Page 45 - Hematology_ Basic Principles and Practice ( PDFDrive )

C H A P T E R 2

EPIGENETICS AND EPIGENOMICS

Jennifer Wu and Myles Brown

Epigenetics can be defined as inheritance of variation above and factors, cofactors, RNA polymerases, and the totality of functional
beyond changes in the DNA sequence. In other words, epigenetics components underlying gene expression.
comprises the study of how cells sharing the same exhaustive DNA It is important to remember some key differences between
blueprint can appear and function so distinctly as white blood cells, genomic and epigenomic research. Whereas the genome is an essen-
hepatocytes, neurons, and so forth. Whereas the genome contains all tially unvarying feature of every cell in an organism (with the
of an organism’s vital information, a cell’s epigenome dynamically important exception of T and B cells that rearrange and mutate their
filters and organizes that information into highly coordinated pro- antigen receptor genes), the epigenome of each cell within that organ-
grams of gene expression. ism is unique. Moreover, epigenomes are fluid throughout a cell’s life
Within the nucleus, DNA interacts with a variety of proteins to span, integrating intrinsic cellular “identity” with contextual signals
form chromatin, which can be broadly classified as highly compacted to specify a program of gene expression. Finally, the mechanics of
and transcriptionally silent (heterochromatin) versus loosely com- DNA replication and cell division necessarily disrupt the protein–
pacted and transcriptionally active (euchromatin). Heterochromatin DNA interactions that comprise the epigenome. How cells reestablish
comprises two distinct classes of DNA: (1) noncoding, often repeti- their epigenetic identity after cell division is not well understood.
tive, “structural” DNA of centromeres and telomeres (constitutive
heterochromatin), and (2) gene-encoding and gene-regulatory “func-
tional” DNA that is selectively rendered inactive in different cell types FUNCTIONAL CHROMATIN DOMAINS
(facultative heterochromatin). When euchromatin is described as
loosely compacted, the information content of its DNA is readily Regulatory, noncoding DNA regions can have a variety of different
accessible to binding the protein and RNA machinery that regulate functions (illustrated in Fig. 2.1A), variously classified as promoters,
gene expression. The aim of the study of epigenetics and chromatin enhancers/silencers, superenhancers, and insulators. Promoters are
therefore is to describe and understand the chromatin dynamics that typically located within 1 to 2 kb of the transcriptional start site
orchestrate the four-dimensional symphony of molecular and cellular (TSS) of a gene. At a minimum, RNA polymerase II–dependent
biology from the (seemingly) one-dimensional score that is the promoters contain binding sites for the general transcription factors
genome. TATA box-binding protein (TBP) and transcription factor IIB
The information contained within chromatin can be grossly (TFIIB), which form the core of the transcriptional complex. Tran-
divided into two main categories: (1) the structural genes themselves, scription factor binding sites within the promoter modulate gene
which are transcribed and translated into proteins or act as functional expression by recruiting histone-modifying enzymes and transcrip-
RNAs, and (2) gene-regulatory regions, which control the timing and tional coactivators or corepressors.
amount of transcription (Fig. 2.1A). The information contained in An enhancer/silencer is a short (50- to 1500-bp) region of DNA
transcribed and translated regions can be interpreted using the that can be bound by transcription factors to increase/decrease the
“genetic code,” wherein the DNA sequence of the gene specifies, likelihood that transcription of a particular gene will occur. Enhancers/
through a messenger RNA (mRNA) intermediate, the amino acid silencers can act both in cis (within a chromosome) and rarely in trans
sequences of resulting proteins. Although there is no genetic code for (between chromosomes), can be located up to 1 Mb away from the
functional RNAs that are not translated into proteins, some, such as gene, and can be upstream or downstream from the TSS. Promoters
ribosomal RNA and transfer RNA genes, have well understood func- physically interact with their associated enhancers or silencers via
tions. There are in addition a number of other types of functional three-dimensional chromatin “looping” facilitated by Mediator and
RNA genes whose functions are only partially elucidated. Transcribed cohesin protein complexes (Fig. 2.1D). Genes may be regulated by
regions comprise approximately 3% of the genome. In contrast, the several enhancers/silencers, and each enhancer/silencer may modulate
information contained in gene-regulatory regions is the “epigenetic expression of one or more genes. A superenhancer is a cluster of
code,” which has yet to be fully deciphered and is based on the physically and functionally associated enhancers that regulates genes
accessibility of those regions to dynamic protein–DNA interactions, critical for cell identity. Superenhancers are marked by high levels of
the identity of those interacting proteins, and the identity of the enhancer-associated histone modification and bind high levels of cell
gene(s) whose expression is being modulated. type–specific and lineage-defining transcription factors (known as
The most dramatic example of chromatin compaction is the “master” transcription factors).
condensation that occurs during mitosis, making individual chromo- Insulators help to restrict the set of genes that can be modulated
somes visible by light microscopy and allowing segregation of repli- by an enhancer by blocking the physical interactions between enhanc-
cates equally among daughter cells. A condensed or compacted ers and promoters. Insulators are bound by cohesin and CTCF
chromosome is folded many times upon itself and is highly protein proteins and form boundaries between silenced and active genes.
bound, affording little or no access to genomic information and Clusters of insulators separate heterochromatin from euchromatin,
remaining transcriptionally silent (Fig. 2.1B). Contrast this with the and the segments of active chromatin bounded by these clusters are
“decondensed” chromatin state that is necessary for DNA replication known as topologic domains—genomic regions within which regula-
during the synthesis phase of the cell cycle. DNA replication requires tion occurs.
unfolding of chromatin, disruption of its protein–DNA interactions,
and “unzipping” the double helix to allow every base in the genome
to be copied. When not dividing, cells maintain their chromatin in DNA METHYLATION
intermediate states of compaction. Actively transcribed genes and
their associated regulatory chromatin regions are “open” and “acces- Methylation of cytosine by DNA methyltransferases (DNMTs)
sible” insofar as the underlying protein–DNA interactions are readily occurs at 60% to 90% of CpG dinucleotides in the mammalian
modified and disrupted to accommodate binding of transcription genome. Methylated DNA is bound by methyl-CpG-binding domain

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