Generally, in progression to cancer, hundreds of genes are silenced or activated. Although silencing of some genes in cancers occurs by mutation, a large proportion of carcinogenic gene silencing is a result of altered DNA methylation (see
DNA methylation in cancer). DNA methylation causing silencing in cancer typically occurs at multiple
CpG sites in the
CpG islands that are present in the
promoters of protein coding genes.
Altered expressions of
microRNA
Micro ribonucleic acid (microRNA, miRNA, μRNA) are small, single-stranded, non-coding RNA molecules containing 21–23 nucleotides. Found in plants, animals, and even some viruses, miRNAs are involved in RNA silencing and post-transcr ...
s also silence or activate many genes in progression to cancer (see
microRNAs in cancer). Altered microRNA expression occurs through hyper/hypo-methylation of
CpG sites in
CpG islands in promoters controlling transcription of the
microRNA
Micro ribonucleic acid (microRNA, miRNA, μRNA) are small, single-stranded, non-coding RNA molecules containing 21–23 nucleotides. Found in plants, animals, and even some viruses, miRNAs are involved in RNA silencing and post-transcr ...
s.
Silencing of DNA repair genes through methylation of CpG islands in their promoters appears to be especially important in progression to cancer (see
methylation of DNA repair genes in cancer).
CpG islands in promoters
In humans, about 70% of
promoters located near the
transcription start site of a gene (proximal promoters) contain a
CpG island.
CpG islands are generally 200 to 2000 base pairs long, have a C:G
base pair
A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA ...
content >50%, and have regions of
DNA
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
where a
cytosine
Cytosine () (symbol C or Cyt) is one of the four nucleotide bases found in DNA and RNA, along with adenine, guanine, and thymine ( uracil in RNA). It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attac ...
nucleotide
Nucleotides are Organic compound, organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both o ...
is followed by a
guanine
Guanine () (symbol G or Gua) is one of the four main nucleotide bases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine ( uracil in RNA). In DNA, guanine is paired with cytosine. The guanine nucleoside ...
nucleotide and this occurs frequently in the linear
sequence
In mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called ''elements'', or ''terms''). The number of elements (possibly infinite) is cal ...
of
bases along its
5′ → 3′ direction.
Genes may also have distant promoters (distal promoters) and these frequently contain CpG islands as well. An example is the promoter of the DNA repair gene ''
ERCC1'', where the CpG island-containing promoter is located about 5,400 nucleotides upstream of the coding region of the ''ERCC1'' gene.
CpG islands also occur frequently in promoters for
functional noncoding RNAs such as
microRNA
Micro ribonucleic acid (microRNA, miRNA, μRNA) are small, single-stranded, non-coding RNA molecules containing 21–23 nucleotides. Found in plants, animals, and even some viruses, miRNAs are involved in RNA silencing and post-transcr ...
s.
Transcription silencing due to methylation of CpG islands
In humans,
DNA methylation
DNA methylation is a biological process by which methyl groups are added to the DNA molecule. Methylation can change the activity of a DNA segment without changing the sequence. When located in a gene promoter (genetics), promoter, DNA methylati ...
occurs at the 5′ position of the
pyrimidine
Pyrimidine (; ) is an aromatic, heterocyclic, organic compound similar to pyridine (). One of the three diazines (six-membered heterocyclics with two nitrogen atoms in the ring), it has nitrogen atoms at positions 1 and 3 in the ring. The oth ...
ring of the cytosine residues within
CpG sites to form
5-methylcytosines. The presence of multiple methylated CpG sites in CpG islands of promoters causes stable inhibition (silencing) of genes.
Silencing of transcription of a gene may be initiated by other mechanisms, but this is often followed by methylation of CpG sites in the promoter CpG island to cause the stable silencing of the gene.
Transcription silencing/activation in cancers
In cancers, loss of
expression of genes occurs about 10 times more frequently by transcription silencing (caused by promoter hypermethylation of CpG islands) than by mutations. As Vogelstein et al. point out, in a colorectal cancer there are usually about 3 to 6
driver mutations and 33 to 66
hitchhiker or passenger mutations.
In contrast, in colon tumors compared to adjacent normal-appearing colonic mucosa, there are about 600 to 800 heavily methylated CpG islands in promoters of genes in the tumors while these CpG islands are not methylated in the adjacent mucosa.
Using
gene set enrichment
Gene set enrichment analysis (GSEA) (also called functional enrichment analysis or pathway enrichment analysis) is a method to identify classes of genes or proteins that are over-represented in a large set of genes or proteins, and may have an a ...
analysis, 569 out of 938
gene sets were hypermethylated and 369 were hypomethylated in cancers. Hypomethylation of CpG islands in promoters results in increased transcription of the genes or gene sets affected.
One study
listed 147 specific genes with colon cancer-associated hypermethylated promoters and 27 with hypomethylated promoters, along with the frequency with which these hyper/hypo-methylations were found in colon cancers. At least 10 of those genes had hypermethylated promoters in nearly 100% of colon cancers. They also indicated 11
microRNA
Micro ribonucleic acid (microRNA, miRNA, μRNA) are small, single-stranded, non-coding RNA molecules containing 21–23 nucleotides. Found in plants, animals, and even some viruses, miRNAs are involved in RNA silencing and post-transcr ...
s whose promoters were hypermethylated in colon cancers at frequencies between 50% and 100% of cancers. MicroRNAs (miRNAs) are small endogenous RNAs that pair with sequences in
messenger RNA
In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein.
mRNA is created during the ...
s to direct
post-transcriptional repression. On average, each microRNA represses or inhibits transcriptional expression of several hundred target genes. Thus microRNAs with hypermethylated promoters may be allowing enhanced transcription of hundreds to thousands of genes in a cancer.
Transcription inhibition and activation by nuclear microRNAs
For more than 20 years,
microRNA
Micro ribonucleic acid (microRNA, miRNA, μRNA) are small, single-stranded, non-coding RNA molecules containing 21–23 nucleotides. Found in plants, animals, and even some viruses, miRNAs are involved in RNA silencing and post-transcr ...
s have been known to act in the cytoplasm to degrade transcriptional expression of specific target gene
messenger RNA
In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein.
mRNA is created during the ...
s (see
microRNA history). However, recently, Gagnon et al.
showed that as many as 75% of microRNAs may be shuttled back into the nucleus of cells. Some nuclear microRNAs have been shown to mediate transcriptional gene activation or transcriptional gene inhibition.
DNA repair genes with hyper/hypo-methylated promoters in cancers
DNA repair genes are frequently repressed in cancers due to hypermethylation of CpG islands within their promoters. In
head and neck squamous cell carcinomas at least 15 DNA repair genes have frequently hypermethylated promoters; these genes are ''XRCC1, MLH3, PMS1, RAD51B, XRCC3, RAD54B, BRCA1, SHFM1, GEN1, FANCE, FAAP20, SPRTN, SETMAR, HUS1,'' and ''PER1''.
About seventeen types of cancer are frequently deficient in one or more DNA repair genes due to hypermethylation of their promoters.
As summarized in one review article, promoter hypermethylation of the DNA repair gene ''
MGMT
MGMT () is an American rock band formed in 2002 in Middletown, Connecticut. It was founded by singers and multi-instrumentalists Andrew VanWyngarden and Benjamin Goldwasser, Ben Goldwasser.
Originally signed to Cantora Records by the nascent ...
'' occurs in 93% of bladder cancers, 88% of stomach cancers, 74% of thyroid cancers, 40%-90% of colorectal cancers and 50% of brain cancers. Promoter hypermethylation of ''
LIG4
DNA ligase 4 also DNA ligase IV, is an enzyme that in humans is encoded by the ''LIG4'' gene.
Function
DNA ligase 4 is an ATP-dependent DNA ligase that joins double-strand breaks during the non-homologous end joining pathway of double-stran ...
'' occurs in 82% of colorectal cancers. This review article also indicates promoter hypermethylation of ''
NEIL1'' occurs in 62% of
head and neck cancer
Head and neck cancer is a general term encompassing multiple cancers that can develop in the head and neck region. These include cancers of the mouth, tongue, gums and lips (oral cancer), voice box ( laryngeal), throat ( nasopharyngeal, orophary ...
s and in 42% of
non-small-cell lung cancer
Non-small-cell lung cancer (NSCLC), or non-small-cell lung carcinoma, is any type of epithelial lung cancer other than small-cell lung cancer (SCLC). NSCLC accounts for about 85% of all lung cancers. As a class, NSCLCs are relatively insensitiv ...
s; promoter hypermetylation of ''
ATM'' occurs in 47% of
non-small-cell lung cancer
Non-small-cell lung cancer (NSCLC), or non-small-cell lung carcinoma, is any type of epithelial lung cancer other than small-cell lung cancer (SCLC). NSCLC accounts for about 85% of all lung cancers. As a class, NSCLCs are relatively insensitiv ...
s; promoter hypermethylation of ''
MLH1
DNA mismatch repair protein Mlh1 or MutL protein homolog 1 is a protein that in humans is encoded by the ''MLH1'' gene located on chromosome 3. The gene is commonly associated with hereditary nonpolyposis colorectal cancer. Orthologs of human ...
'' occurs in 48% of squamous cell carcinomas; and promoter hypermethylation of ''
FANCB'' occurs in 46% of
head and neck cancer
Head and neck cancer is a general term encompassing multiple cancers that can develop in the head and neck region. These include cancers of the mouth, tongue, gums and lips (oral cancer), voice box ( laryngeal), throat ( nasopharyngeal, orophary ...
s.
On the other hand, the promoters of two genes, ''
PARP1'' and ''
FEN1'', were hypomethylated and these genes were over-expressed in numerous cancers. ''PARP1'' and ''FEN1'' are essential genes in the error-prone and mutagenic DNA repair pathway
microhomology-mediated end joining. If this pathway is over-expressed, the excess mutations it causes can lead to cancer.
PARP1 is over-expressed in tyrosine kinase-activated leukemias,
in neuroblastoma,
in testicular and other germ cell tumors,
and in Ewing's sarcoma,
FEN1 is over-expressed in the majority of cancers of the breast,
prostate,
stomach,
neuroblastomas,
pancreatic,
and lung.
DNA damage appears to be the primary underlying cause of cancer.
If accurate DNA repair is deficient, DNA damages tend to accumulate. Such excess DNA damage can increase
mutation
In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, ...
al errors during
DNA replication
In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all life, living organisms, acting as the most essential part of heredity, biolog ...
due to error-prone
translesion synthesis. Excess DNA damage can also increase
epigenetic
In biology, epigenetics is the study of changes in gene expression that happen without changes to the DNA sequence. The Greek prefix ''epi-'' (ἐπι- "over, outside of, around") in ''epigenetics'' implies features that are "on top of" or "in ...
alterations due to errors during DNA repair. Such mutations and epigenetic alterations can give rise to
cancer
Cancer is a group of diseases involving Cell growth#Disorders, abnormal cell growth with the potential to Invasion (cancer), invade or Metastasis, spread to other parts of the body. These contrast with benign tumors, which do not spread. Po ...
(see
malignant neoplasms
Cancer is a group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body. These contrast with benign tumors, which do not spread. Possible signs and symptoms include a lump, abnormal ...
). Thus, CpG island hyper/hypo-methylation in the promoters of DNA repair genes are likely central to progression to cancer.
See also
*
Eukaryotic transcription
*
Gene expression
Gene expression is the process (including its Regulation of gene expression, regulation) by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, proteins or non-coding RNA, ...
*
Transcriptional regulation
*
Cancer epigenetics
Cancer epigenetics is the study of epigenetics, epigenetic modifications to the DNA of cancer cells that do not involve a change in the nucleotide sequence, but instead involve a change in the way the genetic code is expressed. Epigenetic mecha ...
References
{{reflist, 30em
Gene expression
Non-coding RNA
Epigenetics
Cancer epigenetics
DNA
Medical regulation