Alteration of genome folding via contact domain boundary insertion

Zhang, Di; Huang, Peng; Sharma, Malini; Keller, Cheryl A.; Giardine, Belinda; Zhang, Haoyue; Gilgenast, Thomas G.; Phillips-Cremins, Jennifer E.; Hardison, Ross C.; Blobel, Gerd A.

doi:10.1038/s41588-020-0680-8

Cited by 39 publications

(48 citation statements)

References 104 publications

(143 reference statements)

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“…We first tested the structural variant effect predictions of transposon-mediated 2kb TAD boundary element insertions into various genome locations (2kb insertion + 5 kb transposon), which have been measured with in situ Hi-C 24 . We computed the insulation score change at each insertion site and compared with the predicted changes.…”

Section: Resultsmentioning

confidence: 99%

Sequence-based modeling of genome 3D architecture from kilobase to chromosome-scale

Zhou

2021

Preprint

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The structural organization of the genome plays an important role in multiple aspects of genome function. Understanding how genomic sequence influences 3D organization can help elucidate their roles in various processes in healthy and disease states. However, the sequence determinants of genome structure across multiple spatial scales are still not well understood. To learn the complex sequence dependencies of multiscale genome architecture, here we developed a sequence-based deep learning approach, Orca, that predicts genome 3D architecture from kilobase to whole-chromosome scale, covering structures including chromatin compartments and topologically associating domains. Orca also makes both intrachromosomal and interchromosomal predictions and captures the sequence dependencies of diverse types of interactions, from CTCF-mediated to enhancer-promoter interactions and Polycomb-mediated interactions. Orca enables the interpretation of the effects of any structural variant at any size on multiscale genome organization and provides an in silico model to help study the sequence-dependent mechanistic basis of genome architecture. We show that the models accurately recapitulate effects of experimentally studied structural variants at varying sizes (300bp-80Mb) using only sequence. Furthermore, these sequence models enable in silico virtual screen assays to probe the sequence-basis of genome 3D organization at different scales. At the submegabase scale, the models predicted specific transcription factor motifs underlying cell-type-specific genome interactions. At the compartment scale, based on virtual screens of sequence activities, we propose a new model for the sequence basis of chromatin compartments: sequences at active transcription start sites are primarily responsible for establishing the expression-active compartment A, while the inactive compartment B typically requires extended stretches of AT-rich sequences (at least 6-12kb) and can form 'passively' without depending on any particular sequence pattern. Orca thus effectively provides an 'in silico genome observatory' to predict variant effects on genome structure and probe the sequence-based mechanisms of genome organization.

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Section: Resultsmentioning

confidence: 99%

Sequence-based modeling of genome 3D architecture from kilobase to chromosome-scale

Zhou

2021

Preprint

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“…Chromosome conformation capture is a powerful tool for the study of DNA folding within the nucleus. NG Capture-C has been applied to numerous biological questions, including enhancer characterization and super-enhancer dissection 19,[41][42][43][44] , understanding the dynamics of Polycomb Bodies 45,46 and Xchromosome inactivation 47,48 , characterizing CTCF boundaries 24,49,50 , and mapping the effector genes for polygenic human traits 51,52 . Despite their widespread applicability, the sequencing needs and cost of high-resolution methods have limited their use in large-scale experiments.…”

Section: Discussionmentioning

confidence: 99%

High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale

et al. 2021

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Chromosome conformation capture (3C) provides an adaptable tool for studying diverse biological questions. Current 3C methods generally provide either low-resolution interaction profiles across the entire genome, or high-resolution interaction profiles at limited numbers of loci. Due to technical limitations, generation of reproducible high-resolution interaction profiles has not been achieved at genome-wide scale. Here, to overcome this barrier, we systematically test each step of 3C and report two improvements over current methods. We show that up to 30% of reporter events generated using the popular in situ 3C method arise from ligations between two individual nuclei, but this noise can be almost entirely eliminated by isolating intact nuclei after ligation. Using Nuclear-Titrated Capture-C, we generate reproducible high-resolution genome-wide 3C interaction profiles by targeting 8055 gene promoters in erythroid cells. By pairing high-resolution 3C interaction calls with nascent gene expression we interrogate the role of promoter hubs and super-enhancers in gene regulation.

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“…Moreover, deletion or inversion of CTCF-associated boundary elements at the Wnt6-Ihh-Epha4-Pax3 locus caused the Epha4 TAD to wrongly interact with different neighbouring genes, which provides mouse models of human limb malformations 16 . Beyond CRISPR-Cas9 approaches, transposon-mediated insertion of a 2-kb DNA fragment containing a CBS and a transcription start site at various genomic regions in human HAP1 cells led to local, context-dependent conformational changes to chromatin, including formation of new domains, repartitioning of existing domains and switching from B to A compartments 97 . These genome editing experiments demonstrate the importance of CBS location and orientation in defining TAD organization and loop formation 89,93 .…”

Section: Euchromatinmentioning

confidence: 99%