6b NEU

The Polycomb proteins form two complexes, which are PRC1 (Polycomb repressive complex) and
PRC2. Both complexes contain a core and the core includes the enzyme that modify histones and a
number of associated proteins, so that they can form a canonical or several non canonical
complexes. The core of PRC1 can associate with different PCGF proteins (PCGF1-PCGF6) defining
canonical PRC1 complexes (cPRC1) and non canonical PCR1 complexes (ncPCR1). cPRC1 contains PHC
and CBX proteins and the more loosely associated SCMH proteins. ncPRC1 complexes are defined by
the presence of RYBP/YAF2 that associate with additional proteins. Composition of PRC2 complexes.
The core of PRC2 complexes (EZH1/2: enzymatic activity that attaches methyl groups to histones)
associates with different accessory proteins to define the PRC2.1 and PRC2.2 complexes,
respectively. The core of PRC1 also has a histone modifying activity, but it does not methylate
histones, it attaches an ubiquitin modification. Trithorax complexes on the other hand contain
methylases (SET1A/B, MLL 1/2, MLL3/4). Whereas the PRC1/2 complexes modify histones in a
repressive way, the methylation introduced by the Trithorax complexes corresponds to active
chromatin.

The two PRC complexes act together in the classical model, in a way that PRC2 is recruited to
chromatin and it somehow binds to chromatin, then introduces a modification and this modification
is then recognised first of all by another PRC2 complex which adds another modification and not a
PLC to complex that again another modification. This is the way how the repressive modification
which is 3 lysine 27 trimethylation H3K27m3 is propagated to form metal chromatin. In the classical
model PRC1 complex recognises the trimethylated chromatin and then introduce the also repressive.
ubiquitination of lysine 119 in the H2A histone H2AK119.

The alternative model says that the ubiquitination comes first and the ubiquitination is then
recognised by PRC2 and then PRC2 adds the repressive H3K27m3 marks. Trithorax complexes add
the methyl marks that are associated with transcriptional activities and this is the mono and
dimethylation of H3K4m1 and H3K4m2 in enhancers and around core promoters the H3K4me3 is
added.

According to the "classical model," targeting of the PRC2 complex leads to the methylation of H3K27.
This modification is recognized by the Cbx subunit of the canonical PRC1 complex, which in turn
catalyses monoubiquitination of histone H2A at lysine 119 (H2AK119ub). An alternative recruitment
mechanism posits that ncPRC1 is targeted to unmethylated CpG islands through the FBXL10/KDM2B
subunit. ncPRC1 seems to be responsible for the majority of the H2AK119ub modifications present at
PcG-target sites, which might facilitate the recruitment of PRC2. H3K27 methyl marks can be erased
by histone demethylases, such as UTX/KOM6A and JMJD3/KDM6B, while several deuquibitinases
(including BAP1, USP16 and USP21) can remove the monoubiquitin moiety from histone H2A. Set
1A/B COMPASS complexes catalyze mono-, di-, and trimethylation on H3K4 at active promoters. The
activity of the partially redundant COMPASS complexes containing MLL3/KMT2C and MLL4/KMT2D
leads to the deposition of H3K4me1 at enhancers, facilitating the recruitment of other activators such
as CBP/p300. The deposition of methyl marks on H3K4 at bivalent regions is performed by
MLL2/COMPASS. Multiple histone demethylases, including members of KDM1/LSD. KDM2A/FBXL11,
and KDM5/JARID families, are implicated in the removal of methyl groups on H3K4.

The question is, how do these polycomb and trithorax complexes know where to add repressive or
activating marks (histone modification) on chromatin? There are several ways for Trithorax and
Polycomb complexes to be brought to DNA and determine by adding determine or repressive histone
marks, whether are region is transcribed or not transcribed. The whole process is then modified
and/or regulated by the Insulator sequences, which determine where the spreading has to end.
One is mediated by transcription factors and one by DNA sequences (PRE/CGI for binding of
polycomb complexes and TRE/CGI for binding the compass elements, which belong to Trithorax) but
the mode of recruiting the complex is similar except that you know for instance if it's a transcription
factor that recruits the complex than that transcription factor that recruits the PRC complexes will be
different from those that recruit the compass like complex. The first recruitment is either the
polycomb group complexes or the Trithorax complexes are recruited because a transcription Factor
binds to a DNA sequence. If the transcription Factor causes repression of chromatin, it recruits
polycomb complexes and if it is an activator that binds to this element it will recruit the trithorax
complexes, corresponding to the activation of genes.

Another mode of recruiting of polycomb complexes or trothorax complexs is through non-coding

RNA so they are non-coding RNAS that can bind polycombs or compass complexes, that can mediate
the interaction with these DNA sequences.

A third possibility is that both polycomb and trithorax group complexes contain reader domains,
which can recognise chromatin by determining the histone modification. If the chromatin is already
methylated on lysine 27 then that can be recognised by the polycomb group complexes as a way of
propagating the repressive mark and similarly the trithorax complexes can recognise lysine 4
methylation marks that correspond to active genes.

There is also the situation, that there is no DNA sequences and in this case it is called roaming activity
of the PRC2 complexes and that means that the PRC2 will not be stable on DNA and they will not
trimethylate, but only dimethylate on histone H3 lysine 27 because it is a very brief and transient
interaction.

The consequences of PRC complex proteins are than they inhibit chromatin remodelling they inhibit
the binding of Pol II to, lead to chromatin compaction, they inhibit the deposition of the activating
mark H3K27, they stabilise repressive chromatin loops and chromatin domains and they have a
protective function against improper gene activation. So inhibiting genes, that are not supposed to
be transcribed is of course just as important as making sure that they are to transcribed when
necessary.

Global function of what polycomb and trithroax complexes do. What is epigenetic gene regulation
and what is it good for? Epigenetic regulation is what determines cell type specificity and epigenetic
inheritance make sure that each cell type expresses a certain pattern of genes and not others. Role of
trxG complexes in maintaining heritable state of active gene expression in contrast to heritable
silencing by PcG complexes. Transcriptional activator binds to a specific sequence and will recruit Trx
and make sure that the corresponding gene will be turned on. Same with repressors and Polycomb
 concept of cellular memory. Once the complexes have determined which region of the genome
can be transcribed and which cannot be transcribed, this is going to be inherited on daughter cells
and from then on, a pattern of Gene expression has been determined.

Positive control of enhancer activity by lncRNAs is a very general mechanism of gene control.

Original notion was that our genome is transcribed wherever we have genes and where we don’t
have genes, the genome is not transcribed. This is proven to be wrong and we now know that a large
part of our genome is transcribed, no matter whether the region contains a RNA/Protein coding gene
or not. This means transcription has other functions than just generating mRNA or any other RNA.
When a gene is being activated its is not only the gene that is transcribed, but also the enhancer. This
means that RNAs are generated that correspond in their sequence to enhancers.

Mechanism who enhancer RNA is known to contribute to gene activity.

LncRNA allows for the binding of proteins that Bring the enhancer proximal to the TSS via loop
formation. The enhancer RNA stays associated with the enhancer probably by basepairing with the
DNA and the RNA itself binds to proteins, that are involved in DNA loop formation. So we get loop
formation between enhancers and core promoters, genes can be activated.

LncRNA changes nuclear localization of the gene to an active chromosome territory. Enhancer RNAs
can change the localisation of gene within the nucleus.

LncRNA recruit ts activators/chromatin modifiers. Enhancer RNAs that stay associated with the
enhancer can also help to bind transcriptional activators and these would bind to the RNA and not
the enhancer sequence itself.

LncRNA transcribed in the vicinity of a gene delivers activators to the proximal promoter/TSS.
Combination of these mechanisms, a loop and the enhancer RNA recruits a ts activator and this
activator interacts then with the core promoter and in this way helps the gene to be transcribed.

This is still an emerging field, but it has become clear that it contributes to gene expression.