High-resolution analysis of cis-acting regulatory networks at the α-globin locus

Jim Hughes; Karen Lower; Ian Dunham; Stephen Taylor; Marco De Gobbi; Jackie Sloane-Stanley; Simon McGowan; Jiannis Ragoussis; Douglas Vernimmen; Richard Gibbons; Doug Higgs

doi:10.1098/rstb.2012.0361

High-resolution analysis of cis-acting regulatory networks at the α-globin locus

Jim Hughes, Karen Lower, Ian Dunham, Stephen Taylor, Marco De Gobbi, Jackie Sloane-Stanley, Simon McGowan, Jiannis Ragoussis, Douglas Vernimmen, Richard Gibbons, Doug Higgs

Research output: Contribution to journal › Article › peer-review

12 Citations (Scopus)

Abstract

We have combined the circular chromosome conformation capture protocol with high-throughput, genome-wide sequence analysis to characterize the cis-acting regulatory network at a single locus. In contrast to methods which identify large interacting regions (10-1000 kb), the 4C approach provides a comprehensive, high-resolution analysis of a specific locus with the aim of defining, in detail, the cis-regulatory elements controlling a single gene or gene cluster. Using the human α-globin locus as a model, we detected all known local and long-range interactions with this gene cluster. In addition, we identified two interactions with genes located 300 kb (NME4) and 625 kb (FAM173a) from the a-globin cluster.

Original language	English
Pages (from-to)	20120361
Number of pages	11
Journal	Philosophical Transactions of the Royal Society of London Series B: Biological Sciences
Volume	368
Issue number	1620
DOIs	https://doi.org/10.1098/rstb.2012.0361
Publication status	Published - 19 Jun 2013

Keywords

α-globin locus
Chromatin conformation capture
cis-regulatory elements

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10.1098/rstb.2012.0361

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Hughes, J., Lower, K., Dunham, I., Taylor, S., De Gobbi, M., Sloane-Stanley, J., McGowan, S., Ragoussis, J., Vernimmen, D., Gibbons, R., & Higgs, D. (2013). High-resolution analysis of cis-acting regulatory networks at the α-globin locus. Philosophical Transactions of the Royal Society of London Series B: Biological Sciences, 368(1620), 20120361. https://doi.org/10.1098/rstb.2012.0361

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abstract = "We have combined the circular chromosome conformation capture protocol with high-throughput, genome-wide sequence analysis to characterize the cis-acting regulatory network at a single locus. In contrast to methods which identify large interacting regions (10-1000 kb), the 4C approach provides a comprehensive, high-resolution analysis of a specific locus with the aim of defining, in detail, the cis-regulatory elements controlling a single gene or gene cluster. Using the human α-globin locus as a model, we detected all known local and long-range interactions with this gene cluster. In addition, we identified two interactions with genes located 300 kb (NME4) and 625 kb (FAM173a) from the a-globin cluster.",

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Hughes, J, Lower, K, Dunham, I, Taylor, S, De Gobbi, M, Sloane-Stanley, J, McGowan, S, Ragoussis, J, Vernimmen, D, Gibbons, R & Higgs, D 2013, 'High-resolution analysis of cis-acting regulatory networks at the α-globin locus', Philosophical Transactions of the Royal Society of London Series B: Biological Sciences, vol. 368, no. 1620, pp. 20120361. https://doi.org/10.1098/rstb.2012.0361

TY - JOUR

T1 - High-resolution analysis of cis-acting regulatory networks at the α-globin locus

AU - Hughes, Jim

AU - Lower, Karen

AU - Dunham, Ian

AU - Taylor, Stephen

AU - De Gobbi, Marco

AU - Sloane-Stanley, Jackie

AU - McGowan, Simon

AU - Ragoussis, Jiannis

AU - Vernimmen, Douglas

AU - Gibbons, Richard

AU - Higgs, Doug

PY - 2013/6/19

Y1 - 2013/6/19

N2 - We have combined the circular chromosome conformation capture protocol with high-throughput, genome-wide sequence analysis to characterize the cis-acting regulatory network at a single locus. In contrast to methods which identify large interacting regions (10-1000 kb), the 4C approach provides a comprehensive, high-resolution analysis of a specific locus with the aim of defining, in detail, the cis-regulatory elements controlling a single gene or gene cluster. Using the human α-globin locus as a model, we detected all known local and long-range interactions with this gene cluster. In addition, we identified two interactions with genes located 300 kb (NME4) and 625 kb (FAM173a) from the a-globin cluster.

AB - We have combined the circular chromosome conformation capture protocol with high-throughput, genome-wide sequence analysis to characterize the cis-acting regulatory network at a single locus. In contrast to methods which identify large interacting regions (10-1000 kb), the 4C approach provides a comprehensive, high-resolution analysis of a specific locus with the aim of defining, in detail, the cis-regulatory elements controlling a single gene or gene cluster. Using the human α-globin locus as a model, we detected all known local and long-range interactions with this gene cluster. In addition, we identified two interactions with genes located 300 kb (NME4) and 625 kb (FAM173a) from the a-globin cluster.

KW - α-globin locus

KW - Chromatin conformation capture

KW - cis-regulatory elements

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DO - 10.1098/rstb.2012.0361

M3 - Article

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VL - 368

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JO - Philosophical Transactions of the Royal Society of London Series B: Biological Sciences

JF - Philosophical Transactions of the Royal Society of London Series B: Biological Sciences

IS - 1620

ER -

High-resolution analysis of cis-acting regulatory networks at the α-globin locus

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Keywords

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