Spatial genome organization and cognition

Abstract

Nonrandom chromosomal conformations, including promoter-enhancer loopings that bypass kilobases or megabases of linear genome, provide a crucial layer of transcriptional regulation and move vast amounts of non-coding sequence into the physical proximity of genes that are important for neurodevelopment, cognition and behaviour. Activity-regulated changes in the neuronal '3D genome' could govern transcriptional mechanisms associated with learning and plasticity, and loop-bound intergenic and intronic non-coding sequences have been implicated in psychiatric and adult-onset neurodegenerative disease. Recent studies have begun to clarify the roles of spatial genome organization in normal and abnormal cognition.

Figure 1. The 3-dimensional genome, from nucleosome to nucleus

a. Chromatin fibers that surround a DNA inside the nucleus are organized of arrays of the elementary unit, the nucleosome (146 bp of DNA wrapped in 2.5 loops around the core histone octamer). In ‘A compartments’, chromatin is in an open or active conformation and is permissive for transcription. This state is defined by high occupancy of RNA polymerase II complex and transcription factors and increased portions of nucleosome free DNA. In ‘B compartments’, chromatin is condensed and RNA polymerase and transcription factor occupancy is decreased. Each compartment can contain several megabases of 3D genome sequences. Superimposed upon this generalized model of nucleosomal organization is the 3D genome. This includes topological-associated domains (TADs) which extend on average (median size) across 185 kb and that can exist within both A compartments and in B compartments that primarily harbor repressive and condensed chromatin. The constituent loci within TADs come into contact with each other much more frequently than with loci from outside domains. The 3D genome also includes lamina-associated domains (LAD), which are condensed heterochromatin enriched around the nuclear periphery and physically bound to lamin proteins at the inner nuclear lamina.b. In ‘B compartments’, chromatin is condensed and is enriched with a different set of proteins to A compartments, which include, among others, HP1 (heterochromatin-associated protein 1) and (not shown) repressive histone methylation markings (H3K9me3, H4K20me3). c. TAD boundaries, but also specific chromosomal loop formations, including promoter-enhancer loopings, are often demarcated by CTCF and cohesins, and additional proteins which serve to regulate the formation of 3D genome structures. Formation of promoter—enhancer loopings in A compartments, for example, involves a sequence of steps:. (1) transcription factors (TF) bind to promoter and enhancer sequences of DNA; (2) the co-activator Mediator is recruited which in turn recruits the cohesin complex (3), which as ring structure creates or stabilizes the loop. CTCF operates in parallel or synergistically to Mediator. This structure allows activation and modulation of the RNA polymerase II core transcription machinery

Figure 2. Enhancer-mediated regulation of neuronal gene expression

Four models for enhancer-dependent up- and down-regulation of transcription have been described in neurons (see text). The models are not mutually exclusive. (A, top) Protein ‘cargo’ model, which has been demonstrated for the GAD1 gene: Distal enhancer sequences bind transcription factors. Promoter and enhancer sequences are separated and interaction between transcription factors, enhancer and promoter sequences cannot occur, and the rate of transcription is reduced (dashed arrow). Loop formations that enable physical proximity between the enhancer’s target (such as be a gene transcription start site), transcription factors and the proximal promoter region upregulate transcription (bottom). (B, top) enhancer RNA (eRNA) decoy model, which has been demonstrated for the neuronal gene Arc: When the Arc gene promoter is occupied by negative elongation factor (NELF), the action of RNA polymerase II complex is stalled and Arc transcription is low. However, the distal enhancer sequences of the gene produce enhancer RNAs (eRNAs), and when the enhancer region moves via specific loop formations into physical proximity to the Arc promoter, these short non-coding eRNAs bind NELF, which reduces NELF occupancy at the target gene (Arc), thereby liberating RNA polymerase II complex and promoting the transcriptional process (Bottom). (C) Loop competition model, shown for the gene GRIN2B: Two or more non-contiguous (separated by interspersed sequence) cis-regulatory sequences, potentially with opposing effects on transcription (i.e. a promoter sequence and a repressor sequence), are competing to access the GRIN2B gene promoter. Top: When the GRIN2B promoter interacts with a silencer protein occupying loop-bound repressor DNA elements, and transcriptional activity is reduced. Bottom: When the same promoter interacts with an active enhancer element that has bound transcription factors present, GRIN2B expression is increased. (D) Strand break mobilization at the c-fos immediate early gene (IEG) promoter: Promoter activity is low at baseline when the genome is in linear form (bottom). To activate transcription, topoisomerase IIβ enzyme induces DNA strand breaks. This results in the mobilization of promoter sequences into physical proximity with enhancer elements that were previously separated by several kb of interspersed linear genome (bottom). The physical proximity of these promoter and enhancer DNA then leads to synergistic activation of gene expression via enhancer-bound transcription factor proteins.

Figure 3. Dynamic model of chromomosomal conformation at GRIN2B NMDA receptor gene locus

(top) Long-range chromosomal loop formations at the GRIN2B locus are not detectable cells and tissues that do not express the GRIN2B protein. However, in cells that express GRIN2B, the expression can be finely tuned by dynamic competition between multiple chromosomal conformations competing for access to the GRIN2B promoter and transcription start site. Transcription is increased by a loop-bound enhancer formation of DNA, to which IEG transcription factors, NRF-1 and additional activator proteins are bound as a complex. This is counterbalanced by additional chromosomal conformations that carry repressive chromatin into physical proximity to the GRIN2B promoter, This repressive chromatin is characterized by localized enrichments of HP1 (heterochromatin-associated protein 1) and repressive SETDB1 histone methyltransferase, (see text and reference for details).