Comparative analysis of 2D and 3D distance measurements to study spatial genome organization

Finn, Elizabeth H.; Pegoraro, Gianluca; Shachar, Sigal; Misteli, Tom

doi:10.1101/076893

Cited by 8 publications

(19 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We chose pairs of loci ranging from kilobases to megabases apart on chromosome 19. The inter-locus distances of each given pair showed high cell-to-cell variability, in agreement with previous FISH results (Finn et al, 2017a;Finn et al, 2017b;Giorgetti et al, 2016;Fudenberg et al, 2017) but in our case in the live cell mode. To assess local chromosome dynamics during cell cycle progression, we analyzed a pair of loci spaced by 4.6 kb from the center-to-center between the regions labeled by the two CRISPR probes.…”

Section: Discussionsupporting

confidence: 93%

CRISPR-Based DNA Imaging in Living Cells Reveals Cell Cycle-Dependent Chromosome Dynamics

Naseri

et al. 2017

Preprint

View full text Add to dashboard Cite

IN BRIEFDistinct chromosome folding and dynamics during cell cycle progression were dissected by CRISPR-Sirius DNA imaging in living cells. HIGHLIGHTS• CRISPR-Sirius allows tracking of pairs of chromosomal loci having kilobase to megabase inter-locus distances• Pair-wise tracking of loci allows measurement of both local and domain dynamics• Chromosomal fiber relaxation is positively correlated with local dynamics• Genomic region size contributes to local and domain movements• Distinct chromosome dynamics were uncovered during cell cycle progression in interphase . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/195966 doi: bioRxiv preprint first posted online Sep. 29, 2017; 2 SUMMARYIn contrast to the well-studied condensation and folding of chromosomes during mitosis, their dynamics in interphase are less understood. We developed a sensitive, multicolor system, CRISPR-Sirius, allowing the real-time tracking of the dynamics of chromosomal loci. We tracked loci kilobases to megabases apart and found significant variation in the inter-locus distances of each pair, indicating differing degrees of DNA contortion. We resolved two distinct modes of dynamics of loci: saltatory local movements as well as translational movements of the domain. The magnitude of both of these modes of movements increased from early to late G1, whereas the translational movements were reduced in early S. The local fluctuations decreased slightly in early S and more markedly in mid-late S. These newly observed movements and their cell cycle-dependence are indicative of a hitherto unrecognized compaction-relaxation dynamic of the chromosomal fiber operating concurrently with changes in the extent of observed genomic domain movements.

show abstract

Section: Discussionsupporting

confidence: 93%

CRISPR-Based DNA Imaging in Living Cells Reveals Cell Cycle-Dependent Chromosome Dynamics

Naseri

et al. 2017

Preprint

View full text Add to dashboard Cite

show abstract

“…Probes were generated via nick translation as described previously (51) from bacterial artificial chromosomes (BACs) to approximately 100 genomic loci (see Table 1). Mixes, reagents, and conditions are exactly as in Finn (28). All experiments were performed in triplicate.…”

Section: Hifish Imagingmentioning

confidence: 99%

“…Automated analysis of all images was performed based on a modified version of a previously described Acapella 2.6 (PerkinElmer) custom script (28,52,53). This custom script performed automated nucleus detection based on the maximal projection of the DAPI image (ex.…”

Section: D and 3d Image Analysismentioning

confidence: 99%

See 1 more Smart Citation

Heterogeneity and Intrinsic Variation in Spatial Genome Organization

Finn

Pegoraro

Brandão

et al. 2017

Preprint

Self Cite

View full text Add to dashboard Cite

Abstract:The genome is hierarchically organized in 3D space and its architecture is altered in differentiation, development and disease. Some of the general principles that determine global 3D genome organization have been established. However, the extent and nature of cell-to-cell and cell-intrinsic variability in genome architecture are poorly characterized. Here, we systematically probe the heterogeneity in genome organization in human fibroblasts by combining high-resolution Hi-C datasets and high-throughput genome imaging. Optical mapping of several hundred genome interaction pairs at the single cell level demonstrates low steady-state frequencies of colocalization in the population and independent behavior of individual alleles in single nuclei. Association frequencies are determined by genomic distance, higher-order chromatin architecture and chromatin environment. These observations reveal extensive variability and heterogeneity in genome organization at the level of single cells and alleles and they demonstrate the coexistence of a broad spectrum of chromatin and genome conformations in a cell population.

show abstract

“…(d) Distance distributions between five pairs of FISH probes on chr1 in fibroblast cells. The experimental data (histograms) were digitized fromFig.4Bin[58]. The fits using Eq.…”

mentioning

confidence: 99%

A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C

Kim

Bak

Liu

et al. 2019

Preprint

View full text Add to dashboard Cite

Identifying chromatin domains (CDs) from Hi-C data is currently a central problem in genome research. Here we present Multi-CD (https://github.com/multi-cd), a unified method to discover CDs at various genomic scales. Integrating approaches from polymer physics, financial market fluctuation analysis and Bayesian inference, Multi-CD identifies the CDs that best represent the global pattern of correlation manifested in Hi-C, and reveals the multi-scale structure of chromosome. At each scale, the CDs are consistent with the results of existing methods, as well as with biological data from independent sources. CD solutions compared across different scales and cell types allow us to quantify the hierarchy between four major families of CDs, and to glean the principles of chromatin organization: (i) Sub-TADs, TADs, and meta-TADs constitute a robust hierarchical structure. (ii) The assemblies of compartments and TAD-based domains are governed by distinct organizational principles. (iii) Sub-TADs are the common building blocks of chromosome architecture. CDs acquired from our interpretation of Hi-C data using Multi-CD not only provide new insights into chromatin organization, but also offer a quantitative account for its cell-type-dependence and function.with γ ij = (σ ii + σ jj − 2σ ij )/2, where σ ij (= δr i · δr j ) is the positional covariance, determined by the topology of polymer network [42]. Indeed, distance distributions measured using fluorescence measurement between chromatin loci justifies this hypothesis (see Fig. S1). Importantly, our interpretation of chromosome conformation as a locally equilibrated, quasi-stable polymer network enables a one-to-one mapping of the contact probability p ij = rc 0 dxP (x; γ ij ) to the positional covariance σ ij , and hence to the cross-correlation matrix, (C) ij = σ ij / √ σ ii σ jj (see Methods). The cross-correlation matrix C normalizes the wide numer-

show abstract

Comparative analysis of 2D and 3D distance measurements to study spatial genome organization

Cited by 8 publications

References 40 publications

CRISPR-Based DNA Imaging in Living Cells Reveals Cell Cycle-Dependent Chromosome Dynamics

CRISPR-Based DNA Imaging in Living Cells Reveals Cell Cycle-Dependent Chromosome Dynamics

Heterogeneity and Intrinsic Variation in Spatial Genome Organization

A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C

Contact Info

Product

Resources

About