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DNA Repair, Recombination Genome Instability

Lichun Jiang, Ph.D

Laboratory of Dr. Rui Chen

Baylor College of Medicine

Molecular Biology Refresher Course With Bioinformatics 2014 Sep 19, 2014

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DNA Repair, Recombination Genome Stability

Background Lecture (45min) Bioinformatics Lecture (45min)

DNA as Genetics Information Carrier

http://micro.magnet.fsu.edu/cells/nucleus/chromatin.html

1, Replication 2, Transcription

DNA is Packed in Chromatin Structure

Source of DNA damage

• Reactive oxygen species

• Replication errors

• Transcription replication collision

• Spontaneous reactions

• UV radiation

• X-ray

• Mutagenic chemical

• Virus

Endogenous source Exogenous source

Modified from http://www.genomic-instability.org/

Consequence of DNA Damage

DNA repair

Cell cycle arrest (Apoptosis) Mutation(Aging, Genetic Disease and Cancer)

DNA damage

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DNA Repair

• Direct reversal

• Single strand damage repair

• Double strand break repair

Direct Reversal

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Single Strand Damage Repair

• Mismatch Repair (MMR) --undamaged bases(replication and recombination errors)

• Base excision repair (BER) –Damaged but non-bulky bases (oxidized, methylated)

• Nucleotide excision repair (NER) –Bulky, helix-distorting lesions(pyrimidine dimers)

Mismatch Repair

Key components:

MutS- recognizes mismatch

MutL- couples mismatch recognition

by MutS to down-stream steps

MutH- generated a nick at the newly synthesized

strand

http://cmgm.stanford.edu/

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Base Excision Repair

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Nucleotide Excision Repair

http://www.web-books.com/MoBio/Free/Ch7G.htm

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Double Strand Break Repair

• Homologous Recombination(HR)

• Non-Homologous Ending Joining (NHEJ)

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Homologous Recombination

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Non-homologous Ending Joining(NHEJ)

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Mutation Rate

Annu Rev Genomics Hum Genet. 2014 Jun 5

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Catarina D. Campbell, Evan E. Eichler Properties and rates of germline mutations in humans. Trends in Genetics 2013, Volume 29, issue 10, p575-584

Average Number of Mutations of Each Type of Variant Per Birth

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Common Mechanisms Leading to Biases in Mutation

Catarina D. Campbell, Evan E. Eichler Properties and rates of germline mutations in humans. Trends in Genetics 2013, Volume 29, issue 10, p575-584

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G

C

Glu

(d) Run-on mutation

G

C

(a) Silent mutation

Point Mutation

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Sequence Conservation Corresponds

to Intolerant Positions

Ng P C , and Henikoff S Genome Res. 2001;11:863-874

Cold Spring Harbor Laboratory Press

Rare Variants vs Common Variants

Kaiser J. Science 2012 Nov 23;338(6110):1016-7

Allele Frequency is a Good Predict of Function

Marth et al. Genome Biology 2011 12R84

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Informatics

• Identifying genes and mutations associated with a inheritable disease(OMIM, dbSNP, HGMD, LOVD)

• Tell minor allele frequency in different ethnicity group etc (Hapmap, 1000 Genome)

• Function predition of a missen variant (SIFT) • Tell whether a variant is ever seen in tumor

tissues (COSMIC) • Embracing the revolution brought by Next

Generation Sequencing(NGS)

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Search for genes relevant to USHER Syndrome type2 in OMIM

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USHER Syndrome type2 in OMIM

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Description of USH2A gene in OMIM

Table view of variants

View variants in Ensembl

View variants in dbSNP

Concepts in HapMap Project

2014/9/18 Nature 426, 789-796 (18 December 2003) |

HapMap is about common SNPs!

HapMap project website

Search for USH2A gene

Check frequency of SNPs

Download frequency data

2014/9/18

1000 genome

• A deep catalog of human genetic variation

• Low coverage whole genome and exome sequencing

• phase 3: 2535 individuals from 26 different populations

2014/9/18

1000 genome browser

SNPs in USH2A in 1000 genome

2014/9/18

Function prediction of missense variants

2014/9/18

Explore SIFT/PROVEAN

2014/9/18

Cosmic: catalog of somatic mutations

TP53 in COSMIC

Embracing the Revolution Brought by NGS

2014/9/18

My contact:

lchjiang@gmail.com

Thank you!