HDACs complete homology of the series with a note on various HDACs present in mammals and their regulations

1. HDACs
(Histone Deacetylases)
KRVS Chaitanya

2. • Histone deacetylases (HDAC) are a class
of enzymes that remove acetyl groups (O=C-CH3)
from an ε-N-acetyl lysine amino acid on a histone,
allowing the histone to wrap the DNA more tightly.
• This is important because DNA is wrapped around
histone, and DNA expression is regulated by
acetylation and de-acetylation.

3. • Its action is opposite to that of histone
acetyltransferase.
• HDAC proteins are now also called lysine
deacetylases (KDAC), to describe their function
rather than their target, which also includes non-
histone proteins

5. HDAC super family
• Together with the acetyl polyamine
amidohydrolases and the acetoin utilization proteins,
the histone deacetylases form an ancient protein
superfamily known as the histone deacetylases
superfamily.

6. • Classes of HDACs in higher eukaryotes.
• HDACs, are classified in four classes depending on
sequence homology to the yeast original enzymes and
domain organization:

8. Classification of HDACs

11. • HDAC (except class III) contain zinc and are known as
Zn2+-Dependent Histone Deacetylases.
• They feature a classical arginase fold and are structurally
and mechanistically distinct from sirtuins (class III),
which fold into a Rossmann architecture and
are NAD+ dependent.

12. Subtypes
• HDAC proteins are grouped into four classes based on function and DNA
sequence similarity.
• Class I, II and IV are considered "classical" HDACs whose activities are
inhibited by trichostatin A (TSA) and have a zinc dependent active site,
whereas Class III enzymes are a family of NAD+-dependent proteins known
as sirtuins and are not affected by TSA.
• Homologues to these three groups are found in yeast having the names:
reduced potassium dependency 3 (Rpd3), which corresponds to Class I; histone
deacetylases 1 (hda1), corresponding to Class II; and silent information
regulator 2 (Sir2), corresponding to Class III.

13. • Class IV contains just one isoform (HDAC11), which is not
highly homologous with either Rpd3 or hda1 yeast
enzymes, and therefore HDAC11 is assigned to its own class.
• The Class III enzymes are considered a separate type of
enzyme and have a different mechanism of action; these
enzymes are NAD+-dependent, whereas HDACs in other
classes require Zn2+ as a cofactor.

16. Evolution
• HDACs are conserved across evolution, showing orthologs in
all eukaryotes and even in Archaea.
• All upper eukaryotes, including vertebrates, plants and
arthropods, possess at least one HDAC per class, while most
vertebrates carry the 11 canonical HDACs, with the exception
of bone fish, which lack HDAC2 but appears to have an extra
copy of HDAC11, dubbed HDAC12.

18. • Plants carry additional HDACs compared to animals,
putatively to carry out the more complex transcriptional
regulation required by these sessile organisms.
• HDACs appear to be deriving from an ancestral acetyl-binding
domain, as HDAC homologs have been found in bacteria in
the form of Acetoin utilization proteins (AcuC) proteins

19. Sub cellular distribution
• Within the Class I HDACs, HDAC 1, 2, and 3 are found
primarily in the nucleus, whereas HDAC8 is found in both the
nucleus and the cytoplasm, and is also membrane-associated.
• Class II HDACs (HDAC4, 5, 6, 7 9, and 10) are able to shuttle
in and out of the nucleus, depending on different signals.

20. • HDAC6 is a cytoplasmic, microtubule-associated
enzyme.
• HDAC6 deacetylates tubulin, Hsp90, and cortactin,
and forms complexes with other partner proteins, and
is, therefore, involved in a variety of biological
processes.

21. Function
Histone modification:
• Histone tails are normally positively charged due to amine groups
present on their lysine and arginine amino acids.
• These positive charges help the histone tails to interact with and
bind to the negatively charged phosphate groups on the DNA
backbone.
• Acetylation, which occurs normally in a cell, neutralizes the positive
charges on the histone by changing amines into amides and
decreases the ability of the histone to bind to DNA.

22. • This decreased binding allows chromatin expansion,
permitting genetic transcription to take place.
• Histone deacetylases remove those acetyl groups, increasing
the positive charge of histone tails and encouraging high-
affinity binding between the histones and DNA backbone.
• The increased DNA binding condenses DNA structure,
preventing transcription.

23. • Histone deacetylases is involved in a series of pathways
within the living system.
• According to the Kyoto Encyclopaedia of Genes and
Genomes (KEGG), these are:
1. Environmental information processing; signal
transduction; notch signalling pathway
2. Cellular processes; cell growth and death; cell cycle
3. Human diseases; cancers; chronic myeloid leukaemia

24. • Histone acetylation plays an important role in the regulation of
gene expression.
• Hyper acetylated chromatin is transcriptionally active, and
hypoacetylated chromatin is silent.
• A study on mice found that a specific subset of mouse genes
(7%) was deregulated in the absence of HDAC1.

25. • Their study also found a regulatory crosstalk
between HDAC1 and HDAC2 and suggest a novel function
for HDAC1 as a transcriptional coactivator.
• HDAC1 expression was found to be increased in the prefrontal
cortex of schizophrenia subjects negatively correlating with
the expression of GAD67 mRNA.

26. Non-histone effects
• It is a mistake to regard HDACs solely in the context of regulating
gene transcription by modifying histones and chromatin structure,
although that appears to be the predominant function. The function,
activity, and stability of proteins can be controlled by post-
translational modifications.
• Protein phosphorylation is perhaps the most widely studied and
understood modification in which certain amino acid residues are
phosphorylated by the action of protein kinases or dephosphorylated
by the action of phosphatases.

27. • The acetylation of lysine residues is emerging as an
analogous mechanism, in which non-histone proteins are
acted on by acetylases and deacetylases.
• It is in this context that HDACs are being found to
interact with a variety of non-histone proteins—some of
these are transcription factors and co-regulators, some are
not.

28. Note the following four examples:
1. HDAC6 is associated with aggresomes.
– Misfolded protein aggregates are tagged by ubiquitination and removed
from the cytoplasm by dynein motors via the microtubule network to an
organelle termed the aggresome.
– HDAC 6 binds polyubiquitinated misfolded proteins and links to dynein
motors, thereby allowing the misfolded protein cargo to be physically
transported to chaperones and proteasomes for subsequent destruction.
– HDAC6 is important regulator of HSP90 function and its inhibitor
proposed to treat metabolic disorders.

29. 2. PTEN is an important phosphatase involved in cell signaling
via phosphoinositols and the AKT/PI3 kinase pathway.
• PTEN is subject to complex regulatory control via
phosphorylation, ubiquitination, oxidation and acetylation.
• Acetylation of PTEN by the histone acetyltransferase
p300/CBP-associated factor (PCAF) can repress its activity;
on the converse, deacetylation of PTEN by SIRT1 deacetylase
and, by HDAC1, can stimulate its activity.

30. 3. APE1/Ref-1 (APEX1) is a multifunctional protein possessing both
DNA repair activity (on abasic and single-strand break sites) and
transcriptional regulatory activity associated with oxidative stress.
• APE1/Ref-1 is acetylated by PCAF; on the converse, it is stably
associated with and deacetylated by Class I HDACs.
• The acetylation state of APE1/Ref-1 does not appear to affect
its DNA repair activity, but it does regulate its transcriptional
activity such as its ability to bind to the PTH promoter and initiate
transcription of the parathyroid hormone gene.

31. 4. NF-κB is a key transcription factor and effector molecule
involved in responses to cell stress, consisting of a p50/p65
heterodimer.
• The p65 subunit is controlled by acetylation via PCAF and by
deacetylation via HDAC3 and HDAC6.

32. Neurodegenerative diseases
• Inherited mutations in the gene encoding FUS,
an RNA/DNA binding protein, are causally linked
to amyotrophic lateral sclerosis (ALS).
• FUS has a pivotal role in the DNA damage response involving
its direct interaction with histone deacetylase 1 (HDAC1).
• ALS mutant FUS proteins are defective in the DNA damage
response and in recombinational DNA repair, and also show
reduced interaction with HDAC1.

33. • Ataxia-telangiectasia is due to mutation in the Atm gene. Wild-
type Atm encodes a protein kinase employed in chromatin
remodeling and in epigenetic alterations that are required
for repairing DNA double-strand breaks.
• Atm mutation causes neurons to accumulate nuclear histone
deacetylase 4 (HDAC4) resulting in increased histone deacetylation
and altered neuronal gene expression that likely contributes to
the neurodegeneration characteristic of ataxia-telangiectasia.

34. HDAC inhibitors
• Histone deacetylase inhibitors (HDIs) have a long history of use in
psychiatry and neurology as mood stabilizers and anti-epileptics, for
example, valproic acid.
• In more recent times, HDIs are being studied as a mitigator or treatment
for neurodegenerative diseases.
• Also in recent years, there has been an effort to develop HDIs for cancer
therapy.
• Vorinostat (SAHA) was FDA approved in 2006 for the treatment of
cutaneous manifestations in patients with cutaneous T cell
lymphoma (CTCL) that have failed previous treatments.

35. • A second HDI, Istodax (romidepsin), was approved in 2009 for
patients with CTCL. The exact mechanisms by which the
compounds may work are unclear, but epigenetic pathways are
proposed.
• In addition, a clinical trial is studying valproic acid effects on the
latent pools of HIV in infected persons.
• HDIs are currently being investigated as chemosensitizers for
cytotoxic chemotherapy or radiation therapy, or in association with
DNA methylation inhibitors based on in vitro synergy.
• Isoform selective HDIs which can aid in elucidating role of
individual HDAC isoforms have been developed.

36. • HDAC inhibitors have effects on non-histone proteins that
are related to acetylation.
• HDIs can alter the degree of acetylation of these molecules
and, therefore, increase or repress their activity.
• For the four examples given above (see Function) on
HDACs acting on non-histone proteins, in each of those
instances the HDAC inhibitor Trichostatin A (TSA) blocks
the effect.

37. • HDIs have been shown to alter the activity of many
transcription factors, including ACTR, cMyb,
E2F1, EKLF, FEN 1, GATA, HNF-4, HSP90, Ku70,
NFκB, PCNA, p53, RB, Runx, SF1 Sp3, STAT, TFIIE, TCF,
YY1.

38. • The ketone body β-hydroxybutyrate has been shown in mice to
increase gene expression of FOXO3a by histone deacetylases inhibition.
• Histone deacetylases inhibitors may modulate the latency of some viruses,
resulting in reactivation.
• This has been shown to occur, for instance, with a latent human
herpesvirus-6 infection.
• Histone deacetylases inhibitors have shown activity against
certain Plasmodium species and stages which may indicate they have
potential in malaria treatment. It has been shown that HDIs accumulate
acetylated histone H3K9/H3K14, a downstream target of class I HDACs.

39. Thank you