1. Polycomb, trithorax, and maintenance of gene expression
A key feature of development in metameric animals is the definition of body segments where groups of cells with a specified fate will give rise to their relative body structures. Cell fates are specified by particular combinations of homeotic gene products. During early embryogenesis, maternal and segmentation genes regulate homeotic genes by binding to specific regulatory sequences located in the promoter regions.  Later in development, the expression pattern of homeotic genes as well as other important developmental genes are maintained by a cell memory system dependent on two groups of genes. The members of these two groups are able to recognize the active and inactive state of expression and fix it to the cell progeny through many cell divisions. These components have been classified in two genetic groups. The trithorax-group (trxG) maintain the active state of expression, while the Polycomb-group (PcG) counteracts this activation with a stable repressive function.
There is strong evidence that the memory function encoded by these two groups of genes is achieved through regulation of higher order chromatin structures. PcG gene products form large multimeric protein complexes in Drosophila, mouse and human. PcG mediated gene silencing can be directed by DNA elements in cis, defined as PcG response elements (PRE). On the other hand, several trxG members act at elements defined as TRE (that overlap with PRE) via chromatin remodeling and induction of histone modifications that increase chromatin accessibility to transcription factors.
In this set of slides, some of the features of PcG and of trxG factors are summarized and examples of molecular and cell biological approaches to dissect their mechanisms of action are presented.

2. Polycomb, trithorax, and maintenance of gene expression
Early development
OFF ON
Maternal, Gap, Pair-rule, Segment polarity
Establishment of patterns
Ubx
OFF ON
Polycomb-Group
Maintenance phase
trithorax-Group
Transmission of pattern after disappearance of early factors
OFF ON
Intro
haltere
Ubx OFF
Ubx ON
wing
Update: December 2004

3. PcG and trxG proteins associate to multiple genomic lociPH
DAPI
Polytene chromosome staining shows around 100 bands for each PcG protein
Merge

4. PcG and trxG proteins bind to specific DNA elements, named PRE and TRE
Binding leads to maintenance of PcG-dependent repression of reporter genes
Bound by PcG proteins in vivo (in polytene chromosomes and by cross-linking experiments)
Repression is enhanced by homologous pairing of the transgenes
Bound by trxG proteins in vivo
Binding leads to maintenance of trxG-dependent activation of reporter genes
PRE and TRE often overlap in the same genomic region
PcG and trxG proteins bind to specific DNA elements, named PRE and TRE
PRE
TRE

5. Members of the PcG and of the trxG
protein motif
homologs
Members of the PcG and of the trxG
Gene
trithorax (trx)
SET (H3 HMTase)/ PHD-finger
MLL/ALL-1/HRX (human)
brahma (brm)
bromo domain
SWI2/SNF2 (yeast)
(DNA dependent ATPase/helicase)
brg1 (mouse/human); Hbrm (human)
Trithorax-like (Trl)
zinc finger (DNA binding)
BTB/POZ (dimerization)
trxG
PcG
Polycomb (Pc)
chromo domain
(Binding to H3 methyl K9 or K27)
M33 (mouse); hPC (human)
polyhomeotic (ph)
one zinc finger
Mph1/Rae-28 (mouse); hph1; hph2 (human)
Posterior sex combs (Psc)
RING finger
bmi-1 (mouse/human); mel-18 (mouse)
Pleiohomeotic (pho)
Zinc-finger (DNA binding)
hYY-1 (human); mYY-1 (mouse)
Enhancer of zeste (E(z))
SET (H3MTase)
Ezh1; Ezh2 (human); clf (Arabidopsis)
extra sex combs (esc)
WD repeat
Eed (mouse); hEED (human)
PRC1 complex
Esc/E(z)
Complex
Ash-1
SET (H3/H4HMTase)/ PHD-finger
ASH-1 (human); NSD1 (mouse)
TAC1 complex
Brm complex
FACT complex

6. Action of PcG and trxG complexes on chromatin
Nucleosome remodeling
(BRM complex)
trxG ON Ac
Maintenance of active states
(open chromatin)
Histone acetylation and methylation
(TAC1 and ASH1 complexes)
Me K4 H3
Target gene
PRE
OFF
PcG
Me K27 H3
Deacetylation and methylation
(ESC-E(Z) complex)
Maintenance of repressed states
(compact chromatin)
- Chromatin compaction
- H2A Ubiquitination
(PRC1 complex)
Ub H2A

7. Histone H3 methylation and PolycombPc
H3 K9 triMe
Merge
Data from:
Ringrose et al. (2004) Mol. Cell 16, 641 Pc
H3 K27 triMe
Merge
There is a strong but not absolute correlation between trimethylation of K27 (and K9) trimethylation and Polycomb recruitment at target loci. i.e. there is more to Pc recruitment

8. What do « Polycomb » proteins do to chromatin ?
1. Condensation
Recombinant PC-containing complexes can condense an array of 12 nucleosomes in vitro
Condensation requires PSC (not PH) protein, and involves histones but does not necessitate histone tails
Data from: Francis et al. (2004), Science 306, 1574

9. What do « Polycomb » proteins do to chromatin ?
2. H2A Ubiquitination
Data from:
Wang et al. (2004) Nature 431, 873
Purified human PRC1-type complexes can Ubiquitinate H2A in vitro, and the drosophila counterpart of the same complex induces a dRing-dependent H2A Ub at the Ubx PcG target gene

10. Features of PREs and TREs, and examples of how they are studied in drosophila

11. The Bithorax-complex is a target locus for PcG and trxG proteins
Fab-7&8
iab-4
iab2/3
bxd bx
Mcp
Regulatory regions in the Bithorax Complex are shown in red
Target elements for PcG and/or trxG proteins are shown in green

12. 1. Spatial specific maintenance of silencing of homeotic genes
Ubx
HbZYG
Extended germ band stage (6h)
Gastrulation stage (3h)
Wild type embryo
Mutant PcG embryo
---> Anterior derepression, antero-posterior transformation A P
1. Spatial specific maintenance of silencing of homeotic genes
No effect on initiation of silencing in anterior parasegments
Silencing initiates correctly, thanks to early repressors like Hunchback (Hb), but degenerates in the absence of PcG proteins when these repressors disappear

13. 1. Example of PcG-dependent spatial specific silencing of homeotic genes
bxd5.1 UbxlacZ reporter construct
Bxd 5.1 PRE
Ubx prom
LacZ
mini-white
Silencing of a Ubx-lacZ reporter mimicking the wt behaviour of the Ubx gene, which is silenced in parasegments 1 to 5
PcG dependent derepression of a Ubx-lacZ reporter in embryonic territories where it is normally silenced
Data from: Hodgson, J. W., Argiropoulos, B., and Brock, H. W. (2001). Site-specific recognition of a 70-base-pair element containing d(GA)(n) repeats mediates bithoraxoid polycomb group response element-dependent silencing. Mol Cell Biol 21,

14. 2. Pairing Sensitive Silencing
During embryonic development, chromosome homologs pair in diptera. Pairing brings homolog sequences in close physical proximity. This pairing correlates with the strength of PcG and trxG mediated regulation
Weak PcG mediated repression
Strong PcG mediated repression
PRE Heterozygous
PRE Homozygous
2. Pairing Sensitive Silencing

15. The Fab-7 element of the BX-C
Ubx
abd-A
Abd-B
3,6 Kb
Locus BX-C
Chr. III
Boundary
PRE
The Fab-7 element is a 3.6 Kb region that regulates expression of the homeotic gene Abdominal-B (Abd-B), located in the locus named Bithorax Complex (BX-C) in chromosome III of Drosophila. This element is partitioned in a PRE and a so-called “chromatin boundary”, i.e. an element that might segregate independent chromosomal domains from each other.
Fab-7
The Fab-7 element of the BX-C

16. w
Chromosome X
2. An example of Pairing Sensitive Silencing: silencing of the mini-white reporter gene by the Fab-7 element in the Fab-X transgenic line
---> strong mini-white silencing
---> weak silencing of the mini-white reporter gene
Transgenic Fab-7
heterozygous
homozygous P
mini-white
Fab-7
Data from: Bantignies, F., Grimaud, C., Lavrov, S., Gabut, M., and Cavalli, G. (2003). Inheritance of Polycomb-dependent chromosomal interactions in Drosophila. Genes Dev 17,

17. 2. Silencing of mini-white depends on PcG and trxG proteins
Fab-7
Pc +/+
Pc -/+
trx +/+
trx -/+
UAS-lacZ
white

18. 3. Recruitment of PcG and trxG proteins to PREs: analysis in Fab-7 by a combination of immunostaining and FISH in polytene chromosomes (immuno-FISH)
24A
25E5
transgene
DAPI
Immunostaining
of PH protein
FISH
Immuno-FISH
Fab-7
UAS-lacZ
white
Transgene :

19. 4. Recruitment of PcG proteins at PREs: chromatin analysis by Formaldehyde cross-linking and chromatin immunoprecipitation (ChIP)
Sonicate and purify chromatin
(average size = 1 kb)
Add antibody and purify antibody-chromatin complexes on Protein A Sepharose, purify DNA and amplify by Linker-mediated PCR
Cross-link cells or embryos with formaldehyde to induce protein-DNA crosslinks
Use amplified DNA as probe on a Southern of a genomic walk, quantify by PhosphorImager
Genomic walk

20. Example: analysis of PC and GAGA factor binding to Fab-7 by ChIP
1230 bp
778 bp
422 bp
356 bp
GAF Xh E H Xb P F
200
120 40
Boundary
PRE
1 Kb p d 50 30 10 PC
Mock
PC Ip
GAGA Ip
Example: analysis of PC and GAGA factor binding to Fab-7 by ChIP
Quantification of the signals
Data from: Cavalli, G., and Paro, R. (1998). The Drosophila Fab-7 chromosomal element conveys epigenetic inheritance during mitosis and meiosis. Cell 93,

21. Fab-7
UAS-lacZ
white
Hsp 70
GAL4
Driver construct
Reporter construct
The GAL4 system for the study of PRE/TRE function: mimicking the developmental pathway leading to maintenance of homeotic gene expression
Check Eye color
Light Eye color
white repressed
Embryo
Larva
Pupa
1st
2nd
3rd instar
HsGAL4 pulse during early development
Experimental approach ?
5. Maintenance of active as well as repressed states: PREs and TREs form elements named as Cellular Memory Modules

22. Fab-7: a cellular memory module (CMM) that maintains active as well as silenced chromatin throughout development
+HS
-HS
lacZ
white
Fab-7 G
3,6 kb
Gal4
hsp70
GAL4 HS
UAS
Beta-gal stains to study lacZ expression
Data from: Cavalli, G., and Paro, R. (1998). The Drosophila Fab-7 chromosomal element conveys epigenetic inheritance during mitosis and meiosis. Cell 93,

23. Chromatin states can be inherited through meiosis by the following generations

24. Meiotic inheritance of derepressed states
G1, G2, G3...
Repressed
Derepressed G0
GAL4 pulse in embryos
Re-cross red eyed flies

25. Big open questions
What are the precise developmental cues that recruit PcG or trxG proteins to PREs of homeotic genes? Do they also apply for other PREs/TREs?
What are the molecular mechanisms for recruitment of PcG and trxG proteins to PREs and TREs? What are the effects of these recruitments on chromatin?
Once recruited, how can these proteins maintain chromatin states through DNA replication and through mitosis (and meiosis)?
What is the basis of the Pairing Sensitive Effects and of long distance interactions? How does this phenomenon contribute to inheritance of chromatin states?
What is the genome-wide profile of PcG and trxG binding? What is the identity of the corresponding target genes? Are they all regulated like homeotic genes, or are there different categories of regulatory mechanisms?