Biology Reference
In-Depth Information
9.3. Compaction
The state of chromatin compaction, via the binding of PRC1, may strongly
influence the transcriptional competence of
Hox
loci. The maintenance of
the correct compaction state, as well as the decompaction process, in space
and time, is thus essential. The active induction of local chromatin
decompaction may guide transcriptional activities, yet the opposite process
is equally possible, with transcription of the surrounding chromatin inducing
the eviction of Polycomb complexes.
9.4. Compartmentalization
Hox
clusters form dynamic local 3D compartments labeled by either
H3K27me3 or H3K4me3 marks. These compartments physically separate
active from inactive genes and the gene cluster from the surrounding chro-
matin. Polycomb components are concentrated into the inactive compart-
ments, whereas Trithorax components and the transcription machinery are
concentrated into the active compartment, where they likely synergize to
promote and maintain transcription itself. The step-wise transition of
Hox
genes from the inactive to the active compartments may act as a timer
accompanying temporal collinearity. The pace of transition may reflect
the various affinities for the repressive and activating machineries, polarized
toward the two extremities of the gene cluster.
9.5. Contacts
Hox
clusters are involved in positive and negative long-range contacts. Col-
linear programs co-opted along with the radiation of vertebrates generally
involve remote regulatory information, which can override the cluster-
intrinsic repressive polarity. On the other hand, inactive
Hox
genes coated
by H3K27me3 can establish low-frequency contacts with other
Hox
clus-
ters. These arguably stochastic contacts, which occur at Polycomb bodies
in
Drosophila
, may serve to further concentrate the repressive machinery.
ACKNOWLEDGMENTS
We apologize to all authors whose work has been excluded due to space constraints.
Drosophila
ChIP-on-chip data for
Figs. 4.5 and 4.6
was downloaded from
http://cav-ouranos.igh.cnrs.fr/
viewer-0.3_public/index.php
.
Data for Topological domains as discussed in section 4.8 was
obtained from
http://chromosome.sdsc.edu/mouse/hi-c/database.php
.
Wethankmembers
of the Duboule labs for useful discussion and acknowledge the financial support from the
Ecole Polytechnique F
´
d
´
rale (Lausanne), the University of Geneva, the Swiss National
Research Fund, the National Research Centre “Frontiers in Genetics,” and the European
Research Council grant “SystemsHox.ch.”
