A Complex Chromatin Landscape Revealed by Patterns of Nuclease Sensitivity and Histone Modification within the Mouse β-Globin Locus

Bulger, Michael; Schübeler, Dirk; Bender, Michael A.; Hamilton, Joan; Farrell, Catherine; Hardison, Ross C.; Groudine, Mark

doi:10.1128/mcb.23.15.5234-5244.2003

Cited by 147 publications

(162 citation statements)

References 63 publications

(71 reference statements)

Supporting

Mentioning

151

Contrasting

Order By: Relevance

“…It has been noted that olfactory receptor genes located ∼90 kb upstream of the LCR are orthologous to ones located 40 kb upstream of the murine locus (Bulger et al 2000), indicating that these regions are related. In addition, the murine HS-62.5/ HS-60 element is embedded in a sequence that is similar to a sequence located ∼90 kb upstream of the human LCR (Bulger et al 2003). These observations indicate that the region located ∼90 kb upstream of the human LCR is orthologous to the region located ∼40 kb upstream of the murine locus, suggesting that this region may also interact with the LCR in human cells.…”

Section: Interactions Between Hs5 and Upstream Elementsmentioning

confidence: 99%

See 1 more Smart Citation

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

Dostie¹,

et al. 2006

View full text Add to dashboard Cite

Physical interactions between genetic elements located throughout the genome play important roles in gene regulation and can be identified with the Chromosome Conformation Capture (3C) methodology. 3C converts physical chromatin interactions into specific ligation products, which are quantified individually by PCR. Here we present a high-throughput 3C approach, 3C-Carbon Copy (5C), that employs microarrays or quantitative DNA sequencing using 454-technology as detection methods. We applied 5C to analyze a 400-kb region containing the human ␤-globin locus and a 100-kb conserved gene desert region. We validated 5C by detection of several previously identified looping interactions in the ␤-globin locus. We also identified a new looping interaction in K562 cells between the ␤-globin Locus Control Region and the ␥-␦-globin intergenic region. Interestingly, this region has been implicated in the control of developmental globin gene switching. 5C should be widely applicable for large-scale mapping of cis-and trans-interaction networks of genomic elements and for the study of higher-order chromosome structure.

show abstract

Section: Interactions Between Hs5 and Upstream Elementsmentioning

confidence: 99%

“…top, middle, and bottom panels). This region contains three olfactory receptor genes and multiple HS sites (Bulger et al 2003).…”

Section: Interactions Between Hs5 and Upstream Elementsmentioning

confidence: 99%

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

Dostie¹,

et al. 2006

View full text Add to dashboard Cite

show abstract

“…Four genomic regions have been investigated recently in comparable detail to the one presented here: the mouse beta globin locus (19 DHS in 170 kb) (Hardison et al 1997;Bulger et al 2003); the mouse Sprr locus (16 DHS in 260 kb) (Martin et al 2004); the mouse imprinted Igf2/ H19 locus (26 DHS in 130 kb) (Koide et al 1994); and the human imprinted SNRPN locus (eight DHS in 150 kb) (Schweizer et al 1999). The beta globin and Sprr studies also demonstrated a discordance between DHS and ECRs.…”

Section: Evolutionary Conservation Versus Unbiased Approachesmentioning

confidence: 99%

Long-range DNase I hypersensitivity mapping reveals the imprinted Igf2r and Air promoters share cis-regulatory elements

Pauler

Stricker²,

Warczok³

et al. 2005

Genome Res.

View full text Add to dashboard Cite

Epigenetic mechanisms restrict the expression of imprinted genes to one parental allele in diploid cells. At the Igf2r/Air imprinted cluster on mouse chromosome 17, paternal-specific expression of the Air noncoding RNA has been shown to silence three genes in cis: Igf2r, Slc22a2, and Slc22a3. By an unbiased mapping of DNase I hypersensitive sites (DHS) in a 192-kb region flanking Igf2r and Air, we identified 21 DHS, of which nine mapped to evolutionarily conserved sequences. Based on the hypothesis that silencing effects of Air would be directed towards cis regulatory elements used to activate genes, DHS are potential key players in the control of imprinted expression. However, in this 192-kb region only the two DHS mapping to the Igf2r and Air promoters show parental specificity. The remaining 19 DHS were present on both parental alleles and, thus, have the potential to activate Igf2r on the maternal allele and Air on the paternal allele. The possibility that the Igf2r and Air promoters share the same cis-acting regulatory elements, albeit on opposite parental chromosomes, was supported by the similar expression profiles of Igf2r and Air in vivo. These results refine our understanding of the onset of imprinted silencing at this cluster and indicate the Air noncoding RNA may specifically target silencing to the Igf2r promoter.

show abstract

“…subsequently demonstrated to be responsible for this insulator activity of 5 0 HS4 [5]. The human and mouse b-globin loci are also located inside large chromosomal regions of inactive chromatin and are similarly flanked by CTCF-binding sites [17,18]. These were suspected to form a barrier for incoming heterochromatin, but their deletion did not lead to closing or inactivation of the b-globin locus [12,19].…”

Section: Introductionmentioning

confidence: 99%

CTCF: the protein, the binding partners, the binding sites and their chromatin loops

Holwerda

Laat

2013

Phil. Trans. R. Soc. B

198

170

View full text Add to dashboard Cite

CTCF has it all. The transcription factor binds to tens of thousands of genomic sites, some tissue-specific, others ultra-conserved. It can act as a transcriptional activator, repressor and insulator, and it can pause transcription. CTCF binds at chromatin domain boundaries, at enhancers and gene promoters, and inside gene bodies. It can attract many other transcription factors to chromatin, including tissue-specific transcriptional activators, repressors, cohesin and RNA polymerase II, and it forms chromatin loops. Yet, or perhaps therefore, CTCF's exact function at a given genomic site is unpredictable. It appears to be determined by the associated transcription factors, by the location of the binding site relative to the transcriptional start site of a gene, and by the site's engagement in chromatin loops with other CTCF-binding sites, enhancers or gene promoters. Here, we will discuss genome-wide features of CTCF binding events, as well as locus-specific functions of this remarkable transcription factor.

show abstract

A Complex Chromatin Landscape Revealed by Patterns of Nuclease Sensitivity and Histone Modification within the Mouse β-Globin Locus

Cited by 147 publications

References 63 publications

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

Long-range DNase I hypersensitivity mapping reveals the imprinted Igf2r and Air promoters share cis-regulatory elements

CTCF: the protein, the binding partners, the binding sites and their chromatin loops

Contact Info

Product

Resources

About