Targeted Genomics and Transcriptomics
A collection of methods that employ a purification step to selectively enrich for specific DNA/RNA species before sequencing.
What is targeted sequencing?
A mutation/abnormality that is present in all cells, either inherited or de novo?
What are constitutional/germline mutations?
This was a genome editing technology typically used in forward genetic screens (from phenotype to genotype).
What is chemical mutagenesis?
This is the definition of a transgenic animal.
What is an animal carrying a foreign gene(s) introduced by recombinant technology?
This is a mutation that normally results in a nonfunctional or null allele.
What is a knock-out mutation?
This is the basic methodology of how hybridization-based capture works.
What is:
1. hybridization of biotin-labeled antisense probes with their target
2. incubation with streptavidin-coated beads
3. bead capture includes only biotin-tagged targets
This is the class of cancer gene that is usually over activated in cancers.
What is an oncogene?
This is the endonuclease used to introduce double-strand breaks to DNA with zinc fingers and TALE repeats.
What is Fok1?
This is what you would use to express a trans gene in a specific tissue or cell type.
What is a tissue specific promoter?
These are examples of agents that can be used to induce trans gene expression.
What is tamoxifen (Tamoxifen-inducible promoter) or doxycycline (tetracycline-inducible promoter)?
This is how proteins are cross linked to DNA in ChIP-seq.
What is formaldehyde?
The hypothesis that cancer predisposition is dominantly inherited, but at the cellular level it is recessive.
What is Knudson's two-hit hypothesis?
What is a short guide RNA (sgRNA)?
This is the strategy of the Cre-Lox system.
1. The gene/exon of interest is flanked by loxP sites ("floxed") in mouse A
2. Mouse B contains a Cre gene (driven by either ubiquitous or tissue-specific promoter)
3. Mouse A is mated with Mouse B --> cells in progeny mice that express Cre will inactivate the floxed gene
These are two DNA repair pathways activated by double-strand DNA breaks.
What is non-homologous end joining (NHEJ) and homology-directed repair (HR)?
This is how you would determine an enriched region in your CLIP- or ChIP-seq data.
What is peak calling, which is where localized signal enrichment/read density is compared to an input control?
These are often the typical functions of tumor suppressor genes.
What is cell growth inhibition, DNA damage repair, apoptosis mechanisms, etc.?
These are two technologies employing targetable nucleases where target specificity is achieved through protein-DNA interactions.
What are zinc finger nucleases (ZFNs) and TALENs?
This is a description of the Tet-On system.
Transcription of the TRE-regulated target gene is stimulated by rtTA only in the presence of Doxycycline.
These are three common mechanisms of inactivation of tumor suppressor genes.
What are point mutations, chromosome deletion/mitotic recombination, and promoter hypermethylation?
What is a genome-wide CRISPR screen?
This is a description of the genetic event that is loss of heterozygosity.
This is a short genomic sequence located at the 3' end of the target sequence that must be present for Cas9 to be active.
What is a photospacer adjacent motif (PAM)?
This is a description of the Tet-Off system.
Transcription of the TRE-regulated target gene is activated by the presence of tTA. When doxycycline is introduced, tTA cannot activate target gene transcription and the gene is "turned off"
In a genome-wide CRISPR screen, this is what increased sgRNA abundance signal indicates.
What is that loss of the target gene improves cell survival under the given condition?