The radial nuclear positioning of genes correlates with features of megabase-sized chromatin domains

Abstract

A nonrandom radial nuclear organization of genes has been well documented. This study provides further evidence that radial positioning depends on features of corresponding ∼1 Mbp chromatin domains (CDs), which represent the basic units of higher-order chromatin organization. We performed a quantitative three-dimensional analysis of the radial nuclear organization of three genes located on chromosome 1 in a DG75 Burkitt lymphoma-derived cell line. Quantitative real-time polymerase chain reaction revealed similar transcription levels for the three selected genes, whereas the total expression strength (TES) calculated as the sum of transcription of all genes annotated within a surrounding window of about 1 Mbp DNA differed for each region. Radial nuclear position of the studied CDs correlated with TES, i.e., the domain with the highest TES occupied the most interior position. Positions of CDs with stable TES values were stably maintained even under experimental conditions, resulting in genome-wide changes of the expression levels of many other genes. Our results strongly support the hypothesis that knowledge of the local chromatin environment is essential to predict the radial nuclear position of a gene.

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

“…Although they are usually represented as large chromatin globules (for review, see Mirny 2011;Fudenberg and Mirny 2012;Bickmore 2013;de Graaf and van Steensel 2013;Dekker et al 2013;Gibcus and Dekker 2013), direct experimental evidence for the existence of such globules in individual cells is controversial. Using confocal and 3D-SIM microscopy, Cremer and colleagues observed ∼1-Mb globular domains within chromosomal territories (Cremer and Cremer 2001;Kolbl et al 2012;Smeets et al 2014). However, using STORM microscopy, Ricci et al found that chromatin in individual mammalian cells is organized into "clutches" composed of several nucleosomes, and that increased histone acetylation dramatically reduces the size of these clutches (Ricci et al 2015).…”

Gene expression amplification by nuclear speckle association

“…Across multiple species and cell types, lamin-associated domains, as revealed by DamID (DNA adenine methyltransferase identification), show low gene densities and transcriptional activity (Kind et al, 2013). Similarly, across multiple species and cell types, the radial positioning of gene loci within a cell population stochastically closer to the nucleus center is associated with higher transcriptional activity (Kölbl et al, 2012; Takizawa et al, 2008). This stochastic correlation between gene expression and radial positioning may mask a more deterministic relationship between gene expression and gene positioning relative to a specific nuclear body which itself is radially distributed.…”

Transcription amplification by nuclear speckle association

“…Across multiple species and cell types, lamin-associated domains (LADs), 23 as revealed by DamID, show low gene densities and transcriptional activity (Kind et al, 2013). 24 Similarly, across multiple species and cell types, the radial positioning of gene loci within a cell 25 population stochastically closer to the center of the nucleus is associated with higher 26 transcriptional activity (Kolbl et al, 2012;Takizawa et al, 2008). This stochastic correlation 27 between gene expression and radial positioning may mask a more deterministic relationship 28 between gene expression and gene positioning relative to a specific nuclear body which itself is 29 radially distributed.…”