BCH5413 Exam 2 Questions and Answers
RNA-seq - ANSWER-sequencing all RNA in a cell type/tissue
CAGE - ANSWER-cap analysis of gene expression; capture of all 7mG capped RNAs
followed by sequencing of short tag adjacent to cap; identifies TSS
RNA-PET - ANSWER-paired end tags; simultaneous capture of capped,
polyadenylated RNAs; indicative of full length mRNA
siRNA - ANSWER-derived from long dsRNA sequence; bound to and cut up by Dicer
into small ss sequences, forms complex with Ago for sequence specific binding to
mRNA and clevage; requires some degree of homology
miRNA - ANSWER-formed from 70nt shRNA; Drosha complex gives it sticky ends
before exiting nucleus, bound to and cut up by Dicer into small ss sequences, forms
complex with Ago for sequence specific binding to mRNA for
transciptional/translational repression; homology not required
RISC - ANSWER-RNA induced silencing complex; associates with miRNA or siRNA
miR 1-1 - ANSWER-gene that encodes single miRNA
DCGR8/Drosha Complex - ANSWER-recognizes hairpin of miRNA precursor; gives it
2-base, 3' sticky end which is recognized by Exportin 5 for export from nucleus
TRBP/Dicer Complex - ANSWER-recognizes pre miRNA; processes to yield 21-23bp
dsRNA fragment with 2bp 3' sticky ends
Ago-Family Protein - ANSWER-binds to ss miRNA; forming miRNP inhibits
translation of mRNAs
Mechanisms for Translational Repression by miRNA - ANSWER-1) repress initiation
2) de-capping/deadenylation
3)prevent ribosome assembly
4)Inhibit translation, post-initiation
Miravirsen - ANSWER-Drug targetting miR-122 which stabilizes viral mRNA in HepC
Mechanisms of siRNA-Mediated mRNA degradation - ANSWER-siRNA RISC catalyzes
endonuclease clevage of target mRNA
siRNA KD Experiments - ANSWER-1)direct application of dsRNA oligont
2)insertion of an siRNA expression vector
lncRNA - ANSWER-long, non-coding RNA; similar to mRNA but doesnt encode for
proteins; >200nt in length; lower expression than coding mRNAs
,Mechanisms of lncRNA gene regulation - ANSWER-1) production of miRNAs
2)Interactions with PRC2
3) Interactions with coregulators
4)TF Decoy
5)miRNA sponge
6)STATU1-Mediated mRNA decay
ENCODE - ANSWER-identification and analysis of functional elements in 11% of the
human genome (2007); analyzed 147 different cell lines (2013)
ChIP-Seq - ANSWER-chromatin immunoprecipitation followed by DNA sequencing
DNase-seq - ANSWER-DNase I digestion of chromatin followed by isolation of
DNase-digested DNA fragments and DNA sequencing; Identifies DNase HS sites
(i.e. regulatory regions)
FAIRE-seq - ANSWER-formaldehyde-assisted isolation of regluatory regions;
another method for identifying DNA sequences with regulatory function by enriching
for nucleosome-depleted regions of chromatin
RRBS - ANSWER-reduced representation bisulfite sequencing; determines the
methylation levels of individual cytosines in a defines subportion of a genome of
interest
GWAS - ANSWER-genome-wide association studies; results typically fall within
these non-coding regions, suggesting that many genetic variations associated with
disease fall within these non-coding regions
Enhancer RNAs - ANSWER-both adenylated and polyadenylated; chromatin
signatures of eRNA regulatory regions distinct from regulatory regions of genes
SMGs - ANSWER-Significantly mutated genes; cancer related genes involved in
diverse cellular functions and tumor-type-specific mutations; targets for gene
therapy
TILs - ANSWER-Tumor infiltrating lymphocytes; frequently contained within human
melanoma,; recognize autologous tumor; given back to patient for immunotherapy
WES - ANSWER-Tumor Whole Exome Sequencing
Tumor-Specific Mutations - ANSWER-by definition, confined to the tumor;seen as
foreign by the immune system and therefore likely to be immunogenic
Tandem Minigene - ANSWER-string of minigenes encoding the mutated AA flanked
by 12 AAs
Minigenes - ANSWER-sections of DNA encoding tumor non-synonymous point
, mutations
G1 Phase - ANSWER-gap/growth phase 1; cell has 2n chromosomes; increase in
RNA and protein synthesis; prepares for S Phase; DNA damage repaired
S Phase - ANSWER-DNA synthesis phase; each parental chromosome is duplicated
to produce 2 identical sister chromatids
G2 Phase - ANSWER-gap/growth phase 2; cells have 4n chromosomes; guards
entry into mitosis, gives time to ensure replication is complete, allows for cell
growth
M Phase - ANSWER-Mitotic phase; sister chromatids are equally distributed to each
daughter cell
G0 Phase - ANSWER-quiescence (resting state); little protein or DNA synthesis
unless given external signal
Prophase - ANSWER-replicated chromosomes condense and become visible;
centrosome is duplicated; mitotic spindle forms
Prometaphase - ANSWER-Nuclear envelope breakdown; spindle microtubules attach
to kinetochore at centromere; chromosomes begin moving
Metaphase - ANSWER-Microtubule attachment to chromosomes complete;
Condensed chromosomes aligned along mitotic spindle midplane
Anaphase - ANSWER-APC activates and cohesins are degraded; sister chromatids
are partitioned; shortening of spindle microtubules pulls separated chromatids
towards opposite ends of cell
Telophase - ANSWER-Mitotic cyclins degraded by APC; daughter nuclei form,
chromosomes decondense and cell begins to divide; contractile ring forms
Cytokinesis - ANSWER-Contractile ring forms clevage furrow; Actual splitting of cell
into two daughter cells
cdc Mutants - ANSWER-Cell division cycle yeast mutants; yeast mutants used to
explore regulation fo synthesis activation and destruction of regulatory proteins
Checkpoints - ANSWER-surveillance mechanisms used to ensure proper DNA
replication and chromosome segregation; mainly act by controlling cdk activity
MPF - ANSWER-mitosis promoting factor; protein-based signal that sends cells into
mitosis; composed of 2 proteins - Cdk1 and cyclin B which associate to form active
MPF complex
Cdk1 and Cyclin - ANSWER-Associate together to form active MPF signal
RNA-seq - ANSWER-sequencing all RNA in a cell type/tissue
CAGE - ANSWER-cap analysis of gene expression; capture of all 7mG capped RNAs
followed by sequencing of short tag adjacent to cap; identifies TSS
RNA-PET - ANSWER-paired end tags; simultaneous capture of capped,
polyadenylated RNAs; indicative of full length mRNA
siRNA - ANSWER-derived from long dsRNA sequence; bound to and cut up by Dicer
into small ss sequences, forms complex with Ago for sequence specific binding to
mRNA and clevage; requires some degree of homology
miRNA - ANSWER-formed from 70nt shRNA; Drosha complex gives it sticky ends
before exiting nucleus, bound to and cut up by Dicer into small ss sequences, forms
complex with Ago for sequence specific binding to mRNA for
transciptional/translational repression; homology not required
RISC - ANSWER-RNA induced silencing complex; associates with miRNA or siRNA
miR 1-1 - ANSWER-gene that encodes single miRNA
DCGR8/Drosha Complex - ANSWER-recognizes hairpin of miRNA precursor; gives it
2-base, 3' sticky end which is recognized by Exportin 5 for export from nucleus
TRBP/Dicer Complex - ANSWER-recognizes pre miRNA; processes to yield 21-23bp
dsRNA fragment with 2bp 3' sticky ends
Ago-Family Protein - ANSWER-binds to ss miRNA; forming miRNP inhibits
translation of mRNAs
Mechanisms for Translational Repression by miRNA - ANSWER-1) repress initiation
2) de-capping/deadenylation
3)prevent ribosome assembly
4)Inhibit translation, post-initiation
Miravirsen - ANSWER-Drug targetting miR-122 which stabilizes viral mRNA in HepC
Mechanisms of siRNA-Mediated mRNA degradation - ANSWER-siRNA RISC catalyzes
endonuclease clevage of target mRNA
siRNA KD Experiments - ANSWER-1)direct application of dsRNA oligont
2)insertion of an siRNA expression vector
lncRNA - ANSWER-long, non-coding RNA; similar to mRNA but doesnt encode for
proteins; >200nt in length; lower expression than coding mRNAs
,Mechanisms of lncRNA gene regulation - ANSWER-1) production of miRNAs
2)Interactions with PRC2
3) Interactions with coregulators
4)TF Decoy
5)miRNA sponge
6)STATU1-Mediated mRNA decay
ENCODE - ANSWER-identification and analysis of functional elements in 11% of the
human genome (2007); analyzed 147 different cell lines (2013)
ChIP-Seq - ANSWER-chromatin immunoprecipitation followed by DNA sequencing
DNase-seq - ANSWER-DNase I digestion of chromatin followed by isolation of
DNase-digested DNA fragments and DNA sequencing; Identifies DNase HS sites
(i.e. regulatory regions)
FAIRE-seq - ANSWER-formaldehyde-assisted isolation of regluatory regions;
another method for identifying DNA sequences with regulatory function by enriching
for nucleosome-depleted regions of chromatin
RRBS - ANSWER-reduced representation bisulfite sequencing; determines the
methylation levels of individual cytosines in a defines subportion of a genome of
interest
GWAS - ANSWER-genome-wide association studies; results typically fall within
these non-coding regions, suggesting that many genetic variations associated with
disease fall within these non-coding regions
Enhancer RNAs - ANSWER-both adenylated and polyadenylated; chromatin
signatures of eRNA regulatory regions distinct from regulatory regions of genes
SMGs - ANSWER-Significantly mutated genes; cancer related genes involved in
diverse cellular functions and tumor-type-specific mutations; targets for gene
therapy
TILs - ANSWER-Tumor infiltrating lymphocytes; frequently contained within human
melanoma,; recognize autologous tumor; given back to patient for immunotherapy
WES - ANSWER-Tumor Whole Exome Sequencing
Tumor-Specific Mutations - ANSWER-by definition, confined to the tumor;seen as
foreign by the immune system and therefore likely to be immunogenic
Tandem Minigene - ANSWER-string of minigenes encoding the mutated AA flanked
by 12 AAs
Minigenes - ANSWER-sections of DNA encoding tumor non-synonymous point
, mutations
G1 Phase - ANSWER-gap/growth phase 1; cell has 2n chromosomes; increase in
RNA and protein synthesis; prepares for S Phase; DNA damage repaired
S Phase - ANSWER-DNA synthesis phase; each parental chromosome is duplicated
to produce 2 identical sister chromatids
G2 Phase - ANSWER-gap/growth phase 2; cells have 4n chromosomes; guards
entry into mitosis, gives time to ensure replication is complete, allows for cell
growth
M Phase - ANSWER-Mitotic phase; sister chromatids are equally distributed to each
daughter cell
G0 Phase - ANSWER-quiescence (resting state); little protein or DNA synthesis
unless given external signal
Prophase - ANSWER-replicated chromosomes condense and become visible;
centrosome is duplicated; mitotic spindle forms
Prometaphase - ANSWER-Nuclear envelope breakdown; spindle microtubules attach
to kinetochore at centromere; chromosomes begin moving
Metaphase - ANSWER-Microtubule attachment to chromosomes complete;
Condensed chromosomes aligned along mitotic spindle midplane
Anaphase - ANSWER-APC activates and cohesins are degraded; sister chromatids
are partitioned; shortening of spindle microtubules pulls separated chromatids
towards opposite ends of cell
Telophase - ANSWER-Mitotic cyclins degraded by APC; daughter nuclei form,
chromosomes decondense and cell begins to divide; contractile ring forms
Cytokinesis - ANSWER-Contractile ring forms clevage furrow; Actual splitting of cell
into two daughter cells
cdc Mutants - ANSWER-Cell division cycle yeast mutants; yeast mutants used to
explore regulation fo synthesis activation and destruction of regulatory proteins
Checkpoints - ANSWER-surveillance mechanisms used to ensure proper DNA
replication and chromosome segregation; mainly act by controlling cdk activity
MPF - ANSWER-mitosis promoting factor; protein-based signal that sends cells into
mitosis; composed of 2 proteins - Cdk1 and cyclin B which associate to form active
MPF complex
Cdk1 and Cyclin - ANSWER-Associate together to form active MPF signal
