A 4C approach to gene interactions in 3D
1
DOI: 10.1038/nrg2000 URLs Wouter de Laat’s web site: http://www2.eur.nl/fgg/ch1/ delaat.html Rolf Ohlsson’s web site: http://www.fu.uu.se/devbiol/ OhlssonLab/Home.html Entrez gene: HoxB1: http://www.ncbi.nlm. nih.gov/entrez/query.fcgi?db=g ene&cmd=Retrieve&dopt=full_ report&list_uids=15407 β-globin: http://www.ncbi.nlm. nih.gov/entrez/query.fcgi?db=g ene&cmd=Retrieve&dopt=full_ report&list_uids=15127 Rad23A: http://www.ncbi.nlm. nih.gov/entrez/query.fcgi?db=g ene&cmd=Retrieve&dopt=full_ report&list_uids=19358 H19: http://www.ncbi.nlm.nih. gov/entrez/query.fcgi?db=gen e&cmd=Retrieve&dopt=full_ report&list_uids=14955 Igf2: http://www.ncbi.nlm.nih. gov/entrez/query.fcgi?db=gen e&cmd=Retrieve&dopt=full_ report&list_uids=16002 GENE REGULATION A 4C approach to gene interactions in 3D A new method significantly increases our ability to explore how genes are organized in their spatial environ- ments. Three studies have pioneered this approach to show that many interactions between genes take place in the nucleus. They also provide new insights into how such interactions contribute to gene regulation. Chromosome conformation capture (3C) is widely used to tell whether genes are closely positioned in the nucleus. It uses gene-specific PCR primers to generate a product if two genes are close enough to be ligated following chromatin crosslinking. In the new approach, which two of the studies have named 4C, adding a circularization step followed by inverse PCR removes the need for two gene-specific primers. Any sequence that comes into close proximity with a gene of interest can be detected, whether or not such an interaction was previously suspected. Würtele and Chartrand used 4C to probe the spatial environment of the HoxB1 locus in mouse embryonic stem cells by looking at the genomic positions of the 4C PCR products. Loci that lie closest to HoxB1 along the chromosome colocalize with this gene most frequently in the nuclear space. When the cells were induced to express HoxB1, interactions with loci on other chromosomes became more common. This is consistent with models in which inactive genes are constrained within a relatively small space, but explore a larger area when their expression is induced, which can also involve a reposition- ing of the gene in the nucleus. Simonis and colleagues took a similar approach, but used microar- rays to identify interacting loci following PCR. They studied interac- tions with two loci, the tissue-specific β-globin gene and the housekeeping gene Rad23a. Both were found to make many contacts in 3D space, with intrachromosomal interactions being more frequent than interchro- mosomal contacts. Interestingly, in brain tissue, in which the β-globin gene is silenced, it tends to interact with inactive genes, whereas in blood cells, in which β-globin is expressed, it interacts with active genes that are not necessarily tissue-specific. Rad23a makes intra- and interchromosomal contacts with active genes and these contacts seem to be largely conserved between tissues. A third study also used 4C com- bined with microarrays, this time to explore the epigenetic control of physical interactions between loci. The parental origin of an imprinting control region (ICR) upstream of H19 is known to control the forma- tion of a chromatin loop that allows the ICR to contact and silence a neighbouring gene, Igf2. Zhao and colleagues used 4C to investigate whether H19 also contacts other loci. They uncovered an extensive network of interchromosomal and intrachromosomal interactions, with both imprinted and non- imprinted genes, that was linked to either activation or silencing of the interacting genes in different cases. Importantly, many of these interac- tions were epigenetically regulated, relying on the methylation status of the H19 ICR. Although 4C has been applied to just four genes, a complex set of interactions has already been uncovered. A thorough exploration of interactions for many more genes, and a careful analysis of how they relate to gene expression, will be key challenges for the future. Louisa Flintoft ORIGINAL RESEARCH PAPERS Würtele, H. & Chartrand, P. Genome-wide scanning of HoxB1- associated loci in mouse ES cells using an open- ended chromosome confirmation capture methodology. Chromosome Res. 14, 477–495 (2006) | Simonis, M. et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nature Genet. 8 October 2006 (doi: 10.1038/ ng1896) | Zhao, Z. et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nature Genet. 8 October 2006 (doi: 10.1038/ng1891) WEB SITES Wouter de Laat’s web site: http://www2.eur.nl/fgg/ch1/delaat.html Rolf Ohlsson’s web site: http://www.fu.uu.se/ devbiol/OhlssonLab/Home.html RESEARCH HIGHLIGHTS NATURE REVIEWS | GENETICS VOLUME 7 | MONTH 2006 | 1 © 2006 Nature Publishing Group
Transcript of A 4C approach to gene interactions in 3D
DOI:10.1038/nrg2000
URLsWouter de Laat’s web site: http://www2.eur.nl/fgg/ch1/delaat.html Rolf Ohlsson’s web site: http://www.fu.uu.se/devbiol/OhlssonLab/Home.html
Entrez gene:
HoxB1: http://www.ncbi.nlm.
nih.gov/entrez/query.fcgi?db=g
ene&cmd=Retrieve&dopt=full_
report&list_uids=15407
β-globin: http://www.ncbi.nlm.
nih.gov/entrez/query.fcgi?db=g
ene&cmd=Retrieve&dopt=full_
report&list_uids=15127
Rad23A: http://www.ncbi.nlm.
nih.gov/entrez/query.fcgi?db=g
ene&cmd=Retrieve&dopt=full_
report&list_uids=19358
H19: http://www.ncbi.nlm.nih.
gov/entrez/query.fcgi?db=gen
e&cmd=Retrieve&dopt=full_
report&list_uids=14955
Igf2: http://www.ncbi.nlm.nih.
gov/entrez/query.fcgi?db=gen
e&cmd=Retrieve&dopt=full_
report&list_uids=16002
G E N E R E G U L AT I O N
A 4C approach to gene interactions in 3D
A new method significantly increases our ability to explore how genes are organized in their spatial environ-ments. Three studies have pioneered this approach to show that many interactions between genes take place in the nucleus. They also provide new insights into how such interactions contribute to gene regulation.
Chromosome conformation capture (3C) is widely used to tell whether genes are closely positioned in the nucleus. It uses gene-specific PCR primers to generate a product if two genes are close enough to be ligated following chromatin crosslinking. In the new approach, which two of the studies have named 4C, adding a circularization step followed by inverse PCR removes the need for two gene-specific primers. Any sequence that comes into close proximity with a gene of interest can be detected, whether or not such an interaction was previously suspected.
Würtele and Chartrand used 4C to probe the spatial environment of the HoxB1 locus in mouse embryonic stem cells by looking at the genomic positions of the 4C PCR products. Loci that lie closest to HoxB1 along the chromosome colocalize with this
gene most frequently in the nuclear space. When the cells were induced to express HoxB1, interactions with loci on other chromosomes became more common. This is consistent with models in which inactive genes are constrained within a relatively small space, but explore a larger area when their expression is induced, which can also involve a reposition-ing of the gene in the nucleus.
Simonis and colleagues took a similar approach, but used microar-rays to identify interacting loci following PCR. They studied interac-tions with two loci, the tissue-specific β-globin gene and the housekeeping gene Rad23a. Both were found to make many contacts in 3D space, with intrachromosomal interactions being more frequent than interchro-mosomal contacts. Interestingly, in brain tissue, in which the β-globin gene is silenced, it tends to interact with inactive genes, whereas in blood cells, in which β-globin is expressed, it interacts with active genes that are not necessarily tissue-specific. Rad23a makes intra- and interchromosomal contacts with active genes and these contacts seem to be largely conserved between tissues.
A third study also used 4C com-bined with microarrays, this time to explore the epigenetic control of physical interactions between loci. The parental origin of an imprinting control region (ICR) upstream of H19 is known to control the forma-tion of a chromatin loop that allows the ICR to contact and silence a neighbouring gene, Igf2. Zhao and colleagues used 4C to investigate whether H19 also contacts other loci. They uncovered an extensive network of interchromosomal and intrachromosomal interactions, with both imprinted and non-imprinted genes, that was linked to either activation or silencing of the interacting genes in different cases. Importantly, many of these interac-tions were epigenetically regulated, relying on the methylation status of the H19 ICR.
Although 4C has been applied to just four genes, a complex set of interactions has already been uncovered. A thorough exploration of interactions for many more genes, and a careful analysis of how they relate to gene expression, will be key challenges for the future.
Louisa Flintoft
ORIGINAL RESEARCH PAPERS Würtele, H. & Chartrand, P. Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended chromosome confirmation capture methodology. Chromosome Res. 14, 477–495 (2006) | Simonis, M. et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nature Genet. 8 October 2006 (doi: 10.1038/ng1896) | Zhao, Z. et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nature Genet. 8 October 2006 (doi: 10.1038/ng1891)WEB SITES Wouter de Laat’s web site: http://www2.eur.nl/fgg/ch1/delaat.html Rolf Ohlsson’s web site: http://www.fu.uu.se/devbiol/OhlssonLab/Home.html
R E S E A R C H H I G H L I G H T S
NATURE REVIEWS | GENETICS VOLUME 7 | MONTH 2006 | 1© 2006 Nature Publishing Group
