Understanding the regulatory and transcriptional complexity of the genome through structure

Abstract

An expansive functionality and complexity has been ascribed to the majority of the human genome that was unanticipated at the outset of the draft sequence and assembly a decade ago. We are now faced with the challenge of integrating and interpreting this complexity in order to achieve a coherent view of genome biology. We argue that the linear representation of the genome exacerbates this complexity and an understanding of its three-dimensional structure is central to interpreting the regulatory and transcriptional architecture of the genome. Chromatin conformation capture techniques and high-resolution microscopy have afforded an emergent global view of genome structure within the nucleus. Chromosomes fold into complex, territorialized three-dimensional domains in concert with specialized subnuclear bodies that harbor concentrations of transcription and splicing machinery. The signature of these folds is retained within the layered regulatory landscapes annotated by chromatin immunoprecipitation, and we propose that genome contacts are reflected in the organization and expression of interweaved networks of overlapping coding and noncoding transcripts. This pervasive impact of genome structure favors a preeminent role for the nucleoskeleton and RNA in regulating gene expression by organizing these folds and contacts. Accordingly, we propose that the local and global three-dimensional structure of the genome provides a consistent, integrated, and intuitive framework for interpreting and understanding the regulatory and transcriptional complexity of the human genome.

Figure 1.

Examples of proximal enrichments resulting from ChIP-seq. (A) ChIP-seq of a transcription factor (green) results in immunoprecipitation of bound DNA sequence (blue) as well as addition of DNA sequence (orange) in close proximity. Only bound sequence shows evidence of DNase I footprint and binding motif. (B) Immunoprecipitation of DNA sequence associated with large multiprotein complex results in artifactual indirect enrichments for a wide range of transcription factors. (C) Active enhancers exhibit a range of ChIP-seq enrichments as a result of a close spatial proximity to histone modification and transcription factors at promoters.

Figure 2.

Formation of chromatin loops at gene loci permits coordination between processes of transcription initiation, termination, and splicing. Promoter and terminal regions of genes colocalize during transcription, forming a looped structure that enhances transcriptional directionality. Gene loop formation depends on contacts between both promoter-associated transcription factors, such as TFIIB, within the pre-initiation complex and polyadenylation factors, such as Ssu72 and cleavage factor subunits, within the terminator complex. Extensive contacts between the spliceosome and the initiating and elongating polymerase II complex also facilitate cotranscriptional splicing.

Figure 3.

Three-dimensional interpretation (left) of regulatory and transcriptional complexity in one-dimensional genome representation (right). (A) The genome forms large complex clusters and introspective folded clusters with specialized transcription compartments. Each of these clusters correlates to a collection of transcripts and “background” ChIP-seq enrichment. (B) Within each cluster the genome is folded to associate with subnuclear structures containing transcription factors and machinery, splicing, and other accessory proteins. These associations coregulate genes to generate interleaved complex transcriptional networks of coding (blue) and noncoding transcripts (green). Proximal cross-linking with ChIP-seq results in a complex landscape of enrichment across loci that reflect the folded genome structure. (C) Within each gene, local dynamic chromatin folding determines the association of alternative promoters and local noncoding RNAs with a shared regulatory architecture, thereby mediating coregulated gene expression.