Biological implications and regulatory mechanisms of long-range chromosomal interactions

Abstract

Development of high-throughput sequencing-based methods has enabled us to examine nuclear architecture at unprecedented resolution, allowing further examination of the function of long-range chromosomal interactions. Here, we review methods used to investigate novel long-range chromosomal interactions and genome-wide organization of chromatin. We further discuss transcriptional activation and silencing in relation to organization and positioning of gene loci and regulation of chromatin organization through protein complexes and noncoding RNAs.

Keywords: Chromatin; Chromatin Regulation; Chromatin Structure; Chromosome Conformation Capture; Nuclear Organization; Nuclear Structure.

FIGURE 1.

Schematic representation of 3C-based methods. There are many methods derived from the original 3C design. Here, we present a few popular methods. In brief, cells are cross-linked, and chromatin is digested by restriction enzymes or sonicated. The structures of protein complexes containing DNA are preserved. These complexes are then diluted to a very low concentration, and ligation reactions are performed. Different amplification strategies are used to measure the relative cross-linking efficiency between loci. 3C is used to detect one specific interaction. 4C detects all possible interacting regions of one given locus. 5C and HiC provide “many-to-many” interacting efficiencies in a large genomic region or the whole genome. ChIP-PET includes immunoprecipitation to specifically examine the long-range interactions associated with a specific protein.

FIGURE 2.

Transcriptional architecture: from a one-dimensional linear model to a three-dimensional transcription factory model. A, the simplest model of transcription organization considers chromatin structure as one-dimensional and posits that the transcriptional machinery acts mainly on promoters or enhancers immediately upstream of a transcription start site. TF, transcription factor. B, the looping model usually describes interaction between a promoter and a distant upstream enhancer. The cohesin complex is considered essential to maintain the looping structure. C, a transcription factory consists of immobilized and enriched RNAPII foci. DNA loci in cis and in trans are recruited to the factory by specific transcription factors as well as by CTCF and the cohesin complex. Different chromosomes are represented as Chr A and Chr B.

FIGURE 3.

Regulatory mechanisms governing nuclear architecture in various systems. A, β-globin loci in erythroid cells are enriched in Klf1-specialized transcription factories. Other Klf1-coregulated gene loci are dynamically colocalized with the β-globin locus and cotranscribed in specialized transcription factories. B, four categories of CTCF-mediated looping functions. Green arrows indicate genes with active epigenetic marks. Red brackets represent genes with repressive histone modification. Black boxes represent active enhancer elements. C, XIST-mediated XCI. The XIST lncRNA is expressed on Xi and spreads to cover the full chromosome (upper panel). The PRC2 complex is recruited by XIST and also loaded onto Xi. Xi is compacted and forms unique higher order chromosome structure (lower panel), with inactivated genes located inside, and active genes (“escapees” represented by red boxes) located on the outer surface.