Systematic evaluation of chromosome conformation capture assays

Oksuz, Betül Akgöl; Yang, Liyan; Abraham, Sameer; Venev, Sergey V.; Krietenstein, Nils; Parsi, Krishna Mohan; Özadam, Hakan; Oomen, Marlies E.; Nand, Ankita; Mao, Hui Z.; Genga, Ryan M.; Maehr, René; Rando, Oliver J.; Mirny, Leonid A.; Gibcus, Johan H.; Dekker, Job

doi:10.1038/s41592-021-01248-7

Cited by 160 publications

(157 citation statements)

References 37 publications

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“…when the dip is absent) for each value of the fractal dimension. The gray symbols (stars for Micro-C and crosses for Hi-C) correspond to the human differentiated cells based on experimental data from [8] and [9, 10]. (right) A sketch of a typical chromosome surrounded by other chromosomes.…”

Section: Discussionmentioning

confidence: 99%

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Crumpled polymer with loops recapitulates key features of chromosome organization

Polovnikov

Belan

Imakaev

et al. 2022

Preprint

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Chromosomes are exceedingly long polymers compacted in a cell nucleus. While it was long suggested that mammalian chromosomes are folded into loops, experimental detection of such loops has remained a daunting task. The most comprehensive experimental information about chromosome spatial organization is provided by Hi-C experiments that measure the frequency of contacts between all chromosomal positions. The lack of a tractable physical model of a polymer folded into loops limits our ability to interpret experimental data. It thus remains unknown how to obtain accurate and quantitative information about the nature of chromosomal looping from Hi-C. Here, we introduce a model of a polymer with random loops, solve it analytically and extend it by simulations for real chains. Remarkably, our model faithfully reproduces complex shapes of experimental contact probability curves universal among mammalian cells. This agreement suggests that chromosomes are indeed organized into a sequence of randomly positioned loops and allows to estimate loop sizes. We further show that excluded volume in real chains can induce osmotic and topological repulsion between loops. Thus, our new framework allows interpretation of experimental data and suggests that interphase chromosomes are crumpled polymers further folded into a sequence of randomly positioned loops.

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Section: Discussionmentioning

confidence: 99%

“…5B). A cloud of Hi-C data points overlays the theoretical curves on this diagram, allowing to reveal important general character of interphase chromosomes in human cells [8–10].…”

Section: Discussionmentioning

confidence: 99%

Crumpled polymer with loops recapitulates key features of chromosome organization

Polovnikov

Belan

Imakaev

et al. 2022

Preprint

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“…Although in the current CTCC protocol the cryomilled cell fragments are also stabilized by chemical crosslinking for subsequent DNA proximity mapping, the crosslinking of subcellular fragments could be more rapid, efficient and less diffusion biased. Moreover, the crosslinking reagents could be extended from formaldehyde to other chemicals that may not be amenable to in-situ studies but more efficient for in-vitro capturing protein complexes mediating the chromatin interactions(62, 63). Chromatin interaction mapping in cryomilled particles can be enhanced by restriction digestion of the DNA in individual particles, presumably by generating additional DNA ends that can facilitate proximity ligation.…”

Section: Discussionmentioning

confidence: 99%

Cryomilling Tethered Chromatin Conformation Capture reveal new insights into inter-chromosomal interactions

Kumar

Nan

et al. 2022

Preprint

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Traditional methods used to map the three-dimensional organization of chromatin in-situ generally involve chromatin conformation capture by formaldehyde crosslinking, followed by detergent solubilization and enzymatic digestion of DNA. Ligation of proximal DNA fragments followed by next generation sequencing (NGS) generates contact information that enables a global view of the chromatin conformation. Here, we explore the use of cryomilling to physically fragmentize the cells under cryogenic conditions to probe chromatin interactions in the cryomilled cell fragments by the tethered chromatin conformation capture (TCC). Our results show that cryomilling TCC (CTCC) can generate a global contact map similar to that obtained with in-situ Hi-C. This result suggests that summation of chromatin interactions mapped in individual subcellular fragments can reconstitute the global contact map of intact cells in an ensemble manner, paving the way for chromatin conformation analyses of solid tissue by CTCC. Compared with the conventional in-situ methods such as Hi-C, CTCC shows more uniform access to different subcompartments of the folded genome. On the other hand, most inter-chromosomal (trans) contacts are diminished or lost in CTCC except for a group of unique trans contacts that remain intact throughout the cryomilling and in-vitro crosslinking steps. These apparently ultra-stable trans interactions have much enhanced signal in CTCC due to the elimination of signals of most, presumably weak and transient trans interactions. Systematic and comparative analyses between CTCC and in-situ Hi-C provide further insights into the chromatin structure organization and reveal a generally unentangled chromosome interface and the existence of stable inter-chromosomal contacts that may represent intermingled inter-chromosomal interfaces.

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“…3D-modifying variants (above) are linked to genes in their TAD because this provides evidence of physical proximity. TADs are defined as regions between TAD boundaries as defined with MicroC data in HFF from Akgol Oksuz et al [98] (lifted over to hg19). Genes are defined as the longest transcript from protein-coding genes (NM prefix) from NCBI RefSeq downloaded from the UCSC Table Browser [100].…”

Section: Methodsmentioning

confidence: 99%

Reconstructing the 3D genome organization of Neanderthals reveals that chromatin folding shaped phenotypic and sequence divergence

McArthur

Rinker

Gilbertson

et al. 2022

Preprint

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Changes in gene regulation were a major driver of the divergence of archaic hominins (AHs)---Neanderthals and Denisovans---and modern humans (MHs). The three-dimensional (3D) folding of the genome is critical for regulating gene expression; however, its role in recent human evolution has not been explored because the degradation of ancient samples does not permit experimental determination of AH 3D genome folding. To fill this gap, we apply novel deep learning methods for inferring 3D genome organization from DNA sequence to Neanderthal, Denisovan, and diverse MH genomes. Using the resulting 3D contact maps across the genome, we identify 167 distinct regions with diverged 3D genome organization between AHs and MHs. We show that these 3D-diverged loci are enriched for genes related to the function and morphology of the eye, supra-orbital ridges, hair, lungs, immune response, and cognition. Despite these specific diverged loci, the 3D genome of AHs and MHs is more similar than expected based on sequence divergence, suggesting that the pressure to maintain 3D genome organization constrained hominin sequence evolution. We also find that 3D genome organization constrained the landscape of AH ancestry in MHs today: regions more tolerant of 3D variation are enriched for introgression in modern Eurasians. Finally, we identify loci where modern Eurasians have inherited novel 3D genome folding from AH ancestors, which provides a putative molecular mechanism for phenotypes associated with these introgressed haplotypes. In summary, our application of deep learning to predict archaic 3D genome organization illustrates the potential of inferring molecular phenotypes from ancient DNA to reveal previously unobservable biological differences.

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Systematic evaluation of chromosome conformation capture assays

Cited by 160 publications

References 37 publications

Crumpled polymer with loops recapitulates key features of chromosome organization

Crumpled polymer with loops recapitulates key features of chromosome organization

Cryomilling Tethered Chromatin Conformation Capture reveal new insights into inter-chromosomal interactions

Reconstructing the 3D genome organization of Neanderthals reveals that chromatin folding shaped phenotypic and sequence divergence

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