2. Polycomb Protein Complex
• Polycomb are set of proteins that are involved
in selective repression of certain genes in
specific types of cells and maintain repressed
state in progenitor cells too.
• Most of the polycomb proteins are assembled
into two complexes, Polycom repression
complex 1 (PRC1) and polycomb repression
complex 2 (PRC2).
3. • PRC2 complexes contain histone deacetylases
that inhibits transcription.
• They also contain a subunit enhancer of Zest
[E(Z)] having SET domain, which is
enzymatically active domain of histone methyl
transferases.
• This SET domain methylates H3K27,
generating di and tri methyl lysine.
4. • PRC1 complex then binds with methylated
nucleosome through dimeric Pc subunits, each
containing specific methyl lysine binding domain
called chromodomain.
• Binding to dimeric Pc to nearby nucleosomes is
proposed to condense the chromatin into
structure that inhibits transcription.
• PRC1 complex also contains a ubiquitin ligase that
ubiquitinate H2A at lysine 119 in C-terminal tail.
• This modification inhibits POL II elongation
through chromatin by inhibiting association of a
histone chaperone required to remove histone
octamers from DNA.
5. Trithorax complex
• Trithorax complex counteract the repressive
mechanism of polycomb complex.
• Trithorax complexes encode a histone methyl
transferases that trimethylates H2K4, which is
epigenetic mark of active promoter.
• This histone modification creates a binding
sites for histone acetylase and chromatin
remodelling complexes that promote
transcription and TFIID binding.
6. • Nucleosome with H3K4 methylation are also
binding sites for specific histone demthylases
that prevent methylation of H3K9, preventing
the binding of HP1 and at lysine 27,
preventing the binding of PRC repressing
complex.
7.
8.
9. • Lyon first proposed the hypothesis of X
inactivation in 1961 to explain the nature
of Barr body seen in mouse somatic cells.
• The inactivation in eutherians is random and
irreversible, and the inactive X chromosome
or the Barr body was transcriptionally silent
10. • The inactivation process ‘spread’
along the X chromosome from a
single locus (Russel1963), which
was named as the X-inactivation
centre (XIC/Xic) or X-controlling
element (Xce) that act in cis
11. Experimental Evidence
• An autosomal piece inserted in the
chromosome could also get genetically
inactive and late replicating when the
rearranged X chromosome was
inactivated
• A segment of X chromosome when
inserted in an autosome was found to
escape inactivation (Russell 1963)
12. XIST
• XIST is mapped to the XIC and transcribed
exclusively from the inactive X chromosome.
• The mouse Xist RNA is 15 kb with six exons
while the human XIST RNA is 17- kb long with
eight exons.
13. Silencing by XIST
• Xist initially associates with X-chromosome at a
few focal loci from where these transcripts
spread along its length to promote chromosome-
wide heterochromatinization
• Xist in combination with PRC2, a Polycomb group
repressive protein complex comprising of Suz12,
Eed, Rbbp4/7 and the methyltransferase Ezh2
directs H3K27me2/3 of the inactive X
14. • Jarid2, a PRC2 cofactor and RNA-binding
proteins like YY1 or ATRX help in XIST, PCR2
and X interaction.
• X chromosome coated with Xist RNA seems to
be organized into a compact structure through
interaction with SATB1, which enables
efficient formation of the silencing complex
15. • The nuclear matrix-associated SAF-A/ hnRNP U
protein is believed to act as a platform to
immobilize Xist RNA along the X chromosome
• X chromosomal S/MAR sequences might
function as booster elements in the X
chromosome, providing entry sites for
SATB1and SAF-A/hnRNP U to facilitate
formation of the inactivation core complex and
the subsequent chromosome-wide silencing.
16. • Upon initiation of its expression, Xist localizes
to sites on the X chromosome by binding to
the chromatin-interacting SAF-A protein.
Direct interaction of Xist with SHARP at these
sites is suggested to recruit SMRT. The Xist –
SHARP – SMRT complex may recruit HDAC3
directly to the X chromosome
17. • Xist, PRC2 adherence to X chromosome is
followed by association of PRC1 and PRC 1 like
complexes on the X chromosome that induces
the another epigenetic mark of silencing H2A
Ubiquitinition.
18. • Xist directed removal of the activating histone
acetylation triggers compaction of chromatin
and transcriptional silencing. After initiating
the silenced state.
19.
20.
21. Caption of the Diagram
• Chromatin dynamics at the initiation of the XCI. a Composition of the polycomb group 2 and the
polycomb group 1 complexes. PRC2 is composed of three core elements SUZ12, EED and EZH and
several co-factors including PCL2. The PRC1 complex has four core components: CBX, BMI1, RING
and PHC. RING and the BMI1 component can also be found in other kind of complexes that we
mention as PRC1-like complexes. All the alternative components are shown and in bold highlights
the ones that have been documented as enriched in the Xi. b Schematic representation of the
epigenetics events during XCI. In undifferentiated ES cells, the chromatin around the promoter of
an X-linked gene is shown transcribed, with the presence of euchromatic marks such as
H3K4me2/3, H3K36 methylation and H3 and H4 acetylation. Days 2–4: when differentiation is
induced, Xist is upregulated on one X-chromosome and coats the X-chromosome from which it is
expressed in cis. Gene silencing is initiated and Xist-mediated chromatin modifying complexes such
as PRC1 and PRC2 and others are recruited to the Xi, resulting in the accumulation of PTMs typical
of facultative heterochromatin such as H3K27me3, H2AK199ub, H3K9me2 and H4K20me1. The
replication pattern of the Xi changes and the condensation of the Xi become apparent. Days 4–8:
during this period, gene silencing is spread and maintained thereafter. Further epigenetic events
take place such as the acquisition of DNA methylation at the CpGs of the 5′ end of genes and the
incorporation of macroH2A histone variant; chromatin modifications acquired previously are
maintained; there is also the recruitment of different proteins such as SMCHD1, ASH2L, ATRX and
hnRNP U that will lock in the inactive state
22.
23. Initiation of Xist transcription:
panoply of lncRNAs
• Random inactivation of one of the two X
chromosomes in early embryonic stage involves a
decision as to which of the two X chromosomes
would express Xist.
• XIC region produces several other lncRNAs, some of
which promote and some suppress Xist expression.
Balance of these transcripts seems to determine Xist
activity and therefore, choice of the inactive X.
24. • Jpx and Ftx, which are potential activators of
the X inactivation process in mouse. The Jpx
activates Xist by removing the repressive RNA-
binding protein CTCF from the Xist promoter
• RepeatA (RepA) is encoded within the first
exon of Xist and binds independently with the
inactivating PRC2 in vitro. It inhibits the PRC2
from binding with active X
25. • Tsix is yet another lncRNA transcribed from
the Xic on the active X chromosome in
antisense direction from Xist (Lee et al. 1999).
It inhibits the accumulation of Xist transcripts
on the future active X through negative
regulation of expression of Xist in cis, and of
Jpx lncRNA. Tsix also mediate promoter
methylation of XIST on the active X and hence
its transcriptional silencing.
26. • Sustenance of Tsix expression requires
another lncRNA, Xite, which influences Tsix
promoter activity.
• Linx is another lncRNA which may possibly
participate in the control of Tsix expression in
mouse (Nora et al. 2012). However, it may not
be conserved in human.
27. • A novel 251.8-kb long and mostly unspliced
lncRNA in humans is XACT, which is expressed
from a region about 40 Mb from the human
XIC (Vallot et al. 2013). The XACT transcripts
surround the active X chromosome(s) in
human pluripotent and early differentiating
cells, when XCI is still highly dynamic. In the
absence of Xist, XACT can coat both the X
chromosomes. XACT could protect the active X
during the early steps of X inactivation (Vallot
and Rougeulle 2013; Briggs
• and Reijo Pera 2014).
28.
29. Current model of Dosage
compensation
• 40 kb Tsix expressed from both the X
chromosome from early phase of
development from inactivation centre.
• This prevent sysnthesis of XIST from
complementary strand.
• Later in development Tsix becomes
transcribed from active X.
• This mechanism for controlling symetric
transcription is unknown.
30. • Inhibition of TSIX allows RepA synthesis RNA from
complementary DNA strand.
• RepA forms stem loop secondary structure that
interact with PRC2
• That leads to methylation of H3K27
• This in turns activate XIST promoter by some
unknown mechanism.
• The RepA and PRC2 complex then spreaded over
the entire length of X and causes PRC1 binding
and transcription repression.
31. Gene that escape dosage
compensation
• Although most X-linked genes are silenced, the idea
that some are expressed from the inactive X
chromosome was originally hypothesized for genes
with Y gametologs that should be dosage compensated
with two functional copies in males and females (Lyon
1962). Further, aberrant gene dosage of such “escape”
genes explains phenotypes in individuals with X
chromosome aneuploidies, such as Turner Syndrome
(most commonly due to a 45,X karyotype) and
Klinefelter Syndrome (XXY). The existence of escape
genes has been established for some time (Shapiro et
al. 1979), although it is now known that not all have
copies on the Y.
