Biomedical Engineering Reference
In-Depth Information
to be considered. These chemicals are incorporated in newly polymerized genomic
DNA molecules as false substrates in place of cytosines in the process of DNA rep-
lication during cell division and can act as DNMT inhibitors by trapping and inacti-
vating DNMT molecules in the form of a covalent protein-DNA complex (Zhou
et al.
2002
; Lyko and Brown
2005
). Azacytidines are effective DNA methylation
inhibitors for frequently dividing cells, such as cancer cells (Hagemann et al.
2011
)
and stem cells (Balana et al.
2006
). However, since mature neurons are not replaced
and only very few neurons are incorporated into the existing neuronal circuitry by
neurogenesis, azacytidines injected into brains may inhibit tRNA methylation
(Schaefer et al.
2009
). It has been suggested that methylation of tRNA regulates
tRNA folding and stability (Alexandrov et al.
2006
; Schaefer et al.
2010
), and mis-
folded and unstable tRNA may affect the rate of protein synthesis.
Several non-nucleoside compounds can also be available as DNA methyltrans-
ferase inhibitors. One such inhibitor is (−)-epigallocatechin-3-gallate (EGCG), the
main polyphenol compound found in green tea. EGCG inhibits the infectivity of
infl uenza virus (Nakayama et al.
1993
) and affects various biological processes in
cancer (Kuzuhara et al.
2006
,
2009
; Siddiqui et al.
2011
), including the blocking of
DNA methyltransferase activity in cancer cells (Gu et al.
2009
) and recombinant
DNA methyltransferase protein activity (Rajavelu et al.
2011
). Another DNA meth-
yltransferase inhibitor, RG108 (Fig.
10.6d
), inhibits the enzymatic activity of DNA
methyltransferase by docking at the active pocket (Lyko and Brown
2005
). This
compound is effective without incorporation into genomic DNA and may be more
suitable for neurobiological and behavioral experiments. In fact, intra-brain infu-
sion of RG108 disrupts fear memory (Miller et al.
2010
). The design and chemical
synthesis of novel DNA methyltransferase inhibitors are useful in behavioral
researches (Suzuki et al.
2010
).
10.9
Methods for Analyzing Histone Modifi cations
Posttranslational modifi cation of histones and chromatin remodeling are other
essential epigenetic modifi cations that regulate gene expression. Histone modifi ca-
tions include acetylation, methylation, phosphorylation, ubiquitination, and ADP
ribosylation (Levenson and Sweatt
2005
; Schreiber et al.
2006
). Acetylation is the
best studied posttranslational modifi cation of histone molecules, and acetylation of
histones occurs on the amino group of the side chain of a lysine residue, resulting in
effective neutralization of the positive charges of lysine. This modifi cation dramati-
cally alters the tertiary structure of chromatin to expose promoter regions, allowing
greater access of transcriptional machinery, such as RNA polymerases and tran-
scription factors, onto genomic DNA, resulting in enhancement of gene expression.
Histone acetylation is catalyzed by histone acetyltransferases (HATs), which
transfer acetyl groups from acetyl coenzyme A to the amino group of lysine side
chains. HATs are also known to acetylate nonhistone proteins. This modifi cation is
reversible, and deacetylation is controlled by histone deacetylases (HDACs).
