Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor

Ruf, Sandra; Symmons, Orsolya; Uslu, Veli Vural; Dolle, Dirk; Hot, Chloé; Ettwiller, Laurence; Spitz, François

doi:10.1038/ng.790

Cited by 140 publications

(170 citation statements)

References 50 publications

Supporting

Mentioning

163

Contrasting

Order By: Relevance

“…This plasmid was linearized and randomly integrated into the genome of polymorphic Mus musculus/Mus castaneus embryonic stem cells carrying an ms2-tagged Xist ( [Jonkers et al 2008], a gift from Joost Gribnau) using standard procedures. Integration sites of 56 colonies were identified by nested PCR using transgene-specific primers and a partially random primer as described (Ruf et al 2011), followed by Sanger sequencing. LacO tethering experiments were performed on clone 36 (integration site Chr 11: 115,708,347).…”

Section: Generation Of Laco Transgenic Cellsmentioning

confidence: 99%

Characterization and dynamics of pericentromere-associated domains in mice

et al. 2015

View full text Add to dashboard Cite

Despite recent progress in genome topology knowledge, the role of repeats, which make up the majority of mammalian genomes, remains elusive. Satellite repeats are highly abundant sequences that cluster around centromeres, attract pericentromeric heterochromatin, and aggregate into nuclear chromocenters. These nuclear landmark structures are assumed to form a repressive compartment in the nucleus to which genes are recruited for silencing. We have designed a strategy for genome-wide identification of pericentromere-associated domains (PADs) in different mouse cell types. The ∼1000 PADs and non-PADs have similar chromatin states in embryonic stem cells, but during lineage commitment, chromocenters progressively associate with constitutively inactive genomic regions at the nuclear periphery. This suggests that PADs are not actively recruited to chromocenters, but that chromocenters are themselves attracted to inactive chromatin compartments. However, we also found that experimentally induced proximity of an active locus to chromocenters was sufficient to cause gene repression. Collectively, our data suggest that rather than driving nuclear organization, pericentromeric satellite repeats mostly co-segregate with inactive genomic regions into nuclear compartments where they can contribute to stable maintenance of the repressed status of proximal chromosomal regions.[Supplemental material is available for this article.]One of the major challenges in genome biology is to understand how the genome is organized and what factors control the spatiotemporal expression patterns of genes in different cell types. It is well established that higher-order organization of chromatin within the three-dimensional space of the nucleus is an important contributor to regulation of gene expression. In particular, long-range physical interactions of genomic elements in the nuclear space enable functional communication between genes and their regulatory DNA elements that can be hundreds of kilobases apart on the linear

show abstract

Section: Generation Of Laco Transgenic Cellsmentioning

confidence: 99%

Characterization and dynamics of pericentromere-associated domains in mice

et al. 2015

View full text Add to dashboard Cite

show abstract

“…By profiling the contacts of a given gene promoter, 4C-seq technology allows the identification of the genomic territory within a TAD containing all the CREs that regulate that promoter, what is defined as the regulatory landscape (RL) of that particular gene [12]. Indeed, functional studies in mouse embryos using a transposon-associated sensor [13] have shown that these contact profiles correspond to large regulatory domains typically found around developmental genes [14-16·]. This improved knowledge of the genomic organization in animals, much more realistic and biologically informed, poses new questions to our current understanding of transcriptional regulation.…”

Section: Introductionmentioning

confidence: 99%

Cis-regulatory landscapes in development and evolution

Maeso

Acemel

Gómez-Skármeta

2017

Current Opinion in Genetics & Development

View full text Add to dashboard Cite

The recent advances in our understanding of the 3D organization of the chromatin together with an almost unlimited ability to detect cis-regulatory elements genome-wide using different biochemical signatures has provided us with an unprecedented power to study gene regulation. It is now possible to profile the complete regulatory apparatus controlling the spatio-temporal expression of any given gene, the so-called gene Regulatory Landscapes (RLs). Here we review several studies over the last two years demonstrating the functional consequences of altering RL structure in development, disease and evolution. These works clearly shows that a deep understanding of transcriptional regulation is no longer conceivable without considering the 3D modular organization of animal genomes.

show abstract

“…27; and pig,. Genome-wide mutational screens using gene-trap versions of these vectors have also been carried out successfully in several vertebrate species (20,(31)(32)(33)(34).The aim of this study was to evaluate whether DNA transposons can be used to increase the efficiency of the genetic The authors declare no conflict of interest. …”

mentioning

confidence: 99%

“…13 [28][29][30]. Genome-wide mutational screens using gene-trap versions of these vectors have also been carried out successfully in several vertebrate species (20,(31)(32)(33)(34).…”

mentioning

confidence: 99%

Efficient genetic modification and germ-line transmission of primordial germ cells using piggyBac and Tol2 transposons

Macdonald

Taylor

Sherman

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

155

127

View full text Add to dashboard Cite

The derivation of germ-line competent avian primordial germ cells establishes a cell-based model system for the investigation of germ cell differentiation and the production of genetically modified animals. Current methods to modify primordial germ cells using DNA or retroviral vectors are inefficient and prone to epigenetic silencing. Here, we validate the use of transposable elements for the genetic manipulation of primordial germ cells. We demonstrate that chicken primordial germ cells can be modified in vitro using transposable elements. Both piggyBac and Tol2 transposons efficiently transpose primordial germ cells. Tol2 transposon integration sites were spread throughout both the macro-and microchromosomes of the chicken genome and were more prevalent in gene transcriptional units and intronic regions, consistent with transposon integrations observed in other species. We determined that the presence of insulator elements was not required for reporter gene expression from the integrated transposon. We further demonstrate that a gene-trap cassette carried in the Tol2 transposon can trap and mutate endogenous transcripts in primordial germ cells. Finally, we observed that modified primordial germ cells form functional gametes as demonstrated by the generation of transgenic offspring that correctly expressed a reporter gene carried in the transposon. Transposable elements are therefore efficient vectors for the genetic manipulation of primordial germ cells and the chicken genome.poultry | transgenesis | transposition P rimordial germ cells (PGCs) are specified in the early embryo and are the lineage-restricted stem cells for the germ cell population. In the chicken, segregation of PGCs from somatic cells occurs during the early stages of blastoderm formation (1-3). These cells accumulate in the germinal crescent region anterior to the forming head at day 1 of incubation [stage 4 Hamburger and Hamilton (HH)] and subsequently migrate via the circulatory system to the forming gonads on day 3 of incubation (stage 15 HH) (4). Chicken PGCs can be isolated from embryonic blood at this developmental stage and propagated indefinitely in culture (5). When returned to the circulatory system of an equivalent stage host embryo, the cultured PGCs migrated to and populated the forming embryonic gonad. Breeding from the resulting germline chimeras demonstrated that the cultured PGCs formed functional gametes by production of offspring derived from these cells. Germ-line transmission of cultured PGCs has now been demonstrated for three different chicken breeds (5-7).This in vitro system for the long-term propagation of chicken PGCs is the basis of a unique stem cell model for both the investigation of germ cell differentiation and the generation of genetically modified chickens. Thus far, chicken PGCs have proved highly resistant to genetic modification. Stable transfection of PGCs has been achieved by electroporation of plasmid DNA, at a frequency of ∼1 in 10 6 , but expression from integrated reporter constructs depended on t...

show abstract

Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor

Cited by 140 publications

References 50 publications

Characterization and dynamics of pericentromere-associated domains in mice

Characterization and dynamics of pericentromere-associated domains in mice

Cis-regulatory landscapes in development and evolution

Efficient genetic modification and germ-line transmission of primordial germ cells using piggyBac and Tol2 transposons

Contact Info

Product

Resources

About