Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription.

By S. Chambeyron, Wendy A. Bickmore. Genes & Development, 2004

698 citations recorded by the source corpus.

The colinearity of genes in Hox clusters suggests a role for chromosome structure in gene regulation. We reveal programmed changes in chromatin structure and nuclear organization upon induction of Hoxb expression by retinoic acid. There is an early increase in the histone modifications that are marks of active chromatin at both the early expressed gene Hoxb1, and also at Hoxb9 that is not expressed until much later. There is also a visible decondensation of the chromatin between Hoxb1 and Hoxb9 at this early stage. However, a further change in higher-order chromatin structure, looping out of genes from the chromosome territory, occurs in synchrony with the execution of the gene expression program. We suggest that higher-order chromatin structure regulates the expression of the HoxB cluster at several levels. Locus-wide changes in chromatin structure (histone modification and chromatin decondensation) may establish a transcriptionally poised state but are not sufficient for the temporal program of gene expression. The choreographed looping out of decondensed chromatin from chromosome territories may then allow for activation of high levels of transcription from the sequence of genes along the cluster.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1173ca1a6f382e2e25d8cd32a960244b97d715aa

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

A decade of 3C technologies: insights into nuclear organization. (2012, positive): “This idea is supported by DNA fluorescence in situ hybridization (FISH) observations that certain genes (e.g., HoxB and uPA) loop out of their chromosome territory upon activation (Chambeyron and Bickmore 2004; Ferrai et al. 2010b).”
Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions (2007, result): “This is consistent with a previous report that used FISH, which showed that during ES cell differentiation the Hoxb1 locus is repositioned away from its chromosome territor”
Chromatin in pluripotent embryonic stem cells and differentiation (2006, methodology): “A similar chromosomal extrusion was observed for the HoxB locus in mouse ES cells after differentiation was induced with retinoic acid (RA”
Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation (2009, background): “Studies using ESCs suggest that bivalent modifications maintain the activation or silencing potential of critical differentiation genes (Azuara et al., 2006; Bernstein et al., 2006).”
Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells (2009, background): “However, chromosomal regions often loop out of their chromosome territories in association with activatio”
Beyond the sequence: cellular organization of genome function. (2007, positive): “Similarly, extrachromosomal loops are induced upon activation of the mouse Hox cluster (Chambeyron and Bickmore, 2004).”
A bivalent chromatin structure marks key developmental genes in embryonic stem cells. (2006, background): “Embryonic stem (ES) cell differentiation is accompanied by changes in chromatin accessibility at several key developmental genes, including a large-scale opening of the HoxB locus (Chambeyron and Bickmore, 2004; Perry et al., 2004).”
Three-dimensional folding and functional organization principles of the Drosophila genome. (2012, result): “This supported and extended previous findings on the relationship between transcriptional activity and position within chromosome territories (Chambeyron and Bickmore, 2004; Würtele and Chartrand, 2006).”
Nuclear organization of the genome and the potential for gene regulation (2007, background): “or, in some instances, when gene expression is induce”
Active genes dynamically colocalize to shared sites of ongoing transcription (2004, background): “An expressed gene is preferentially located outside of its chromosome territory, whereas a closely linked, inactive gene is located insid”
Genomic maps and comparative analysis of histone modifications in human and mouse. (2005, background): “…the interrogated regions constitute approxi- foreskin) that do not express 3 HoxA and HoxB genes. mately 2% of the human genome, they are not known Chambeyron and Bickmore (2004) recently described a to contain large gene clusters and are not representative visible decondensation of chromatin at…”