The genome in three dimensions

A new frontier in human brain research

Amanda C. Mitchell, Rahul Bharadwaj, Catheryne Whittle, Winfried Krueger, Karoly Mirnics, Yasmin Hurd, Theodore Rasmussen, Schahram Akbarian

Research output: Contribution to journalReview article

31 Citations (Scopus)

Abstract

Less than 1.5% of the human genome encodes protein. However, vast portions of the human genome are subject to transcriptional and epigenetic regulation, and many noncoding regulatory DNA elements are thought to regulate the spatial organization of interphase chromosomes. For example, chromosomal "loopings" are pivotal for the orderly process of gene expression, by enabling distal regulatory enhancer or silencer elements to directly interact with proximal promoter and transcription start sites, potentially bypassing hundreds of kilobases of interspersed sequence on the linear genome. To date, however, epigenetic studies in the human brain are mostly limited to the exploration of DNA methylation and posttranslational modifications of the nucleosome core histones. In contrast, very little is known about the regulation of supranucleosomal structures. Here, we show that chromosome conformation capture, a widely used approach to study higher-order chromatin, is applicable to tissue collected postmortem, thereby informing about genome organization in the human brain. We introduce chromosome conformation capture protocols for brain and compare higher-order chromatin structures at the chromosome 6p22.2-22.1 schizophrenia and bipolar disorder susceptibility locus, and additional neurodevelopmental risk genes, (DPP10, MCPH1) in adult prefrontal cortex and various cell culture systems, including neurons derived from reprogrammed skin cells. We predict that the exploration of three-dimensional genome architectures and function will open up new frontiers in human brain research and psychiatric genetics and provide novel insights into the epigenetic risk architectures of regulatory noncoding DNA.

Original languageEnglish (US)
Pages (from-to)961-969
Number of pages9
JournalBiological Psychiatry
Volume75
Issue number12
DOIs
StatePublished - Jun 15 2014

Fingerprint

Epigenomics
Genome
Chromosomes
Brain
Human Genome
Research
Chromatin
Transcriptional Silencer Elements
Chromosome Structures
Genetic Research
Nucleosomes
Transcription Initiation Site
DNA
Interphase
DNA Methylation
Post Translational Protein Processing
Prefrontal Cortex
Bipolar Disorder
Histones
Psychiatry

Keywords

  • Chromatin fiber
  • chromosomal looping
  • chromosome conformation capture
  • genome in 3D
  • higher-order chromatin
  • human brain

ASJC Scopus subject areas

  • Biological Psychiatry

Cite this

Mitchell, A. C., Bharadwaj, R., Whittle, C., Krueger, W., Mirnics, K., Hurd, Y., ... Akbarian, S. (2014). The genome in three dimensions: A new frontier in human brain research. Biological Psychiatry, 75(12), 961-969. https://doi.org/10.1016/j.biopsych.2013.07.015

The genome in three dimensions : A new frontier in human brain research. / Mitchell, Amanda C.; Bharadwaj, Rahul; Whittle, Catheryne; Krueger, Winfried; Mirnics, Karoly; Hurd, Yasmin; Rasmussen, Theodore; Akbarian, Schahram.

In: Biological Psychiatry, Vol. 75, No. 12, 15.06.2014, p. 961-969.

Research output: Contribution to journalReview article

Mitchell, AC, Bharadwaj, R, Whittle, C, Krueger, W, Mirnics, K, Hurd, Y, Rasmussen, T & Akbarian, S 2014, 'The genome in three dimensions: A new frontier in human brain research', Biological Psychiatry, vol. 75, no. 12, pp. 961-969. https://doi.org/10.1016/j.biopsych.2013.07.015
Mitchell, Amanda C. ; Bharadwaj, Rahul ; Whittle, Catheryne ; Krueger, Winfried ; Mirnics, Karoly ; Hurd, Yasmin ; Rasmussen, Theodore ; Akbarian, Schahram. / The genome in three dimensions : A new frontier in human brain research. In: Biological Psychiatry. 2014 ; Vol. 75, No. 12. pp. 961-969.
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