Advances in profiling chromatin architecture shed light on the regulatory dynamics underlying brain disorders
Introduction
When measured linearly, the approximately 3 billion DNA base pairs comprising the human genome extend 2 m in length. Despite the relatively large size as compared to other organisms, it contains a similar number of protein coding genes which account for just 2% of its total content. Traditionally, it was thought the other 98% of DNA sequences were “junk DNA”. However, it has become increasingly understood that many of these non-coding regions orchestrate gene regulation via functioning as enhancers, silencers, insulators, and/or non-coding RNAs. It is now estimated that these non-coding regions harbor ~90% of genetic variants associated with human diseases [1], and therefore, detailed characterization of the non-coding genome is imperative for advancing our understanding of disease biology. While large-scale efforts to characterize the non-coding genome such as ENCODE are actively underway [2], deciphering the functional consequences of non-coding variation has been challenging due to its vast size, limited conservation across species, and lack of a generalizable rubric to predict effects from sequence variation. The advent of next generation sequencing technologies and adaptations of genome engineering tools have enabled development of various multi-omic approaches that can be used to decode the regulatory grammar of the genome, or “regulome” [3]. One key approach for better interpreting the non-coding genome is generation of three-dimensional (3-D) contact maps of chromatin conformation, as the coordinated manner in which 2 m-sized DNA is compacted into a nucleus approximately 200,000 times smaller in size is reflective of gene regulatory principles.
In this review, we highlight recent advances in available techniques for assaying chromosome conformation, which provides a roadmap to interrogate the functional consequences of non-coding genetic variants. We also introduce perturbation assays that complement chromatin architecture by experimentally validating variant effects on gene regulation. We conclude by describing key gaps in our knowledge of the dynamic gene regulatory landscape and how filling these gaps can provide a path forward for gleaning mechanistic understanding of disease pathogenesis.
Section snippets
Mapping three-dimensional chromatin configuration
Decoding the chromatin configuration remains a fundamental question in molecular biology. To date, one of the most popular genomic approaches to identify chromatin configuration is to use chromosome conformation capture (3C)-based techniques [4]. Hi-C is one such technique which profiles chromosome conformation at a genome-wide scale [5], and relies on fixation of DNA to preserve chromosome configuration, followed by restriction enzyme mediated digestion and proximity ligation to link points of
Gene regulatory architecture functions as a blueprint for inferring SNP-gene relationships
Genome-wide association studies (GWAS) and whole genome sequencing (WGS) studies have identified hundreds to thousands of genetic variants associated with various human traits and diseases [41], [42]. The vast majority of these variants are located in the non-coding genome, and high-resolution maps of chromatin architecture may function as a reference atlas to decipher the functional consequences of these risk variants. The basic assumption is that risk variants can regulate distal genes when
Experimental validation to elucidate functional impact of SNPs
Despite tremendous strides in predictive methodologies for inferring SNP-gene relationships, a gap remains in experimentally validating the functional outcome of these relationships. Therefore, the next fundamental step is to functionally characterize the variant effects on gene regulation. However, traditional approaches such as luciferase assays and single gene knock-out experiments are no longer suitable for systematic characterization of thousands of genetic variants associated with human
Toward a more complete map of gene regulatory architecture in the human brain
Chromatin configuration of the human brain has been profiled across key developmental epochs and cell types (Table 1). These rich datasets of 3-D chromatin architecture generated from the human brain provided a cornerstone for predicting the functional impact of non-coding variants and elucidating biological underpinnings of various psychiatric and neurodegenerative disorders [48], [67], [68], [69], [70]. Despite these resources, we are far from understanding the comprehensive landscape of gene
Declaration of Competing Interest
Authors declare no conflict of interest.
Acknowledgements
This review was supported by the National Institute of Mental Health (R00MH113823, DP2MH122403, H.W.), the National Institute on Drug Abuse (R21DA051921, H.W.), the Pharmacological Sciences T32 Training Program (T32GM135095, B.M.P.), and the NARSAD Young Investigator Award from the Brain and Behavior Research Foundation (H.W.).
References (85)
- et al.
Formation of chromosomal domains by loop extrusion
Cell Rep.
(2016) - et al.
Architectural protein subclasses shape 3D organization of genomes during lineage commitment
Cell
(2013) - et al.
A compendium of chromatin contact maps reveals spatially active regions in the human genome
Cell Rep.
(2016) - et al.
FIREcaller: detecting frequently interacting regions from Hi-C data
Comput. Struct. Biotechnol. J.
(2021) - et al.
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping
Cell
(2014) Principles of chromosome architecture revealed by Hi-C
Trends Biochem. Sci.
(2018)- et al.
Resolving the 3D landscape of transcription-linked mammalian chromatin folding
Mol. Cell.
(2020) - et al.
Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus
Cell
(2018) - et al.
Sci-Hi-C: a single-cell Hi-C method for mapping 3D genome organization in large number of single cells
Methods
(2020) - et al.
The three-dimensional landscape of the genome in human brain tissue unveils regulatory mechanisms leading to schizophrenia risk
Schizophr. Res.
(2020)
Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assay
Cell
Neurobiology of addiction: a neurocircuitry analysis
Lancet Psychiatry
Functional changes of the basal ganglia circuitry in Parkinson’s disease
Prog. Neurobiol.
A global overview of pleiotropy and genetic architecture in complex traits
Nat. Genet.
Expanded encyclopaedias of DNA elements in the human and mouse genomes
Nature
Integrative analysis of 111 reference human epigenomes
Nature
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data
Nat. Rev. Genet.
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
Science
Chromosome territories
Cold Spring Harb. Perspect. Biol.
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Nature
On the existence and functionality of topologically associating domains
Nat. Genet.
Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements
Nat. Genet.
Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq
Cell Res.
Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
Nat. Genet.
Multi-omics Analysis of Chromatin Accessibility and Interactions With Transcriptome by HiCAR
Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome
Nat. Methods
HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution
Genome Biol.
DeepHiC: a generative adversarial network for enhancing Hi-C data resolution
PLoS Comput. Biol.
Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus
Nat. Commun.
Complex multi-enhancer contacts captured by genome architecture mapping
Nature
Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin
Nat. Methods
Single-cell imaging of genome organization and dynamics
Mol. Syst. Biol.
Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes
Proc. Natl. Acad. Sci. U.S.A.
In situ super-resolution imaging of genomic DNA with OligoSTORM and OligoDNA-PAINT
Methods Mol. Biol.
Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells
Science
Integrated spatial genomics reveals global architecture of single nuclei
Nature
Single-cell Hi-C reveals cell-to-cell variability in chromosome structure
Nature
Cell-cycle dynamics of chromosomal organization at single-cell resolution
Nature
Massively multiplex single-cell Hi-C
Nat. Methods
A human cell atlas of fetal gene expression
Science
A human cell atlas of fetal chromatin accessibility
Science
Joint profiling of DNA methylation and chromatin architecture in single cells
Nat. Methods
Cited by (6)
3D genome organization, genetic variation and disease
2022, Seminars in Cell and Developmental BiologyRegulation of loop extrusion on the interphase genome
2023, Critical Reviews in Biochemistry and Molecular BiologyAnnotating genetic variants to target genes using H-MAGMA
2023, Nature ProtocolsFocus on your locus with a massively parallel reporter assay
2022, Journal of Neurodevelopmental DisordersGene-Regulatory Networks in Brain Development
2022, Neuroscience in the 21st Century: From Basic to Clinical: Third Edition