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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
