An insulator embedded in the chicken α-globin locus regulates chromatin domain configuration and differential gene expression

Furlan-Magaril, Mayra; Rebollar, Eria A.; Guerrero, Georgina; Fernández, Almudena; Moltó, Eduardo; González-Buendía, Edgar; Cantero, Marta; Montoliu, Lluı́s; Recillas‐Targa, Félix

doi:10.1093/nar/gkq740

Cited by 26 publications

(16 citation statements)

References 47 publications

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“…Of possible relevance to this is the presence in the ENCODE database [17] of SNP rs11164648, which is in perfect LD with rs2615977 and which is located within a CTCF-binding site that is predicted to act as a transcriptional insulator. CTCF is a transcriptional repressor and CTCF-dependent insulators have been shown to regulate gene expression by modulating chromatin conformation during development [18]. If cartilage tissues were to become available from an adequate number of young donors then assessing COL11A1 AEI relative to genotype at rs2615977 or rs11164648 may be insightful.…”

Section: Discussionmentioning

confidence: 99%

Allelic expression analysis of the osteoarthritis susceptibility gene COL11A1 in human joint tissues

Raine

Dodd

Reynard

et al. 2013

BMC Musculoskelet Disord

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BackgroundThe single nucleotide polymorphism (SNP) rs2615977 is associated with osteoarthritis (OA) and is located in intron 31 of COL11A1, a strong candidate gene for this degenerative musculoskeletal disease. Furthermore, the common non-synonymous COL11A1 SNP rs1676486 is associated with another degenerative musculoskeletal disease, lumbar disc herniation (LDH). rs1676486 is a C-T transition mediating its affect on LDH susceptibility by modulating COL11A1 expression. The risk T-allele of rs1676486 leads to reduced expression of the COL11A1 transcript, a phenomenon known as allelic expression imbalance (AEI). We were keen therefore to assess whether the effect that rs1676486 has on COL11A1 expression in LDH is also observed in OA and whether the rs2615977 association to OA also marked AEI.MethodsUsing RNA from OA cartilage, we assessed whether either SNP correlated with COL11A1 AEI by 1) measuring COL11A1 expression and stratifying the data by genotype at each SNP; and 2) quantifying the mRNA transcribed from each allele of the two SNPs. We also assessed whether rs1676486 was associated with OA susceptibility using a case–control cohort of over 18,000 individuals.ResultsWe observed significant AEI at rs1676486 (p < 0.0001) with the T-allele correlating with reduced COL11A1 expression. This corresponded with observations in LDH but the SNP was not associated with OA. We did not observe AEI at rs2615977.ConclusionsCOL11A1 is subject to AEI in OA cartilage. AEI at rs1676486 is a risk factor for LDH, but not for OA. These two diseases therefore share a common functional phenotype, namely AEI of COL11A1, but this appears to be a disease risk only in LDH. Other functional effects on COL11A1 presumably account for the OA susceptibility that maps to this gene.

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Section: Discussionmentioning

confidence: 99%

Allelic expression analysis of the osteoarthritis susceptibility gene COL11A1 in human joint tissues

Raine

Dodd

Reynard

et al. 2013

BMC Musculoskelet Disord

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“…The facet-strawberry sequence insulates the Notch gene from flanking chromatin (Vazquez and Schedl, 2000) white The Wari insulator next to the white gene is present in mini-white constructs (Chetverina et al, 2008) Five out of eight sites from the genome-wide map of insulators binding CTCF revealed strong enhancerblocking activity (Nègre et al, 2011) Vertebrates -globin Insulator embedded in the chicken -globin locus regulates chromatin domain configuration and differential gene expression (Furlan-Magaril et al, 2010) -spectrin Insulator with barrier-element activity promotes humanspectrin gene expression in erythroid cells (Gallagher et al, 2009)…”

Section: Notchmentioning

confidence: 99%

CTCF: insights into insulator function during development

2012

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The genome of higher eukaryotes exhibits a patchwork of inactive and active genes. The nuclear protein CCCTC-binding factor (CTCF) when bound to insulator sequences can prevent undesirable crosstalk between active and inactive genomic regions, and it can also shield particular genes from enhancer function, a role that has many applications in development. Exciting recent work has demonstrated roles for CTCF in, for example, embryonic, neuronal and haematopoietic development. Here, we discuss the underlying mechanisms of developmentally regulated CTCF-dependent transcription in relation to model genes, and highlight genome-wide results indicating that CTCF might play a master role in regulating both activating and repressive transcription events at sites throughout the genome. Key words: Igf2/H19, Cohesin, Homeotic gene, Imprint, Insulator IntroductionAs early as the 1950s, the existence of genomic insulators has been postulated based on several observations, such as the phenomenon of position effect variegation (see Glossary, Box 1), in which gene activity is dependent on its genomic location (Lewis, 1950). These locations were later identified as heterochromatic, or inactive, chromatin regions, which, upon translocation, inversion or deletion of chromosomal fragments, may repress the expression of a neighbouring gene (Baker, 1968). The interpretation of this observation was that the genomic rearrangement might have deleted insulators that normally protect genes from the repressive effect of flanking heterochromatin. To add weight to this notion, the biophysical analysis of the Drosophila genome argued for the presence of insulator sequences that separate supercoiled genomic domains (Benyajati and Worcel, 1976). More recently, functional tests with transgenes (see Glossary, Box 1) revealed the existence of three properties of insulators (see Glossary, Box 1): (1) to provide a barrier (or boundary; see Glossary, Box 1) function to prevent repressive heterochromatin from spreading into a neighbouring domain; (2) to provide an enhancer-blocking (see Glossary, Box 1) function when positioned between the enhancer and promoter (see Glossary, Box 1) (Sun and Elgin, 1999), allowing insulators to produce opposite effects either by facilitating the maintenance of a transcriptionally active state or by inhibiting the action of enhancers; (3) to allow three-dimensional looping of genomic regions, a property that is possibly inherent to insulator function, as discussed throughout this review.The first proteins identified that bind to insulator sequences and mediate the insulating function were boundary element-associated factor of 32 kDa (BEAF32) (Zhao et al., 1995), Su(Hw) (Holdridge and Dorsett, 1991;Geyer and Corces, 1992) and zeste-white 5 (Zw5; dwg -FlyBase) (Gaszner et al., 1999) in Drosophila. In vertebrates, CCCTC-binding factor (CTCF) was first shown to mediate insulation (Bell et al., 1999) and was later demonstrated to be highly conserved and also found in Drosophila (dCTCF) (Moon et al., 2005). The DNA-binding do...

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“…The appearance of geneediting nucleases allows one now to easily direct the integration of transgenes to anywhere in the genome, provided the target site is unique. Several types of geneediting nucleases have been developed, namely: Zn-finger nucleases (ZFNs), TALENs, and CRISPR-Cas nucleases (Gaj et al, 2013;Wei et al, 2013;see Chapter 8). The use of gene-editing nucleases will have profound effects and will change the way we plan our experiments.…”

Section: Discussionmentioning

confidence: 99%

“…A simple ratio would then be used to estimate the number of transgene copies integrated in the host genome (Furlan-Magaril et al, 2011).…”

Section: How To Detect Transgene Integration Part 2: Southern Blomentioning

confidence: 99%

Analysis of Transgene Integration

Vicente-García

Fernández

Montoliu

2014

Transgenic Animal Technology

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An insulator embedded in the chicken α-globin locus regulates chromatin domain configuration and differential gene expression

Cited by 26 publications

References 47 publications

Allelic expression analysis of the osteoarthritis susceptibility gene COL11A1 in human joint tissues

Allelic expression analysis of the osteoarthritis susceptibility gene COL11A1 in human joint tissues

CTCF: insights into insulator function during development

Analysis of Transgene Integration

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