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73 Cards in this Set
- Front
- Back
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molecular enhancer
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a region of DNA that positively regulates gene expression, often in a spatial and/or temporal specific manner. Also called a "cis-acting regulatory element." Binds DNA binding proteins (transcription factors) that regulate transcription
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in situ hybridization
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looking for expression of a specific gene using a labeled anti-sense RNA probe. The probe will bind to the complementary sequence in fixed embryos or tissues
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immunolocalization of protein expression
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detects protein; use an antibody to tag the protein of interest; amplify signal with additional probes or secondary antibody
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Experiment to analyze enahncers
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Use reporters
Steps: 1. isolate enhancer DNA fragments 2. clone fragments into DNA vector with general promoter and reporter gene 3. inject recombinant constructs into host embryos (make transgenic by insertion into germ line) 4. analyze spatial expression of reporter gene by staining enzyme or by fluorescence |
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Homeosis
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changes in segmental identity
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Genome browser
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illustrate the gene of interest in cartoon; shows conserved sequences (sequences are more highly conserved in exons vs. introns
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genomic mapping
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1. cut genome with restriction enzymes
2. clone in circular vectors 2. sequence each fragment and use overlapping sequences to piece them together 3. overlapping sequences are called contigs 4. order contigs into a linear sequence using paired end reads |
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whole genome shotgun sequencing
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1.based on piecing together contigs
2. look for regions that are 100% identical and link contigs into scaffolds using paired-end reads in a long insert vector |
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contigs
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contiguous DNA sequence
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scaffold
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super-contigs
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Physical map
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1. DNA fingerprint created by cutting different clones with a restriction enzyme and running the pieces on a gel
2. look for bands of identical size and use the number of identical pieces to find clones that overlap |
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strategy for ordered clone sequencing
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Steps:
1. order large insert clones by overlapping fingerprints to create a physical map 2. select clones with minimal overlap 3. divide into subclones 4. sequence subclones 5. assemble subclones to create the genome sequence |
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enhancer
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genetic locus that enhances the phenotype of another locus, a region of DNA that can activate gene expression, and a cis-regulatory element
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paired-end reads
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are at the ends of cloned inserts and can connect two contigs into a scaffold
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synteny
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situation in which genes are arranged in similar blocks in different species
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EST
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expressed sequence tags (sequence reads from both ends of a cDNA); used to annotate where exons are
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Identifying exons and introns in a gene of interest
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1. make cDNA
2. harvest mRNA through cloning 3. sequence entire clone and computationally align the cDNA sequence to the genomic DNA 4. allows you to ID where all the exons and introns are |
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open reading frame
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region of mRNA that codes for a protein
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mRNA
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RNA transcript after the removal of introns
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BLAST
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basic local alignment search tool
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homolog
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closely related genes in different organisms
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paralog
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genes related by gene duplication
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synteny
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the conserved order of orthologous sequences
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orthologs
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genes in which the same genetic locus has been inherited from a common ancestor
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finding enhancers
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non-coding, conserved regions can be used to find enhancers
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transposon
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mobile genetic element
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how a transposon inserts itself
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1. staggered cuts are made in the target DNA
2. a transposable element inserts itself into the DNA 3. staggered cuts leave short, ss pieces of DNA 4. replication of this ssDNA creates the flanking direct repeats |
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retrotransposons
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retrotransposon sequence is transcribed into RNA; undergoes reverse transcription to produce dsDNA, staggered cuts are made in the target DNA, retrotransposon integrates into host DNA at new site, replication fills in the gaps at the site of insertion and creates the flanking direct repeats
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point mutation
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alteration of a single base pair
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synonymous mutation
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altered codon specifies the same amino acid
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missense mutation (conservative)
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altered codon specifies a chemically similar amino acid
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missense mutation (non-conservative)
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altered codon specifies a chemically dissimilar amino acid
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nonsense mutation
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altered codon signals chain termination
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indel
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either an insertion/deletion
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single nucleotide polymorphism
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one nucleotide changes anywhere in the genome
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translocation
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a chunk of one chromosome is moved onto another chromosome
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reciprocal translocation
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rearrangement where two non-homologous chromosomes trade acentric fragments
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balanced translocation
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one that changes gene order but does not remove/duplicate DNA
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Robertsonian translocation
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rearrangement involving fusion of two acrocentric chromosomes
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metacentric chromosomes
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have centromeres in middle
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submetacentric
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off center centromeres which result in one longer and one shorter arm
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acrocentric
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centromeres near end
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Robertsonian translocation
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rearrangement involving the fusion of two acrocentric chromosomes
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comparative genomic hybridization
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used to detect duplications, deletions, and tandem amplifications in an individuals genome
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population genetics
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the study of genetic variation and how it changes in time and space
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Hardy-Weinburg equilibrium
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in the absence of disturbing forces, the amount of genetic variation remains constant generation after generation
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disturbing forces that can change genotype frequencies
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1. non-random mating
2. mutation 3. migration 4. selection 5. genetic drift |
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haplotype
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tightly linked polymorphisms not separated by historical meioses in a natural population; do not follow Mendel's second law because they are linked
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quantitative genetics
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the genetic analysis of complex traits
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continuous (quantitative or non-Mendelian trait)
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a continuous trait characteristic exhibits a range of phenotypes
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discontinuous trait
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exhibits only a few easily distinguished phenotypes (mendelian trait)
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meristic trait
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quantitative trait determined by multiple genetic and environmental factors and can be measured by whole numbers
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threshold traits
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measured by presence or absence
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polygenic inheritance
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refers to quantitative traits controlled by the cumulative effects of many genes
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frequency distribution
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shows the distribution of a trait within a population
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variance
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variability in a group of measurements
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quantitative trait loci
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chromosome regions containing a gene or genes that influence a quantitative trait
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experimental approach to finding a QTL
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1. cross animals with different phenotypes (or whatever you're looking at)
2. build genetic map 3. map OTL (short tandem repeats or SNPs are used as molecular markers) 4. clone genes to determine their function |
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Reression
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predicting the value of one variable if the value of the other is given
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regression coefficient
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slope of regression line
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heritability
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proportion of the total phenotypic variation that is due to genetic differences
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why is knowing heritability important?
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1. predict response to selection
2. determine contributions of genetics/environment for human disease |
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genetic-environmental interaction variance
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obtained when the effect of a gene depends on the specific environment in which it is found
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broad-sense heritability
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proportion of the phenotypic variance that is due to genetic variance (if H2 = 0, then none of the phenotypic variance is caused by genetic variance)
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narrow-sense heritability
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proportion of the phenotypic variance that is due to additive genetic variance (determines response to selection)
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breeder's equation
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predicts response to selection
R = h2 x S |
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pseudogene
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open reading frame or partial open reading frame that are nonfunctional or inactive due to mutations
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copy number variation
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segment of DNA that is 1 kb or greater and is present at a variable copy number in comparison with a reference genome
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segmental duplication
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a segment greater than 1 kb in size that occurs in two or more copies per haploid genome with the different copies sharing greater than 90% sequence identity
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whole-mount ISH
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detects mRNA expression in tissue
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fluorescent ISH
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detects specific DNA sequences in chromosomes in cells
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fiber FISH
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detects specific DNA sequences in chromosomes in cells at high resolution by stretching out chromosomes
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copy number variation
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deleted or duplicated regions of DNA is widespread in the human genome
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