Biology Reference
In-Depth Information
CHAPTER FOUR
Chromatin Architectures and
Hox
Gene Collinearity
,1
*
National Research Centre “Frontiers in Genetics”, School of Life Sciences, Ecole Polytechnique F´d´rale,
Lausanne, Switzerland
†
National Research Centre “Frontiers in Genetics”, Department of Genetics and Evolution, University of
Geneva, Geneva, Switzerland
1
Corresponding author: e-mail address: denis.duboule@epfl.ch
,
†
Daan Noordermeer
*
, Denis Duboule
*
Contents
1.
Introduction
114
2.
Hox Gene Function and Genomic Organization
115
3. The Many Faces of Collinearity
119
4. Are Polycomb and Trithorax Mediators of Collinearity?
122
5. Downstream of Polycomb and Trithorax: A Compacted Chromatin Architecture
128
6. 3D Chromatin Organization and Collinearity in Drosophila
130
7. A 3D Chromatin Timer for Vertebrate Collinearity?
133
8. A Regulatory Archipelago and Collinearity in Developing Digits
136
9. Clustering, Coating, Compaction, Compartmentalization, and Contacts:
The Five C's of Collinearity?
139
9.1 Clustering
139
9.2 Coating
139
9.3 Compaction
140
9.4 Compartmentalization
140
9.5 Contacts
140
Acknowledgments
140
References
141
Abstract
Ever since the observation that collinearity, that is, the sequential activity of Hox genes
based on their relative positions within their gene clusters, is conserved throughout
most of the animal kingdom, the question has been raised as to what are the underlying
molecular mechanisms. In recent years, technological advances have allowed to
uncover changes in chromatin organization that accompany collinearity at Hox gene
clusters. Here, we discuss insights in the dynamics of histone modifications and 3D orga-
nization in Drosophila and mammals and relate these findings to genomic organization
of Hox gene clusters. Using these findings, we propose a framework for collinearity,
based on five components: clustering, coating, compaction, compartmentalization,
and contacts. We argue that these five components may be sufficient to provide a
mechanistic ground for the readout of collinearity in
Drosophila
and vertebrates.
