The Genetics of Aging

DNA Repair Genes 2

A Table of the so far identified

Human DNA Repair Genes 

NER-related

 

CKN1 (CSA)

Cockayne syndrome; Needed for transcription-coupled NER
CKN1, ERCC6, XAB2

5q12.1

NM_000082

ERCC6 (CSB)

10q11.23

NM_000124

XAB2 (HCNP)

19p13.2

NM_020196

DDB1

Complex defective in XP group E
DDB1, DDB2

11q12.2

NM_001923

DDB2

11p11.2

NM_000107

MMS19L (MMS19)

Transcription and NER

10q24.1

NM_022362

 

Homologous recombination

 

RAD51

Homologous pairing

15q15.1

NM_002875

RAD51L1 (RAD51B)

Rad51 homolog

14q24.1

NM_002877

RAD51C

Rad51 homolog

17q23.2

NM_002876

RAD51L3 (RAD51D)

Rad51 homolog

17q12

NM_002878

DMC1

Rad51 homolog, meiosis

22q13.1

NM_007068

XRCC2

DNA break and crosslink repair
XRCC2, XRCC3

7q36.1

NM_005431

XRCC3

14q32.33

NM_005432

RAD52

Accessory factors for recombination
RAD52, RAD54L, RAD54B

12p13.33

NM_002879

RAD54L

1p34.1

NM_003579

RAD54B

8q22.1

NM_012415

BRCA1

Accessory factor for transcription and recombination, E3 Ubiquitin ligase

17q21.31

NM_007295

BRCA2

Cooperation with RAD51, essential function

13q13.1

NM_000059

SHFM1 (DSS1)

BRCA2 associated

7q21.3

NM_006304

RAD50

ATPase in complex with MRE11A, NBS1

5q23.3

NM_005732

MRE11A

3' exonuclease

11q21

NM_005590

NBS1

Mutated in Nijmegen breakage syndrome

8q21.3

NM_002485

MUS81

A structure-specific DNA nuclease
MUS81, MMS4

11q13.1

NM_025128

EME1 (MMS4L)

17q21.33

NM_152463

 

Non-homologous end-joining

 

G22P1 (Ku70)

DNA end binding
Ku70, Ku80

22q13.2

NM_001469

XRCC5 (Ku80)

2q35

NM_021141

PRKDC

DNA-dependent protein kinase catalytic subunit

8q11.21

NM_006904

LIG4

Ligase

13q33.3

NM_002312

XRCC4

Ligase accessory factor

5q14.2

NM_003401

DCLRE1C (Artemis)

Nuclease

10p13

NM_022487

XLF (Cernunnos, NHEJ1)

XRCC4-LIG4 interacting factor

2q35

NM_024782

 

Modulation of nucleotide pools

 

NUDT1 (MTH1)

8-oxoGTPase

7p22.3

NM_002452

DUT

dUTPase

15q21.1

NM_001948

RRM2B (p53R2)

p53-inducible ribonucleotide reductase small subunit 2 homolog

8q22.3

NM_015713

 

DNA polymerases (catalytic subunits)

 

POLB

BER in nuclear DNA

8p11.21

NM_002690

POLG

BER in mitochondrial DNA

15q26.1

NM_002693

POLD1

NER and MMR
POLD1, POLE1

19q13.33

NM_002691

POLE

12q24.33

NM_006231

PCNA

Sliding clamp for pol delta and pol epsilon

20p12.3

NM_002592

REV3L (POLZ)

DNA pol zeta catalytic subunit, essential function

6q21

NM_002912

MAD2L2 (REV7)

DNA pol zeta subunit

1p36.22

NM_006341

REV1L (REV1)

dCMP transferase

2q11.2

NM_016316

POLH

XP variant

6p21.1

NM_006502

POLI (RAD30B)

Lesion bypass

18q21.2

NM_007195

POLQ

DNA crosslink repair

3q13.33

NM_006596

POLK (DINB1)

Lesion bypass

5q13.3

NM_016218

POLL

Gap-filling during non-homologous end-joining

10q24.32

NM_013274

POLM

Gap filling during non-homologous end-joining

7p13

NM_013284

POLN (POL4P)

DNA crosslink repair?

4p16.3

NM_181808

 

Editing and processing nucleases

 

FEN1 (DNase IV)

5' nuclease

11q12.2

NM_004111

TREX1 (DNase III)

3' exonuclease
3' alternative ORF of the TREX1/ATRIP gene

3p21.31

NM_033629

TREX2

3' exonuclease

Xq28

NM_007205

EXO1 (HEX1)

5' exonuclease

1q43

NM_003686

SPO11

endonuclease

20q13.32

NM_012444

FLJ35220 (ENDOV)

incision 3' of hypoxanthine and uracil

17q25.3

NM_173627

 

Rad6 pathway

 

UBE2A (RAD6A)

Ubiquitin-conjugating enzyme

Xq24-q25

NM_003336

UBE2B (RAD6B)

Ubiquitin-conjugating enzyme

5q31.1

NM_003337

RAD18

E3 ubiquitin ligase

3p25.3

NM_020165

UBE2V2 (MMS2)

Ubiquitin-conjugating complex
UBE2V2, UBE2N

8q11.21

NM_003350

UBE2N (UBC13)

12q22

NM_003348

 

Chromatin Structure

 

H2AFX (H2AX)

Histone, phosphorylated after DNA damage

11q23.3

NM_002105

CHAF1A (CAF1)

Chromatin assembly factor

19p13.3

NM_005483

 

Genes defective in diseases associated with sensitivity to DNA damaging agents

 

BLM

Bloom syndrome helicase

15q26.1

NM_000057

WRN

Werner syndrome helicase / 3' - exonuclease

8p12

NM_000553

RECQL4

Rothmund-Thompson syndrome

8q24.3

NM_004260

ATM

ataxia telangiectasia

11q22.3

NM_000051

Fanconi anemia

 

FANCA

Involved in tolerance or repair of DNA crosslinks
FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCL

16q24.3

NM_000135

FANCB

Xp22.31

NM_152633

FANCC

9q22.32

NM_000136

FANCD2

3p25.3

NM_033084

FANCE

6p21.31

NM_021922

FANCF

11p14.3

NM_022725

FANCG (XRCC9)

9p13.3

NM_004629

FANCL

2p16.1

NM_018062

FANCJ (BRIP1, BACH1)

BRCA1-associated DNA helicase

17q23.2

NM_032043

FANCM

DNA helicase and possible nuclease in the XPF-Hef-Mus81 family

14q21.3

XM_048128

 

Other identified genes with a suspected DNA repair function

 

DCLRE1A (SNM1)

DNA crosslink repair

10q25.3

NM_014881

DCLRE1B (SNM1B)

Related to SNM1

1p13.2

NM_022836

RPA4

Similar to RPA2

Xp21.33

NM_013347

APTX (aprataxin)

Processing of DNA single-strand interruptions

9p21.1

NM_175073

NEIL3

Resembles NEIL1 and NEIL2

4q34.3

NM_018248

RECQL (RECQ1)

DNA helicase

12p12.1

NM_002907

RECQL5

DNA helicase

17q25.1

NM_001003715

HEL308

DNA helicase

4q21.23

NM_133636

RAD52B (RDM1)

Similar to RAD52

17q12

NM_145654

 

Other conserved DNA damage response genes

 

ATR

ATM- and PI-3K-like essential kinase

3q23

NM_001184

RAD1

PCNA-like DNA damage sensors
RAD1, RAD9, HUS1

5p13.2

NM_002853

RAD9A

11q13.2

NM_004584

HUS1

7p12.3

NM_004507

RAD17 (RAD24)

RFC-like DNA damage sensor

5q13.2

NM_002873

CHEK1

Effector kinases
CHEK1, CHEK2

11q24.2

NM_001274

CHEK2

22q12.1

NM_007194

TP53

Regulation of the cell cycle

17p13.1

NM_000546

ATRIP (TREX1)

ATR-interacting protein
5' alternative ORF of the TREX1/ATRIP gene

3p21.31

NM_130384

 

Genes Associated with Aging

‘A great deal of genes are involved in the process of aging’

The above statement might seem simplistic, but it is essentially true.  A large number of genes play a role in modulating the metabolic processes which are involved in the eventual degradation of DNA and cellular structures.  Some of these genes are involved with the processes of DNA repair, some with managing the levels of free radicals and some with regulating the speed of metabolism itself.  Together the varying rates at which these genes are expressed, results in an overall affect of the longevity of the organism itself.

Below is a list of the currently confirmed genes that have been associated through experimentation with cellular longevity.  They all have there own mechanisms of action and several of them will be discussed in detail in this section of the site.  Some particularly have been found to play extremely important roles in the speed of aging and therefore the eventual lifespan of the organism.  

Lifespan and general vigour have been increased in a number of species.  From the nematode Caenorhabditis Elegans, the fruit fly Drosophila Melanogaster and the mouse Mus musculus, by the modulation of certain of these genes.  In some cases longevity has been increased by a substantial degree!

Confirmed Longevity Genes

 

Podospora

Saccharomyces

Caenorhabditis

Drosophila

Mouse

grisea

LAG1

daf-2

sod1

Prop-1

 

LAC1

age-1/daf-23

cat1

p66shc

 

RAS1

daf-18

mth

 

 

RAS2

akt-1/akt-2

 

 

 

PHB1

daf-16

 

 

 

PHB2

daf-12

 

 

 

CDC7

ctl-1

 

 

 

BUD1

old-1

 

 

 

RTG2

spe-26

 

 

 

RPD3

clk-1

 

 

 

HDA1

mev-1

 

 

 

SIR2

 

 

 

 

SIR4-42

 

 

 

 

UTH4

 

 

 

 

YGL023

 

 

 

 

SGS1

 

 

 

 

RAD52

 

 

 

 

FOB1

 

 

 

The major genetic model organisms used in aging research are the filamentous fungus ('Podospora anserina'), bakers' yeast ('Saccharomyces cerevisiae'), the soil roundworm ('Caenorhabditis elegans'), the fruit fly ('Drosophila melanogaster'), and the mouse ('Mus musculus').  http://en.wikipedia.org/wiki/Longevity_genes

DNA Damage and Repair

DNA is the mechanism by which all of our physical characteristics and an increasingly large number of proven mental and social characteristics are passed on from one generation to the next.  This applies to all living organisms, with the exception of a few basic forms, which use RNA to pass on their genetic information and thus characteristics, from one generation to the next.

As the genetic information is passed on between parent and offspring and during the course of an individual organisms lifetime, damage can and does occur to the DNA and thus to the genes.  This damage as it occurs can result (depending also on a number of prevailing environmental factors) in the evolution of a species.  This is broadly done in general accordance with the principles of Charles Darwin’s Natural Selection.  When this damage occurs in a cumulative way through the course of an individual organisms lifetime however, the process eventually results in aging of the cells, tissues and organs, resulting eventually in cellular senescence and death.

A number of mechanisms have evolved in order to repair the damage to an organisms DNA.  The purpose of this section of the site is to outline the different types of damage that can occur to DNA and what mechanisms are in place to limit the affects of this damage and to repair damage once it inevitably does occur.

So before outlining the state of the art knowledge on this very broad subject, here first are a few definitions.

Definition of DNA

Deoxyribonucleic acid; a nucleic acid that consists of two long chains of nucleotides twisted together into a double helix and joined by hydrogen bonds between complementary bases adenine and thymine or cytosine and guanine; it carries the cell's genetic information and hereditary characteristics via its nucleotides and their sequence and is capable of self-replication and RNA synthesis.  http://www.answers.com/topic/dna

Note that where animal research is concerned, a distinction needs to be made between the DNA contained in the Nucleus of the cell, coiled up around beadlike histone proteins and coiled further into chromosomes and the DNA of the Mitochondria.  To aid in this distinction, please find below a definition of Mitochondrial DNA (mtDNA).

Definition of Mitochondrial DNA

Mitochondrial DNA (mtDNA) is DNA that is located in mitochondria. This is in contrast to most DNA of eukaryotic organisms, which is found in the nucleus. It is often stated that 100% of the mtDNA contribution to a zygote is inherited from the mother, although this is controversial and may not be true for all organisms.

Unlike most of the cell, the function of which is defined by nuclear DNA, mitochondria have their own DNA and are assumed to have evolved separately. Human mitochondrial DNA consists of 5-10 rings of DNA and appears to carry 16,568 base pairs with 37 genes (13 proteins, 22 tRNAs and two rRNAs) which are concerned with the production of proteins involved in cellular respiration. However many proteins found in the mitochondria are encoded by nuclear DNA: some, if not most, are thought to have been originally part of the mitochondrial DNA but have since been transferred to the nucleus during evolution.

There is little change in the mtDNA from parent to offspring, unlike nuclear DNA which changes by 50% each generation. Since the mutation rate is easily measured, mtDNA is a powerful tool for tracking matrilineage, and has been used in this role for tracking many species back hundreds of generations.  http://en.wikipedia.org/wiki/Mitochondrial_DNA

A Summary of DNA Damage and Repair

DNA repair is an integrated process whereby damage to the DNA of the cells genome is identified and then corrected.  This DNA damage can occur as a result of a large number of normal metabolic activities.  For example free radicals such as Hydrogen Peroxide H2O2 produced during cellular respiration can damage DNA quite severely.  Also a variety of environmental factors, such as UV radiation and carcinogenic chemicals can and do result in damage to DNA.

This damage can result in lesions that may prevent the cell from being able to transcribe its genes, resulting in a loss of functionality of the cell.  Other lesions can cause damage which does not affect the functionality of the cell itself, but does have an affect on any daughter cells that are produced following Mitosis.  Perhaps resulting in the daughter cells functioning abnormally or being unable to survive.

Fortunately there are a number of DNA repair processes which strive to limit the affects of this damage.  DNA repair is not perfect however.  This means that over time the repair process will fail and a cell will enter one of the following states.

1.  Apoptosis or cellular suicide.  This is a process by which the cell destroys itself
2.  Senescence.  A process whereby the cell becomes irreversibly dormant
3.  Uncontrolled cellular division.  This can result in tumor formation and cancer

The effectiveness of the DNA repair mechanisms in a species have a direct relation to the average and maximum life expectancy of that species.

Articles

  • I think it might be worth defining on this site (just so there is no confusion) what exactly the science of Gerontology is.

    The subject known as Gerontology is the study of the process of aging throughout the lifespan of an individual. This multi-disciplinary subject analyses a variety of aspects of aging, including the physical, mental and social changes in individuals as they grow older. Professionals from a variety of diverse, but interconnected fields are known collectively as gerontologists.

    Gerontology covers such varied subjects as the effects of our aging population on society, including the financial effects of pensions, health insurance and retirement planning. How society itself views the elderly is also encompassed in this field.

    Gerontology distinguishes itself from geriatrics, the branch of medicine that studies the diseases of the old.

    12:18 10 October 2007
  • There are several other ways that are being looked into that may offer may anti-aging/life extension benefits that have not been mentioned as yet. IGF-1 has shown to be extraordinarily effective in reversing the aging process (up to 10X more effective than HGH). Resveratrol (found in red grape skins and hence red wine) has shown much promise in many studies; to the extent that several MIT researches doing one of the studies started supplimenting with it. Folate and B12 taken daily over a few months has been shown to drastically reduce the damage/mutation that can occur to DNA.

    With regard to calorie restriction Many studies suggest that it is not infact the calorie restriction as previously thought but rather maintaining low insulin levels, which happens to be a by product. So it is as much about what you eat as how much you eat. You could still each 3000 calories a day as long as they were from foods that didnt spike your insulin levels and mess with your insulin sensetivity ie not eating many simple carbohydrates etc

    There is also the energetic side of body or life force or call it what you will that when boosted has been shown to reverse chronic illness and aging with no form of supplements etc. Most of the centurian populations like the hunza etc incorporated some sort of meditation or practice that maintained their life force either knowingly or otherwise along with a good diet, exercise, sun etc and low stress.

    On a final note the human body is so remarkable and truely an amazing creation and we are still only so limited in our understanding of it and how it really works that rather than mess with it and start trying to fix or add this or that or think we can make part of it better we should instead address the cause of most of these problems. We drive ourselves and our bodies into the ground eat rubbish etc and program ourselve with mindless entertainment and wonder why we are falling apart and expect to be able to take a few pills and make it all better.

    We are creating and living in a society that is becoming void of any real sustanance whether it be nutritional, emotional or intellecutal. I am not pretending that i have all the answers but i know that if we keep heading in this direction i wouldnt want to live forever even if it were possible. What you do with your life is probably more important than how long it is. In any case given the right environment the body will flourish and the fact that it is still doing as well as it is despite what it is now subjected to is nothing more than a testement to how great it actually is.

    Rhonda Watson

    12:07 17 September 2007