The era of 3D and spatial genomics

Bouwman, Britta A. M.; Crosetto, Nicola; Bienko, Magda

doi:10.1016/j.tig.2022.05.010

Cited by 41 publications

(19 citation statements)

References 125 publications

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“…Methods for spatial mono-omics have progressed tremendously in the last decade with excellent reviews existing for spatial transcriptomics 165 , 171 – 173 , (epi)genomics 166 , 174 , proteomics 86 , 167 and metabolomics 168 , 175 . Here, we briefly highlight the basic principles of the approaches that currently form the basis for most ongoing spatial multi-omics developments.…”

Section: Spatial Multi-omics Methodsmentioning

confidence: 99%

Methods and applications for single-cell and spatial multi-omics

et al. 2023

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The joint analysis of the genome, epigenome, transcriptome, proteome and/or metabolome from single cells is transforming our understanding of cell biology in health and disease. In less than a decade, the field has seen tremendous technological revolutions that enable crucial new insights into the interplay between intracellular and intercellular molecular mechanisms that govern development, physiology and pathogenesis. In this Review, we highlight advances in the fast-developing field of single-cell and spatial multi-omics technologies (also known as multimodal omics approaches), and the computational strategies needed to integrate information across these molecular layers. We demonstrate their impact on fundamental cell biology and translational research, discuss current challenges and provide an outlook to the future.

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Section: Spatial Multi-omics Methodsmentioning

confidence: 99%

Methods and applications for single-cell and spatial multi-omics

et al. 2023

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“…While short-and long-read sequencing have enhanced our capabilities for understanding genetic variation along the linear genome sequence, considerable advances are being made in the concept and interpretation of how the genome is dynamically and hierarchically organized using adjunct sequencing methods. [84][85][86] A number of methodologies, generally based around chromosome conformation capture and subsequent next-generation sequencing, are utilized to interrogate chromosomal interactions, which underpin gene regulation, DNA replication, and DNA repair. 87 The influences of local and long-range chromosomal interactions add considerable complexity to genome structure and regulation, particularly for gene expression.…”

Section: Frontiers In the Lab And Clinicmentioning

confidence: 99%

The Next, Next-Generation of Sequencing, Promising to Boost Research and Clinical Practice

Kumar,

Cowley,

Davis

2024

Semin Thromb Hemost

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“…The investigation of 3D genome topology has dramatically evolved over the past decade: technological advances have boost the field to an unprecedented level ( Bouwman et al, 2022 ). Ongoing efforts are made in providing more accurate data analysis for a better understanding and interpretation of the functional consequence of these changes.…”

Section: C-derived Technologies To Map the 3d Genomementioning

confidence: 99%

Chromosome conformation capture approaches to investigate 3D genome architecture in Ankylosing Spondylitis

et al. 2023

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Ankylosing Spondylitis (AS) is a chronic inflammatory arthritis of the spine exhibiting a strong genetic background. The mechanistic and functional understanding of the AS-associated genomic loci, identified with Genome Wide Association Studies (GWAS), remains challenging. Chromosome conformation capture (3C) and derivatives are recent techniques which are of great help in elucidating the spatial genome organization and of enormous support in uncover a mechanistic explanation for disease-associated genetic variants. The perturbation of three-dimensional (3D) genome hierarchy may lead to a plethora of human diseases, including rheumatological disorders. Here we illustrate the latest approaches and related findings on the field of genome organization, highlighting how the instability of 3D genome conformation may be among the causes of rheumatological disease phenotypes. We suggest a new perspective on the inclusive potential of a 3C approach to inform GWAS results in rheumatic diseases. 3D genome organization may ultimately lead to a more precise and comprehensive functional interpretation of AS association, which is the starting point for emerging and more specific therapies.

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The era of 3D and spatial genomics

Cited by 41 publications

References 125 publications

Methods and applications for single-cell and spatial multi-omics

Methods and applications for single-cell and spatial multi-omics

The Next, Next-Generation of Sequencing, Promising to Boost Research and Clinical Practice

Chromosome conformation capture approaches to investigate 3D genome architecture in Ankylosing Spondylitis

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