DNA Damage Repair: Guardian of the genome and its

association with diseases

Meenakshi Anurag, PhDLester and Sue Smith Breast Center

Baylor College of medicine

Background

DNA damage repair

Sources

Types mechanism

Aberrations & instability

Diseases

Genome browser

Mutational database

Integrating genomic & clinical info

Bioinformatics

Canonical DNA repair pathways

Types of single-strand repair mechanisms

• Direct Reversal

• Base Excision Repair

• Nucleotide Excision Repair

• Mismatch Repair

Hoeijmakers, 2009.DNA Damage, Aging, and Cancer. 1483.

Direct Reversal Repair

Direct reversal repair is a mechanism of repair where the damaged area or lesion is repaired directly by

specialized proteins in our body. It is the simplest form of DNA repair and also, the most energy efficient

method. It does not require a reference template unlike the other single-strand repair mechanism.

Moreover, it does not involve the process of breaking the phosphodiester backbone of the DNA.

An example of reversible DNA damage repairable via

Direct Repair is Alkylation which can be repaired via direct

removal of the Alkyl groups.

Alkylating agents are carcinogens that is capable of alkylating DNA in our body. It is widely used to create medicines (e.g., treatment of leukemia, tumors ) and industrial chemicals.Alkylated DNA bases resulted in improper base pairing

and ultimately, lead to cell death.

An example of Alkylation is Methylation which is the addition of a methyl group (CH3) to a guanine (G) nucleotide. This resulted in a complementary pairing to thymine (T) instead of cytosine (C).

Direct Reversal Repair

Base excision repairBase Excision Repair (BER) is a repair mechanism that corrects damaged DNA by identifying damaged bases and replacing damaged bases with the correct nucleotide.The correct nucleotide can be identified by referencing the complementary strand in the DNA pair based on the Watson-Crick DNA base pairing.DNA bases are constantly subjected to damages like deamination or alkylation. The damaged base is often called the "Abasic Site" or "AP site".Damaged bases are first identified by DNA glycosylases. DNA glycosylases are enzymes that are capable of detecting initial lesions of DNA.Upon detection, glycosylases will enlist the help of AP endonuclease, enzymes that can identify and remove AP sites from the DNA phosphodiester backbone so as to allow DNA polymerase to initiate repair synthesis.With the removal of damaged bases, DNA polymerase synthesize the correct nucleotide to fill the region. Lastly, DNA ligase helps to close and seal the bond

Nucleotide Excision Repair

While base excision repair is a specialized type of repair that identifies damages to DNA bases, nucleotide excision repair (NER) is a generic type of excision repair mechanism

NER detects damages based on the overall structure integrity of the DNA double helix. This allows NER to be able to support and repair multiple types of DNA damage.

NER recognizes distortion in the double helix with the aid of damage surveillance protein complexes like XPC–RAD23B

Bergink S, Toussaint W, Luijsterburg MS, Dinant C, Alekseev S, Hoeijmakers JH, Dantuma NP, Houtsmuller AB, Vermeulen W, 2012

• Helicases encoded by the XPB and XPD gene opens the region around the damaged DNA base, creating a bigger distortion.

• This process helps to further verify the occurrence of the DNA damage.

• Upon confirmation of damage, incision is performed by endonuclease enzymes like XPF gene to remove the region of damage base(s) and its surrounding neighbors.

• With the removal of damaged bases, DNA polymerase synthesize the correct nucleotide to fill the region. Lastly, DNA ligase helps to close and seal the bond.

Nucleotide Excision RepairDamage detection

Damage Verification

Damage Removal

Replacement

Mismatch Repair

While DNA replication is able to achieve an extremely high rate of accuracy with an error rate estimated to be 10–7 to 10–8

(Thomas A. Kunkel, 2004), an occurrence of an incorrect base requires an immediate repair of the mismatch base pairing. This repair mechanism is called Mismatch Repair (MMR)

During replication, an event known as proof-reading helps to monitor any mismatch pairing. As the daughter strand is only methylated after the proof-reading is completed, the DNA repair enzymes are able to determine the daughter strand from the parent strand on the event of an mismatch pairing identification.

Mismatch Repair

Double Strand breaks

There are 2 types of mechanism which repairs this type of double strand DNA

damage, namely homologous recombination (HR) and non-homologous end

joining (NHEJ). The latter is more dangerous as although it repairs the break, some

information of nucleotides are usually lost at repair site and it is almost impossible

to replicate back the original nucleotide information.

Whether homologous recombination or NHEJ is used to repair double-strand

breaks is largely determined by the phase of cell cycle. NHEJ occurs mainly in

G0/G1 and early S phase, whereas HR occurs during the late S and G2 phases

(Takata et al.,1998). More will be discussed in the following sections.

Homologous Recombination

This mechanism of repair only takes place only when 2 DNA double stranded

(duplex) contains extensive region of homology. As a result of this, the

damaged DNA can access to the homologous area of duplex DNA and does a

complementary pair of base pairing.

Homologous recombination repairs DNA before the cell enters M phase of

mitosis. It occurs during and shortly after DNA replication, in the S and G2

phases of the cell cycle as shown below. This is when duplex DNA strands are

more easily available and close to each other.

HR

Non-homologous end joining

Non-Homologous End Joining (NHEJ) is a mechanism that repairs the double strand DNA damage by ligating the broken ends without the need for a template or homologous region. As a result of this information at the break cannot be completely retrieved.

NHEJ typically utilizes short homologous DNA sequences called microhomologies to guide repair. These microhomologies are often present in single-stranded overhangs on the ends of double-strand breaks. When the overhangs are perfectly compatible, NHEJ usually repairs the break accurately. Imprecise repair leading to loss of nucleotides can also occur, but is much more common when the overhangs are not compatible. Inappropriate NHEJ can lead to translocations and telomere fusion, hallmarks of tumor cells.

NHEJ

Summary of DNA damage repair mechanisms

When DNA repair fails

Genomic aberrations & genomic instability

Different types of mutations

Point Mutations

Wiki

Types of chromosomal rearrangements

Abdullah K. Alqallaf, Fuad M. Alkoot and Mash’el S. Aldabbous (2013)

Overview of the major mechanisms to maintain genomic stability during the cell cycle.

Zhiyuan Shen J Mol Cell Biol 2011;3:1-3

Genomic Instability

Rao & Yamada, 2013

DNA damage repair & association with diseases

Role of the DNA damage response in the development of cancer.

How DNA damage response pathways may lead to cancer?

DDR mutations in cancer

Bioinformatics resources

Resources

Resources

Catalogue of somatic mutations in cancer

cBioportal

Integrating genomic and clinical data

MMRdefMMRComp

Haricharan et al, in review Do not reproduce

We are still learning!

Thanks