CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

Guo, Ya; Xu, Qiang; Canzio, Daniele; Shou, Jia‐Wen; Li, Jinhuan; Gorkin, David U.; Jung, Inkyung; Wu, Haiyang; Zhai, Yanan; Tang, You-sheng; Lu, Yichao; Wu, Yonghu; Jia, Zhilian; Li, Wei; Zhang, Michael Q.; Ren, Bing; Krainer, Adrian R.; Maniatis, Tom; Wu, Qiang

doi:10.1016/j.cell.2015.07.038

Cited by 905 publications

(988 citation statements)

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“…Within this hierarchical organization, conserved TAD and sub-TAD structures frame the majority of enhancer-promoter interactions (Dekker et al 2013;Tang et al 2015;Dekker and Mirny 2016). The CCCTCbinding factor (CTCF) regulates each nested level of genomic organization (Guo et al 2015;Hnisz et al 2016), from local enhancer-promoter looping events within the protocadherin clusters to broader genomic neighborhoods and TADs (Guo et al 2012;Rao et al 2014).…”

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confidence: 99%

CTCF-mediated topological boundaries during development foster appropriate gene regulation

et al. 2016

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The genome is organized into repeating topologically associated domains (TADs), each of which is spatially isolated from its neighbor by poorly understood boundary elements thought to be conserved across cell types. Here, we show that deletion of CTCF (CCCTC-binding factor)-binding sites at TAD and sub-TAD topological boundaries that form within the HoxA and HoxC clusters during differentiation not only disturbs local chromatin domain organization and regulatory interactions but also results in homeotic transformations typical of Hox gene misregulation. Moreover, our data suggest that CTCF-dependent boundary function can be modulated by competing forces, such as the self-assembly of polycomb domains within the nucleus. Therefore, CTCF boundaries are not merely static structural components of the genome but instead are locally dynamic regulatory structures that control gene expression during development.

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confidence: 99%

CTCF-mediated topological boundaries during development foster appropriate gene regulation

et al. 2016

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“…In this regard, the generation of chromatin interaction data from a much broader taxonomic sampling will be necessary in combination with careful examination and detailed functional dissection of many more examples of RLs. The use of novel genomic editing tools, such as the CRISPR/CAS9 system, will undoubtedly contribute to this endeavor, as highlighted by the increasing number of works that have benefited from these approaches to shed light into the molecular mechanisms underlying TAD boundaries and the establishment of chromatin loops [19,[47][48][49]. …”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Cis-regulatory landscapes in development and evolution

Maeso

Acemel

Gómez-Skármeta

2017

Current Opinion in Genetics & Development

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The recent advances in our understanding of the 3D organization of the chromatin together with an almost unlimited ability to detect cis-regulatory elements genome-wide using different biochemical signatures has provided us with an unprecedented power to study gene regulation. It is now possible to profile the complete regulatory apparatus controlling the spatio-temporal expression of any given gene, the so-called gene Regulatory Landscapes (RLs). Here we review several studies over the last two years demonstrating the functional consequences of altering RL structure in development, disease and evolution. These works clearly shows that a deep understanding of transcriptional regulation is no longer conceivable without considering the 3D modular organization of animal genomes.

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“…For example, FISH was used to visualize the colocalization of olfactory receptor allele and an enhancer element in individual neurons [117]. CRISPR/Cas9-based technology [118,119] in conjuncted with 3C derivatives, can be used to study chromatin organization [120,121,122] in an elegant way. With the power of SRM, 3C-based methods and FISH/CRISPR technology are offering us more solutions to understand how the dynamics and organization of chromatin structure are functionally translated into the regulation of gene transcription, repair, and expression.…”

Section: Resultsmentioning

confidence: 99%

Developing bioimaging and quantitative methods to study 3D genome

et al. 2016

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The recent advances in chromosome configuration capture (3C)-based series molecular methods and optical superresolution (SR) techniques offer powerful tools to investigate three dimensional (3D) genomic structure in prokaryotic and eukaryotic cell nucleus. In this review, we focus on the progress during the last decade in this exciting field. Here we at first introduce briefly genome organization at chromosome, domain and sub-domain level, respectively; then we provide a short introduction to various super-resolution microscopy techniques which can be employed to detect genome 3D structure. We also reviewed the progress of quantitative and visualization tools to evaluate and visualize chromatin interactions in 3D genome derived from Hi-C data. We end up with the discussion that imaging methods and 3C-based molecular methods are not mutually exclusive ----actually they are complemental to each other and can be combined together to study 3D genome organization.Keywords: 3D Genome; quantitative methods; bioimaging; super resolution INTRODUCTIONIn eukaryotic nucleus, the organization of chromatin is very complex. Highly condensed chromatin and huge numbers of components, such as transcription factors, chromatin proteins and RNA-processing factors, cram together in a very small volume. Essential nuclear processes such as transcription, replication, and repair occur at spatially defined locations in the nucleus. Accumulating evidence suggests that the expression of many genes is correlated with their positions in cell nucleus, and the spatial organization of chromatins has played essential role in regulating transcriptional activity [1]. How these could be done is one of the greatest challenges in molecular biology. 1 DNA helix is hierarchically packaged into chromatin in an elegant way, and eventually form a chromosome in the eukaryotic nucleus over several levels of higher-order structures [1], indicating that a range of microscopy techniques with spatial and temporal scales that cover several orders of magnitude are necessary to understand the organization principles at different levels in a chromosome. For example, the structure of nucleosomes, the fundamental organization unit of chromatin, has been elucidated by X-ray crystals at nanometer scale [2]. The structure of "beads-on-a-string" fiber, which has a diameter of 11-nm and is the very first level of chromatin organization, is also well-understood through Electron Microscope [33]. However, substructure at the scale of 10-200 nm is poorly understood, especially in live cells, partly due to the requirement of biological system that the dynamics, process and function in biology need to be measured with high spatial (approximately nanometer) and temporal (approximately microsecond to millisecond) † These authors contributed equally to this work.

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CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

Cited by 905 publications

References 53 publications

CTCF-mediated topological boundaries during development foster appropriate gene regulation

CTCF-mediated topological boundaries during development foster appropriate gene regulation

Cis-regulatory landscapes in development and evolution

Developing bioimaging and quantitative methods to study 3D genome

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