genome (from few hundred thousands to millions ). It is equally important to understand the interplay between the different elements present at a locus and how their different inputs are integrated and conveyed to target gene(s). Yet, compared to enhancers, other cis-regulatory elements such as silencers are much more elusive, despite their essential role in gene expression. Similarly important are the mechanisms that define the range and specificity of enhancer-promoter interactions. Indeed, changes in the relative position of genes and regulatory elements by chromosomal rearrangements and structural variations can alter gene expression with dramatic consequences [36–40]. Understanding these situations and the associated mechanisms requires approaches that complement the available catalogues of elements and provide a functional integrated view of the genome regulatory architecture.
For this purpose, we have developed an approach based on the distribution of a regulatory sensor gene throughout the mouse genome  (Figure 1B). The regulatory sensor consists of a LacZ reporter gene, which is driven by a minimal promoter that has no specific activity on its own but responds faithfully to endogenous enhancers. This regulatory sensor therefore uncovers the regulatory potential associated with a given genomic position, which results from the collective action of the different regulatory elements that act on this position. It thus reveals, in an operational manner, the gene regulatory activities within poorly characterized regions, or where annotation for activity is indirect (eg. chromatin profiling) or out of the proper genomic context (eg. transgenic assays). Importantly, the minimal promoter used does not display any obvious tissue- or enhancer-type bias, and the observed expression patterns often overlap with the ones of neighbouring genes . The basic principle of the strategy is analogous to an enhancer-trap ; however, the sensor used in our approach has minimal impact on endogenous gene expression  and therefore reveals regulatory activities without titrating them away from their natural target genes.
This regulatory sensor is carried in a Sleeping Beauty transposon, which can be distributed randomly in the mouse genome, by remobilisation in the male germline . Owing to the efficiency of this in vivo transposition system, we have recovered, identified and characterized a large number of insertions that provide a direct view of the regulatory activities associated with specific genomic regions. Furthermore, as the transposons used also carry a loxP site, the different lines can be used for in vivo chromosomal engineering, to generate mice with targeted deletions or duplications, or segmental aneuploidies [2, 42–44]. The local hopping behaviour of Sleeping Beauty makes each line a potential starting point to scan a region of interest : with our germline-specific transposase transgene, the remobilization rate ranges from 10 to 45%, depending on the starting site, and more than 15% of new insertions are within 1 Mb of the starting point. Thus, a research group with access to a limited number of cages can nonetheless set up a regional screen for its region of interest.
To provide a simple and useful access to the expression patterns and the mouse insertion strains generated with this on-going project, we have designed the Transposon- and Recombinase-Associated Chromosomal Engineering Resource (TRACER) database. This new database is freely accessible at http://tracerdatabase.embl.de/. It constitutes a substantial improvement over the previous one that was established to display the data from a limited pilot screen . The new database comprises novel features that allow users to browse and perform refined searches of insertion sites by position and/or expression patterns. The dataset is also now much larger (4-fold increase, with about 1500 insertions in July 2012), and is growing steadily. This web-based database not only provides information on regulatory activities present along the mouse genome but also gives access to a large collection of mice for engineering chromosomal rearrangements in non-genic intervals.
Construction and content
Methodology and population of database
As well as the external user interfaces described below, the TRACER database has internal interfaces restricted to contributing members and requiring login for authentication. These internal interfaces have all the LIMS (laboratory information management system) components required for uploading data, curation of lines and various administration purposes.
The main internal interface allows lab staff to add all the text annotation, and insert sequence and image files associated with a particular TRACER line. There is also a batch upload interface for multiple insert sequences. The backend code automatically cuts the sequence down to just the insert, verifies the mutagen tag is present and the genomic sequence starts with ‘TA’. The batch sequence submission tool is automatically coupled to the UCSC BLAT service with standard parameters (http://genome.ucsc.edu/) to determine the best alignment and genomic location for each insert. When there are multiple good alignments, user intervention is possible to select the best genomic location. An input form is then populated for the aligned sequence along with any existing data for the line. A similar batch upload interface exists for the parsing of the expression image and annotation files. Internal users can also edit annotations for existing lines using a separate curation interface.
Many of the interfaces utilise a controlled vocabulary of terms to populate the drop-down menus, reducing the number of typos in the database and preserving the integrity of the data stored in TRACER. An administrative database exists to edit these controlled vocabularies.
The external interface allows users to register interest in particular lines, or - if the user’s genomic region of interest is not yet covered - to wish for such a line when it becomes available. These requests are captured in the database and matching lines are displayed for the curators so they can contact the requesting researcher. For user-defined regions of interest, new matching lines are automatically searched every week, or when triggered through the curator interface.
Searching the TRACER database
Display and download of data
The internal identifier of the mouse line in the TRACER database.
The genomic position of the insertion (chr/position ; based on MGSCv37/mm9 genome assembly).
The orientation of the loxP site in the transposon. “Plus” corresponds to the following orientation: centromere – 5′-ATAACTTCGTATAGCATACATTATACGAAGTTAT- 3′ telomere. For comparison, loxP sites targeted by the International Knockout Mouse Consortium in genes transcribed from the plus strand (http://www.knockoutmouse.org/about/targeting-strategies) have the same orientation than TRACER “plus” loxP. Depending on the specific transposon, the orientation of the other features (transposon ends, reporter gene) varies: they are indicated and represented in the expanded view available by clicking on the “expand” icon.
An icon and text, indicating whether expression analysis has been performed and whether LacZ reporter expression has been detected. The developmental stage(s) for which information is available are indicated in the next column. Expression assay is “positive” if the insertion showed LacZ staining at least at one of the stages assessed.
The status of the insertion, indicating whether animals carrying the insertion are available. Insertions that were identified in F0 embryos, that couldn’t be established from the founder or were discontinued, are labelled as “not maintained”. Insertions “available” for further use or analysis fall under three categories: “alive” (line established with mice available in small numbers), “cryopreserved” (either as embryos or sperm) and “new” (usually corresponding to a new insertion, with only the founder animal). The status of an insertion is dynamic: not all “new” insertions are established, and depending on circumstances, “alive” ones may become “cryopreserved” or “not maintained”.
Transposon type: most of the available lines harbour a simple regulatory sensor with a lacZ reporter and a single loxP site, in one or the other orientation relative to the transposon ends (SB8 and SB9). New transposons with additional features have been constructed (see Figure 2), and lines containing them are being established and will be added to the resource. Detailed maps and sequences of available transposons are available on the Tracer website.
The final two columns display a checkbox to download the complete set of information available for an insertion, and an email link to indicate interest in a specific insertion. The toolbar buttons above the results table can be used to filter the search results, and to show only available lines and/or lines with expression data.
Further details on a given insertion can be seen by clicking the expand icon next to each record (Figure 4B). The first section describes the genomic context of the insertion. It lists whether the insertion is located in a gene desert (a gene-free region larger than 500 kb), intergenic (less than 500 kb-long), intronic or exonic region, specifies the orientation of the reporter gene, and the parental insertion line from which the insertion was obtained. This section also contains a schematic of the transposon construct, the genomic environment and flanking genes in a snapshot from the Ensembl genome browser  along with links to view the insertion point in Ensembl or the UCSC genome browser .
The second section shows the LacZ expression patterns obtained for the insertion, when available. Mousing over each thumbnail image show a zoomed-in, trackable high-resolution view of the image. In addition, the stage and viewpoint of the image is recorded along with annotations using the expression domain categories detailed above. One can switch from one image to another one by clicking on the corresponding thumbnail.
The final section shows details regarding how the genomic position of the insertion was determined, such as the flanking sequence(s) obtained (trimmed to the TA dinucleotide duplicated upon Sleeping Beauty insertion ), and where this sequence mapped where this sequence mapped to genome using BLAT . When available, primers that have been used to genotype embryos and mice for this specific insertion are indicated.
The left hand panel of the expanded section contains an interface that displays lines with insertion points within 5 Mb (or a user-selected range) (Figure 4B). Users can select one or more of these lines, and open a new tab displaying these flanking lines. This feature is particularly useful to compare regulatory activities across large regions, and to delineate the extent of regulatory domains.
Finally, the toolbar below the search interface allows data to be downloaded for the whole TRACER database, the search results, user selected lines or just the lines described in publications referring to the dataset. Additionally, all available images can be downloaded. Requests for higher resolution photos and other questions can be sent to email@example.com. Most LacZ stained embryos has been archived, albeit in limited numbers for each insertion, and may be made available upon request.
User wish list
A functional view of the genome with TRACER
The introduction of a “regulatory sensor” in the genome provides a direct operational readout of the activities that can contribute to gene expression, which surround the insertion point. Similar enhancer-trap screens have widely been used in Drosophila and to some extent in zebrafish [55–58], providing information about genes and genomes, as well as a series of useful markers and tools. Their use in mice has been limited [59, 60], in part due to the low throughput of transgenesis, and technical difficulties of generating single-copy insertions. The development of robust and efficient in vivo transposition systems [2, 61–63], as shown here, or the use of lentiviral transgenesis, as recently described elsewhere , open new exciting possibilities to conduct such screens in an efficient and affordable manner.
By querying the database for a gene or a region of interest, one can identify expression patterns and regulatory activities associated with that location and its surroundings. The observed activity may indicate possible developmental or tissue-specific regulation of genes, and shed light on their physiological roles in vivo (Figure 6A). However, we wish to emphasize that the regulatory sensor sometimes reflects only a subset of the expression domains of a given gene . Although the sensor responds accurately to influences from long-range remote enhancers, it is less likely to capture the input of promoter elements that have a limited range of action: tissue-restricted expression of the sensor may therefore represent a tissue-specific modulation of an otherwise broadly expressed gene; yet, this modulation may correspond to important biological functions.
Also, the expression pattern associated with an insertion does not necessarily imply that a corresponding enhancer lies nearby, as illustrated by the shared expression of distant insertions (Figure 6A,C; other examples in ). Instead, the sensor reports the collective input at a given position of both positive and negative regulatory elements. Accordingly, comparing the expression pattern of neighbouring insertions to each other and to known enhancer activities [21, 65] can reveal important regulatory features. These include the range of action of enhancers, the boundaries of expression domains, the presence of silencers or other repressive or insulating elements that modulate enhancer activity and cannot be obtained from other types of datasets and approaches. In essence, TRACER provides an operational view of the regulatory structure of the mammalian genome, and delineates the extent of the large regulatory landscapes that subdivide the genome into functional units. It constitutes a functional counterpart to views obtained by different methods; including, for example, Genome Regulatory Blocks that are delineated by the density of conserved non-coding elements and synteny conservation [66, 67], Topological Associated Domains defined by chromosomal interaction biases [68, 69], and Enhancer-Promoter Units that are revealed by clusters of coincident promoter-enhancer chromatin signatures .
The data present in TRACER identifies genomic positions where an inserted transgene will adopt a highly specific expression profile (Figure 6B). Transgenes that drive the expression of markers to label specific cells (such as fluorescent markers) or of effector genes (for example Cre recombinase) in defined cell-types or embryonic tissues have proven very useful to dissect biological and genetic processes. “Position-effects” (the action of endogenous regulatory elements on transgenes) are usually considered as a problem for transgenic experiments because they lead to partially unpredictable outcomes. With the information displayed in TRACER, one can instead exploit position effects, and select genomic sites that will convey an expression pattern of interest. Importantly, many of these sites are located far from genes, implying that their use would have less functional impact than a gene knock-in. The sensor integrates the inputs of both enhancers and silencers that are acting at its position: consequently, the observed pattern is often more restricted than the one driven by enhancer-only constructs or displayed by the neighbouring genes . Hence, retargeting positions identified in TRACER with a transgene of interest should provide a reliable method to create new tissue- and cell-type specific transgenes. This can be done by homologous recombination in mouse ES cells, but the rapid development of Zinc-Finger or TALE Nuclease-associated targeted transgenesis may offer more efficient alternatives [46, 71, 72].
In addition to maps of genomic “regulatory landscapes”, TRACER provides access to a large and growing collection of mice with different transposon insertions (around 200 in July 2012). Only few insertions are likely to disrupt genes or key/highly conserved regulatory elements directly. Instead, these mice can be used for other purposes, and in particular for engineering aneuploidies and structural variants. Chromosomal aneuploidies are often found in patients suffering developmental malformations and/or neuropsychiatric disorders. In some cases, single gene-knockout can reproduce the phenotypes observed in human patients; however, for numerous other conditions, such as contiguous gene diseases, chromosomal duplications or rearrangements in non-coding intervals, gene-based alleles do not provide accurate models. Because Sleeping Beauty transposons frequently re-insert in the vicinity of their initial position, it is possible to use one insertion in a region of interest to generate additional local re-insertions. These insertions can be (re)combined owing to the associated loxP sites, to produce a series of rearrangements of this locus that model genomic alterations found in human patients, and help determine the causal elements or genes (Figure 6C). Such a use of the TRACER resource and GROMIT strategy can be particularly well suited for large gene clusters (eg. proto-cadherins, KRAB-zinc finger genes, olfactory receptors) or gene-deserts associated with human pathologies, complementing the gene-centric resource provided by the International Knockout Mouse Consortium. Given the growing recognition of the biological importance of genomic structural variants for human diseases, we anticipate that TRACER will be a useful resource to rapidly engineer allelic series of structural variants in mouse orthologous intervals, helping to create novel models of human genomic disorders.
TRACER database and community
Owing to the dynamic nature of transposon elements, the resource present in TRACER will expand steadily with the number of users. Each lab using this transposon technology to investigate a region of interest by “local” hopping will produce a substantial number of by-products (~ 80% of the new insertions). Even if these insertions may not be useful for the producing lab, they can be of interest for others. TRACER is designed to serve as a central “virtual” repository to share those mice. Further information, including references, detailed maps and sequences of the different transposons and transgenes in use, and protocols for mapping of new insertions are available through the pages of the TRACER website.
To facilitate exchanges, the TRACER database incorporates several features and internal interfaces for contributing groups (automated insertion mapping, annotation and administration). In particular, the “User wish list” feature offers a simple manner to readily “tag” newly generated mice of interest without a major investment or commitment of the producing labs.
Availability and requirements
The database is accessible at the web addresses:
Websites – links
UCSC Genome Browser: http://genome.ucsc.edu/index.html
The authors thank the members of the EMBL Laboratory Animal Resource, in particular Andrea Schulz, Silke Feller, Michaela Wesch and Klaus Schmitt; the development and maintenance of this mouse resource would not be possible without their dedication and constant support. We thank as well Manuela Borchert and Anne Hermelin for advice and design of the TRACER webpages. The TRACER database and resource is funded by EMBL. The production of some of the strains described in the database was made in the course of projects supported by the European Commission-FP7 (grant Health 223210/CISSTEM) and Human Frontier Science Program (grant RGY0081/2008-C) to FS.
- Alexander RP, Fang G, Rozowsky J, Snyder M, Gerstein MB: Annotating non-coding regions of the genome. Nat Rev Genet. 2010, 11: 559-571. 10.1038/nrg2814.View ArticlePubMed
- Ruf S, Symmons O, Uslu VV, Dolle D, Hot C, Ettwiller L, Spitz F: Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor. Nat Genet. 2011, 43: 379-386. 10.1038/ng.790.View ArticlePubMed
- Visel A, Rubin EM, Rubin EM, Pennacchio LA, Pennacchio LA: Genomic views of distant-acting enhancers. Nature. 2009, 461: 199-205. 10.1038/nature08451.PubMed CentralView ArticlePubMed
- Jeong Y, El-Jaick K, Roessler E, Muenke M, Epstein DJ: A functional screen for sonic hedgehog regulatory elements across a 1 Mb interval identifies long-range ventral forebrain enhancers. Development. 2006, 133: 761-772. 10.1242/dev.02239.View ArticlePubMed
- Zuniga A, Michos O, Spitz F, Haramis A-PG, Panman L, Galli A, Vintersten K, Klasen C, Mansfield W, Kuc S, Duboule D, Dono R, Zeller R: Mouse limb deformity mutations disrupt a global control region within the large regulatory landscape required for Gremlin expression. Genes Dev. 2004, 18: 1553-1564. 10.1101/gad.299904.PubMed CentralView ArticlePubMed
- Spitz F, Gonzalez F, Duboule D: A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell. 2003, 113: 405-417. 10.1016/S0092-8674(03)00310-6.View ArticlePubMed
- Montavon T, Soshnikova N, Mascrez B, Joye E, Thevenet L, Splinter E, de Laat W, Spitz F, Duboule D: A regulatory archipelago controls Hox genes transcription in digits. Cell. 2011, 147: 1132-1145. 10.1016/j.cell.2011.10.023.View ArticlePubMed
- Nobrega MA, Ovcharenko I, Afzal V, Rubin EM: Scanning human gene deserts for long-range enhancers. Science. 2003, 302: 413-10.1126/science.1088328.View ArticlePubMed
- Lettice LA, Heaney SJH, Purdie LA, Li L, de Beer P, Oostra BA, Goode D, Elgar G, Hill RE, de Graaff E: A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. J Neurosci Res. 2003, 12: 1725-1735.
- Uchikawa M, Ishida Y, Takemoto T, Kamachi Y, Kondoh H: Functional analysis of chicken Sox2 enhancers highlights an array of diverse regulatory elements that are conserved in mammals. Dev Cell. 2003, 4: 509-519. 10.1016/S1534-5807(03)00088-1.View ArticlePubMed
- Kleinjan DA, Seawright A, Mella S, Carr CB, Tyas DA, Simpson TI, Mason JO, Price DJ, van Heyningen V: Long-range downstream enhancers are essential for Pax6 expression. Dev Biol. 2006, 299: 563-581. 10.1016/j.ydbio.2006.08.060.PubMed CentralView ArticlePubMed
- Lettice LA, Horikoshi T, Heaney SJH, van Baren MJ, van der Linde HC, Breedveld GJ, Joosse M, Akarsu N, Oostra BA, Endo N, Shibata M, Suzuki M, Takahashi E, Shinka T, Nakahori Y, Ayusawa D, Nakabayashi K, Scherer SW, Heutink P, Hill RE, Noji S: Disruption of a long-range cis-acting regulator for Shh causes preaxial polydactyly. Proc Natl Acad Sci USA. 2002, 99: 7548-7553. 10.1073/pnas.112212199.PubMed CentralView ArticlePubMed
- Kleinjan DA, van Heyningen V: Long-range control of gene expression: emerging mechanisms and disruption in disease. Am J Hum Genet. 2005, 76: 8-32. 10.1086/426833.PubMed CentralView ArticlePubMed
- Jeong Y, Leskow FC, El-Jaick K, Roessler E, Muenke M, Yocum A, Dubourg C, Li X, Geng X, Oliver G, Epstein DJ: Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein. Nat Genet. 2008, 40: 1348-1353. 10.1038/ng.230.PubMed CentralView ArticlePubMed
- Benko S, Fantes JA, Amiel J, Kleinjan D-J, Thomas S, Ramsay J, Jamshidi N, Essafi A, Heaney S, Gordon CT, McBride D, Golzio C, Fisher M, Perry P, Abadie V, Ayuso C, Holder-Espinasse M, Kilpatrick N, Lees MM, Picard A, Temple IK, Thomas P, Vazquez M-P, Vekemans M, Crollius HR, Hastie ND, Munnich A, Etchevers HC, Pelet A, Farlie PG: Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence. Nat Genet. 2009, 41: 359-364. 10.1038/ng.329.View ArticlePubMed
- Rahimov F, Marazita ML, Visel A, Cooper ME, Hitchler MJ, Rubini M, Domann FE, Govil M, Christensen K, Bille C, Melbye M, Jugessur A, Lie RT, Wilcox AJ, Fitzpatrick DR, Green ED, Mossey PA, Little J, Steegers-Theunissen RP, Pennacchio LA, Schutte BC, Murray JC: Disruption of an AP-2alpha binding site in an IRF6 enhancer is associated with cleft lip. Nat Genet. 2008, 40: 1341-1347. 10.1038/ng.242.PubMed CentralView ArticlePubMed
- Tuupanen S, Turunen M, Lehtonen R, Hallikas O, Vanharanta S, Kivioja T, Björklund M, Wei G, Yan J, Niittymäki I, Mecklin J-P, Järvinen H, Ristimäki A, Di-Bernardo M, East P, Carvajal-Carmona L, Houlston RS, Tomlinson I, Palin K, Ukkonen E, Karhu A, Taipale J, Aaltonen LA: The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling. Nat Genet. 2009, 41: 885-890. 10.1038/ng.406.View ArticlePubMed
- Wasserman NF, Aneas I, Nobrega MA: An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer. Genome Res. 2010, 20: 1191-1197. 10.1101/gr.105361.110.PubMed CentralView ArticlePubMed
- Visser M, Kayser M, Palstra RJ: HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter. Genome Res. 2012, 22: 446-455. 10.1101/gr.128652.111.PubMed CentralView ArticlePubMed
- Harismendy O, Notani D, Song X, Rahim NG, Tanasa B, Heintzman N, Ren B, Fu X-D, Topol EJ, Rosenfeld MG, Frazer KA: 9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response. Nature. 2011, 470: 264-268. 10.1038/nature09753.PubMed CentralView ArticlePubMed
- Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA: ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature. 2009, 457: 854-858. 10.1038/nature07730.PubMed CentralView ArticlePubMed
- Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B: Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature. 2009, 459: 108-112. 10.1038/nature07829.PubMed CentralView ArticlePubMed
- Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, Boyer LA, Young RA, Jaenisch R: Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA. 2010, 107: 21931-21936. 10.1073/pnas.1016071107.PubMed CentralView ArticlePubMed
- Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J: A unique chromatin signature uncovers early developmental enhancers in humans. Nature. 2011, 470: 279-283. 10.1038/nature09692.PubMed CentralView ArticlePubMed
- Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, Hong S, Zhang Z, Landt S, Raha D, Euskirchen G, Wei C-L, Ge W, Wang H, Davis C, Fisher-Aylor KI, Mortazavi A, Gerstein M, Gingeras T, Wold B, Sun Y: Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012, 148: 84-98. 10.1016/j.cell.2011.12.014.PubMed CentralView ArticlePubMed
- Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE: Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011, 473: 43-49. 10.1038/nature09906.PubMed CentralView ArticlePubMed
- Consortium TEP: An integrated encyclopedia of DNA elements in the human genome. Nature. 2012, 489: 57-74. 10.1038/nature11247.View Article
- Visel A, Minovitsky S, Dubchak I, Pennacchio LA: VISTA Enhancer Browser–a database of tissue-specific human enhancers. Nucleic Acids Res. 2007, 35: D88-92. 10.1093/nar/gkl822.PubMed CentralView ArticlePubMed
- Finger JH, Smith CM, Hayamizu TF, McCright IJ, Eppig JT, Kadin JA, Richardson JE, Ringwald M: The mouse Gene Expression Database (GXD): 2011 update. Nucleic Acids Res. 2011, 39: D835-41. 10.1093/nar/gkq1132.PubMed CentralView ArticlePubMed
- Heintz N: Gene expression nervous system atlas (GENSAT). Nat Neurosci. 2004, 7: 483-10.1038/nn0504-483.View ArticlePubMed
- Yokoyama S, Ito Y, Ueno-Kudoh H, Shimizu H, Uchibe K, Albini S, Mitsuoka K, Miyaki S, Kiso M, Nagai A, Hikata T, Osada T, Fukuda N, Yamashita S, Harada D, Mezzano V, Kasai M, Puri PL, Hayashizaki Y, Okado H, Hashimoto M, Asahara H: A systems approach reveals that the myogenesis genome network is regulated by the transcriptional repressor RP58. Dev Cell. 2009, 17: 836-848. 10.1016/j.devcel.2009.10.011.PubMed CentralView ArticlePubMed
- Richardson L, Venkataraman S, Stevenson P, Yang Y, Burton N, Rao J, Fisher M, Baldock RA, Davidson DR, Christiansen JH: EMAGE mouse embryo spatial gene expression database: 2010 update. Nucleic Acids Res. 2010, 38: D703-9. 10.1093/nar/gkp763.PubMed CentralView ArticlePubMed
- Visel A, Thaller C, Eichele G: GenePaint.org: an atlas of gene expression patterns in the mouse embryo. Nucleic Acids Res. 2004, 32: D552-6. 10.1093/nar/gkh029.PubMed CentralView ArticlePubMed
- Diez-Roux G, Banfi S, Sultan M, Geffers L, Anand S, Rozado D, Magen A, Canidio E, Pagani M, Peluso I, Lin-Marq N, Koch M, Bilio M, Cantiello I, Verde R, De Masi C, Bianchi SA, Cicchini J, Perroud E, Mehmeti S, Dagand E, Schrinner S, Nürnberger A, Schmidt K, Metz K, Zwingmann C, Brieske N, Springer C, Hernandez AM, Herzog S: A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol. 2011, 9: e1000582-10.1371/journal.pbio.1000582.PubMed CentralView ArticlePubMed
- Neidhardt L, Gasca S, Wertz K, Obermayr F, Worpenberg S, Lehrach H, Herrmann BG: Large-scale screen for genes controlling mammalian embryogenesis, using high-throughput gene expression analysis in mouse embryos. Mech Dev. 2000, 98: 77-94. 10.1016/S0925-4773(00)00453-6.View ArticlePubMed
- Klopocki E, Ott C, Benatar N, Ullmann R, Mundlos S, Lehmann K: A microduplication of the long range SHH limb regulator (ZRS) is associated with triphalangeal thumb-polysyndactyly syndrome. J Med Genet. 2008, 45: 370-375. 10.1136/jmg.2007.055699.View ArticlePubMed
- Sun M, Ma F, Zeng X, Liu Q, Zhao X, Wu F, Wu G, Zhang Z, Gu B, Zhao Y, Tian S, Lin B, Kong X, Zhang X, Yang W, Lo W: Triphalangeal thumb-polysyndactyly syndrome and syndactyly type IV are caused by genomic duplications involving the long-range, limb-specific SHH enhancer. J Med Genet. 2008, 45: 589-595. 10.1136/jmg.2008.057646.View ArticlePubMed
- Dathe K, Kjaer KW, Brehm A, Meinecke P, Nürnberg P, Neto JC, Brunoni D, Tommerup N, Ott CE, Klopocki E, Seemann P, Mundlos S: Duplications involving a conserved regulatory element downstream of BMP2 are associated with brachydactyly type A2. Am J Hum Genet. 2009, 84: 483-492. 10.1016/j.ajhg.2009.03.001.PubMed CentralView ArticlePubMed
- Dimitrov BI, de Ravel T, Van Driessche J, de Die-Smulders C, Toutain A, Vermeesch JR, Fryns JP, Devriendt K, Debeer P: Distal limb deficiencies, micrognathia syndrome, and syndromic forms of split hand foot malformation (SHFM) are caused by chromosome 10q genomic rearrangements. J Med Genet. 2010, 47: 103-111. 10.1136/jmg.2008.065888.View ArticlePubMed
- Kurth I, Klopocki E, Stricker S, van Oosterwijk J, Vanek S, Altmann J, Santos HG, van Harssel JJT, de Ravel T, Wilkie AOM, Gal A, Mundlos S: Duplications of noncoding elements 5' of SOX9 are associated with brachydactyly-anonychia. Nat Genet. 2009, 41: 862-863. 10.1038/ng0809-862.View ArticlePubMed
- Bellen HJ: Ten years of enhancer detection: lessons from the fly. Plant Cell. 1999, 11: 2271-2281.PubMed CentralView ArticlePubMed
- Hérault Y, Rassoulzadegan M, Cuzin F, Duboule D: Engineering chromosomes in mice through targeted meiotic recombination (TAMERE). Nat Genet. 1998, 20: 381-384. 10.1038/3861.View ArticlePubMed
- Wu S, Ying G, Wu Q, Capecchi MR: Toward simpler and faster genome-wide mutagenesis in mice. Nat Genet. 2007, 39: 922-930. 10.1038/ng2060.View ArticlePubMed
- Spitz F, Herkenne C, Morris MA, Duboule D: Inversion-induced disruption of the Hoxd cluster leads to the partition of regulatory landscapes. Nat Genet. 2005, 37: 889-893. 10.1038/ng1597.View ArticlePubMed
- Keng VW, Yae K, Hayakawa T, Mizuno S, Uno Y, Yusa K, Kokubu C, Kinoshita T, Akagi K, Jenkins NA, Copeland NG, Horie K, Takeda J: Region-specific saturation germline mutagenesis in mice using the Sleeping Beauty transposon system. Nat Methods. 2005, 2: 763-769. 10.1038/nmeth795.View ArticlePubMed
- Meyer M, de Angelis MH, Wurst W, Kühn R: Gene targeting by homologous recombination in mouse zygotes mediated by zinc-finger nucleases. Proc Natl Acad Sci USA. 2010, 107: 15022-15026. 10.1073/pnas.1009424107.PubMed CentralView ArticlePubMed
- Venken KJT, Schulze KL, Haelterman NA, Pan H, He Y, Evans-Holm M, Carlson JW, Levis RW, Spradling AC, Hoskins RA, Bellen HJ: MiMIC: a highly versatile transposon insertion resource for engineering Drosophila melanogaster genes. Nat Methods. 2011, 8: 737-743. 10.1038/nmeth.1662.PubMed CentralView ArticlePubMed
- Smih F, Rouet P, Romanienko PJ, Jasin M: Double-strand breaks at the target locus stimulate gene targeting in embryonic stem cells. Nucleic Acids Res. 1995, 23: 5012-5019. 10.1093/nar/23.24.5012.PubMed CentralView ArticlePubMed
- Groner AC, Meylan S, Ciuffi A, Zangger N, Ambrosini G, Dénervaud N, Bucher P, Trono D: KRAB-zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading. PLoS Genet. 2010, 6: e1000869-10.1371/journal.pgen.1000869.PubMed CentralView ArticlePubMed
- Chung JH, Whiteley M, Felsenfeld G: A 5' element of the chicken beta-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila. Cell. 1993, 74: 505-514. 10.1016/0092-8674(93)80052-G.View ArticlePubMed
- Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri AK, Keefe D, Keenan S, Kinsella R, Komorowska M, Koscielny G, Kulesha E, Larsson P, Longden I, McLaren W, Muffato M, Overduin B, Pignatelli M, Pritchard B, Riat HS: Ensembl 2012. Nucleic Acids Res. 2012, 40: D84-90. 10.1093/nar/gkr991.PubMed CentralView ArticlePubMed
- Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ: The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 2010, 39: D876-D882.PubMed CentralView ArticlePubMed
- Ivics Z, Hackett PB, Plasterk RH, Izsvák Z: Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells. Cell. 1997, 91: 501-510. 10.1016/S0092-8674(00)80436-5.View ArticlePubMed
- Kent WJ: BLAT–-The BLAST-Like Alignment Tool. Genome Res. 2002, 12: 656-664.PubMed CentralView ArticlePubMed
- Kawakami K, Abe G, Asada T, Asakawa K, Fukuda R, Ito A, Lal P, Mouri N, Muto A, Suster ML, Takakubo H, Urasaki A, Wada H, Yoshida M: zTrap: zebrafish gene trap and enhancer trap database. BMC Dev Biol. 2010, 10: 105-10.1186/1471-213X-10-105.PubMed CentralView ArticlePubMed
- Balciunas D, Davidson AE, Sivasubbu S, Hermanson SB, Welle Z, Ekker SC: Enhancer trapping in zebrafish using the Sleeping Beauty transposon. BMC Genomics. 2004, 5: 62-10.1186/1471-2164-5-62.PubMed CentralView ArticlePubMed
- Choo BGH, Kondrichin I, Parinov S, Emelyanov A, Go W, Toh W-C, Korzh V: Zebrafish transgenic Enhancer TRAP line database (ZETRAP). BMC Dev Biol. 2006, 6: 5-10.1186/1471-213X-6-5.PubMed CentralView ArticlePubMed
- Ellingsen S, Laplante MA, König M, Kikuta H, Furmanek T, Hoivik EA, Becker TS: Large-scale enhancer detection in the zebrafish genome. Development. 2005, 132: 3799-3811. 10.1242/dev.01951.View ArticlePubMed
- Allen ND, Cran DG, Barton SC, Hettle S, Reik W, Surani MA: Transgenes as probes for active chromosomal domains in mouse development. Nature. 1988, 333: 852-855. 10.1038/333852a0.View ArticlePubMed
- Gossler A, Joyner AL, Rossant J, Skarnes WC: Mouse embryonic stem cells and reporter constructs to detect developmentally regulated genes. Science. 1989, 244: 463-465. 10.1126/science.2497519.View ArticlePubMed
- Ding S, Wu X, Li G, Han M, Zhuang Y, Xu T: Efficient transposition of the piggyBac (PB) transposon in mammalian cells and mice. Cell. 2005, 122: 473-483. 10.1016/j.cell.2005.07.013.View ArticlePubMed
- Horie K, Yusa K, Yae K, Odajima J, Fischer SEJ, Keng VW, Hayakawa T, Mizuno S, Kondoh G, Ijiri T, Matsuda Y, Plasterk RHA, Takeda J: Characterization of Sleeping Beauty transposition and its application to genetic screening in mice. Mol Cell Biol. 2003, 23: 9189-9207. 10.1128/MCB.23.24.9189-9207.2003.PubMed CentralView ArticlePubMed
- Mátés L, Chuah MKL, Belay E, Jerchow B, Manoj N, Acosta-Sanchez A, Grzela DP, Schmitt A, Becker K, Matrai J, Ma L, Samara-Kuko E, Gysemans C, Pryputniewicz D, Miskey C, Fletcher B, Vandendriessche T, Ivics Z, Izsvák Z: Molecular evolution of a novel hyperactive Sleeping Beauty transposase enables robust stable gene transfer in vertebrates. Nat Genet. 2009, 41: 753-761. 10.1038/ng.343.View ArticlePubMed
- Kelsch W, Stolfi A, Lois C: Genetic labeling of neuronal subsets through enhancer trapping in mice. PLoS One. 2012, 7: e38593-10.1371/journal.pone.0038593.PubMed CentralView ArticlePubMed
- Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, Couronne O, Eisen MB, Visel A, Rubin EM: In vivo enhancer analysis of human conserved non-coding sequences. Nature. 2006, 444: 499-502. 10.1038/nature05295.View ArticlePubMed
- Kikuta H, Laplante M, Navratilova P, Komisarczuk AZ, Engström PG, Fredman D, Akalin A, Caccamo M, Sealy I, Howe K, Ghislain J, Pezeron G, Mourrain P, Ellingsen S, Oates AC, Thisse C, Thisse B, Foucher I, Adolf B, Geling A, Lenhard B, Becker TS: Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res. 2007, 17: 545-555. 10.1101/gr.6086307.PubMed CentralView ArticlePubMed
- Engström PG, Fredman D, Lenhard B: Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes. Genome Biol. 2008, 9: R34-10.1186/gb-2008-9-2-r34.PubMed CentralView ArticlePubMed
- Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B: Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012, 485: 376-380. 10.1038/nature11082.PubMed CentralView ArticlePubMed
- Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berkum NL, Meisig J, Sedat J, Gribnau J, Barillot E, Blüthgen N, Dekker J, Heard E: Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature. 2012, 485: 381-385. 10.1038/nature11049.PubMed CentralView ArticlePubMed
- Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B: A map of the cis-regulatory sequences in the mouse genome. Nature. 2012, 488: 116-120. 10.1038/nature11243.PubMed CentralView ArticlePubMed
- Kim E, Kim S, Kim DH, Choi B-S, Choi I-Y, Kim J-S: Precision genome engineering with programmable DNA-nicking enzymes. Genome Res. 2012, 22: 1327-1333. 10.1101/gr.138792.112.PubMed CentralView ArticlePubMed
- Wang J, Friedman G, Doyon Y, Wang NS, Li CJ, Miller JC, Hua KL, Yan JJ, Babiarz JE, Gregory PD, Holmes MC: Targeted gene addition to a predetermined site in the human genome using a ZFN-based nicking enzyme. Genome Res. 2012, 22: 1316-1326. 10.1101/gr.122879.111.PubMed CentralView ArticlePubMed
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.