RESEARCH HIGHLIGHTS Nature Reviews Genetics | AOP, published online 20 May 2014; doi:10.1038/nrg3762
CHROMOSOMES
Dynamically in the loop
BRAND X PICTURES
Various chromosome conformation capture (3C)-derived methods have been developed to detect physical contacts between chromosomal regions genome wide. Mostly carried out on bulk populations of cells, these methods have uncovered the presence of topologically associating domains (TADs). These submegabase-sized regions are characterized by frequent chromosomal contacts within TADs but infrequent contacts between TADs. The variability of TAD structures among single cells in a population has been poorly characterized, but a new study has used computational structural models and high-resolution microscopy to identify TAD structural variability, which has implications for transcriptional regulation. Giorgetti et al. devised a theoretical simulation in which regions of chromosomes are modelled as flexible polymers represented as beads on a string. Thousands of conformations of these polymers are generated to produce their equilibrium ensembles, and the interaction among beads is optimized until the physical contacts in this molecular population are consistent with experimentally determined contacts which, in this case, are from chromosome conformation capture carbon copy (5C) data.
The authors focused their efforts on two TADs that span the mouse X chromosome inactivation centre (Xic) — where the constituent transcription units and putative regulatory elements have been characterized — and sought to experimentally verify predictions that arose from the modelling. The model suggested large cell-to-cell heterogeneity in intra-TAD structure and contacts, which the authors confirmed was the case using three-dimensional DNA fluorescence in situ hybridization (3D DNA FISH) in mouse embryonic stem cells. Moreover, the range and distribution of possible structures suggested by the model accounted better for the different sets of experimental data than previous theoretical models. To test the relative importance of different chromosomal regions for the TAD structure, Giorgetti et al. modelled the forced ‘silencing’ (that is, inability to form contacts) of individual beads. Although silencing of most beads had only minor effects on the predicted TAD structure, silencing of a few ‘master’ beads was predicted to result in polymer unfolding, leading to a major loss of intra-TAD contacts and to inappropriate inter-TAD interactions. Indeed, this was confirmed experimentally using 3D DNA FISH
NATURE REVIEWS | GENETICS
following genome editing to delete one of the proposed master loci. These master loci are enriched in binding sites for CCCTC-binding factor (CTCF) and cohesin, both of which are known to have roles in controlling TAD architecture. Thus, the emerging picture is that key genomic sites within TADs may be responsible for recruiting DNA-binding proteins to determine both the TAD structure and the fidelity of inter-TAD boundaries. Finally, the authors combined DNA FISH with quantitative RNA FISH to show correlations between the TAD compactness and the levels of nascent RNAs transcribed from the loci, which indicated that the variable chromosome conformations have consequences for gene expression. Such findings may have widespread implications, as the senior authors Guido Tiana and Edith Heard point out. “These fluctuating structures may be exploited to provide variability that can participate in setting up monoallelic gene expression (in the case of X chromosome inactivation) or differential gene expression states (in a developmental context),” proposes Heard. Darren J. Burgess ORIGINAL RESEARCH PAPER Giorgetti, L. et al. Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription. Cell 157, 950–963 (2014) FURTHER READING Dekker, J., Marti-Renom, M. A. & Mirny, L. A. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nature Rev. Genet. 14, 390–403 (2013)
VOLUME 15 | JULY 2014 © 2014 Macmillan Publishers Limited. All rights reserved
CHROMOSOMES
Dynamically in the loop
BRAND X PICTURES
Various chromosome conformation capture (3C)-derived methods have been developed to detect physical contacts between chromosomal regions genome wide. Mostly carried out on bulk populations of cells, these methods have uncovered the presence of topologically associating domains (TADs). These submegabase-sized regions are characterized by frequent chromosomal contacts within TADs but infrequent contacts between TADs. The variability of TAD structures among single cells in a population has been poorly characterized, but a new study has used computational structural models and high-resolution microscopy to identify TAD structural variability, which has implications for transcriptional regulation. Giorgetti et al. devised a theoretical simulation in which regions of chromosomes are modelled as flexible polymers represented as beads on a string. Thousands of conformations of these polymers are generated to produce their equilibrium ensembles, and the interaction among beads is optimized until the physical contacts in this molecular population are consistent with experimentally determined contacts which, in this case, are from chromosome conformation capture carbon copy (5C) data.
The authors focused their efforts on two TADs that span the mouse X chromosome inactivation centre (Xic) — where the constituent transcription units and putative regulatory elements have been characterized — and sought to experimentally verify predictions that arose from the modelling. The model suggested large cell-to-cell heterogeneity in intra-TAD structure and contacts, which the authors confirmed was the case using three-dimensional DNA fluorescence in situ hybridization (3D DNA FISH) in mouse embryonic stem cells. Moreover, the range and distribution of possible structures suggested by the model accounted better for the different sets of experimental data than previous theoretical models. To test the relative importance of different chromosomal regions for the TAD structure, Giorgetti et al. modelled the forced ‘silencing’ (that is, inability to form contacts) of individual beads. Although silencing of most beads had only minor effects on the predicted TAD structure, silencing of a few ‘master’ beads was predicted to result in polymer unfolding, leading to a major loss of intra-TAD contacts and to inappropriate inter-TAD interactions. Indeed, this was confirmed experimentally using 3D DNA FISH
NATURE REVIEWS | GENETICS
following genome editing to delete one of the proposed master loci. These master loci are enriched in binding sites for CCCTC-binding factor (CTCF) and cohesin, both of which are known to have roles in controlling TAD architecture. Thus, the emerging picture is that key genomic sites within TADs may be responsible for recruiting DNA-binding proteins to determine both the TAD structure and the fidelity of inter-TAD boundaries. Finally, the authors combined DNA FISH with quantitative RNA FISH to show correlations between the TAD compactness and the levels of nascent RNAs transcribed from the loci, which indicated that the variable chromosome conformations have consequences for gene expression. Such findings may have widespread implications, as the senior authors Guido Tiana and Edith Heard point out. “These fluctuating structures may be exploited to provide variability that can participate in setting up monoallelic gene expression (in the case of X chromosome inactivation) or differential gene expression states (in a developmental context),” proposes Heard. Darren J. Burgess ORIGINAL RESEARCH PAPER Giorgetti, L. et al. Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription. Cell 157, 950–963 (2014) FURTHER READING Dekker, J., Marti-Renom, M. A. & Mirny, L. A. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nature Rev. Genet. 14, 390–403 (2013)
VOLUME 15 | JULY 2014 © 2014 Macmillan Publishers Limited. All rights reserved
