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Cell biology III > Chapter 1 : Genomics and Regulation in Eukaryotes > Flashcards

Chapter 1 : Genomics and Regulation in Eukaryotes Flashcards

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1
Q

What is the genome?

A

organisms complete set of DNA, including chromosomal and mitochondrial DNA

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2
Q

Describe Genomics?

A
  • study of the genomes of organisms, including determination of the entire DNA sequence of organisms and fine-scale genetic mapping
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3
Q

Describe the human genome project?

A
  • international research effort to sequence and mapp all of the genes of the human genome
  • used for biomedical studies
  • used to look for genetic variation that increases risk of specific diseases such as cancer
  • discover the genetic basis for health and disease
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4
Q

Compare the genomes of E.coli, nematode and homo sapien

A
  • similar in number of protein encoding genes, large difference in amount of non-coding regions in the genome
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5
Q

Explain the surprising results of the post-genomic era

A
  • number of protein encoding genes did not correlate with complexity as expected
  • (humans substantially fewer protein-coding genes)
  • prevalence of the use of other mechanisms that increase complexity and variation without increasing number of coding genes
  • recognition of a complex regulatory network
  • “junk DNA” serves a purpose
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6
Q

What is gene expression

A
  • information from a gene is used in the synthesis of a functional gene product (often proteins)
  • in non-protein coding genes (tRNA, snRNA),product is a functional RNA
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7
Q

What are some steps where regulation of gene expression can occur

A
  • regulation of transcription
  • RNA processing
  • RNA transport and localization
  • mRNA sequestration and degredation
  • translation
  • post-translational modifications
  • protein degredation
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8
Q

What are the complex cellular networks involved in regulation of the human genomr

A
  • differential gene expression
  • combinatorial gene control and protein interaction networks
  • complex signal transduction pathways
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9
Q

How can a single fertilized egg give rise to a complex organism with cells of varied phenotypes?

A
  • all cells have same genetic info
  • differences in cells result from differences in gene expression
  • multicellular development, differences in gene expression are set up and maintained by epigenetic mechanisms
  • epigenetic control provides for cell differentiation and perpetuation of expression states and cell memory
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10
Q

Epigenetics is….

A

the study of biological mechanisms that will switch genes on and off
- NOT a change in DNA sequence

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11
Q

What is an epigenetic mark?

A

modification of DNA or histones

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12
Q

What is included as an epigenetic mark?

A
  • dna Methylation
  • Histone modifications
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13
Q

What is an epigenetic pattern?

A
  • patterns of DNA methylation and histone modifications
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14
Q

Are patterns heritable?

A

yes

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15
Q

What are some factors that may influence epigenetic patterns?

A

-

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16
Q

What are some factors that may influence epigenetic patterns?

A
  • Diet
  • geography
  • sleep
    -exercise patterns
  • aging
  • environmental & behavioral factors
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17
Q

Are epigenetics reversible?

A
  • yes
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18
Q

What is a non-coding RNA (ncRNA)

A
  • An RNA molecule not translated into a protein
  • it is possible that many ncRNAs are non functional, but they could also not be
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19
Q

What are the functions of regulatory RNAs?

A
  • bind to DNA to block transcription of the target gene
  • target specific mRNAs for destruction
  • block translation of the mRNA
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20
Q

What are the two broad classes of regulatory RNAs?

A
  • micro RNAs (microRNAs)
  • Long noncoding RNAs (lncRNAs)
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21
Q

Describe early and late stage regulation?

A
  • early stage: economical, but it takes time (only transcribes proteins that it actually needs)
  • late stage: very fast, not economical
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22
Q

Do eukaryotic polymerases recognize their core promotor sequences?

A

no

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23
Q

What is the function of a trans-acting regulatory protein?

A
  • bind cis-acting regulatory sequences to control eukaryotic transcription
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24
Q

Describe regulatory DNA sequences?

A
  • cis-acting
  • core promotor region
  • proximal elements
  • enhancer sequences
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25
Q

What are enhancer sequences?

A
  • ## enable genes to be transcribed only when proper transcriptional activators are present
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26
Q

What are silencers?

A
  • decrease in gene activity when bound to a TF
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27
Q

What are topologically associated domans?

A

(TADS) are relatively large sections of DNA
- enhancers and silences can act within these areas
- TAD boundaries are “insulators” which prevent enhancers and silences in one TAD from affecting transcription of genes in another

28
Q

What are transcription factors?

A
  • TFs are proteins that bind DNA regulatory regions to activate/stimulate or repress transcription
  • trans-acting regulatory proteins
29
Q

What is the general role of a transcription factor?

A
  • bind to the promotor region
  • required for RNA polymerase binding
30
Q

What are two examples of a TF?

A
  • activator
  • repressor
31
Q

How are TF’s grouped into families?

A
  • DNA binding domains
32
Q

Describe transcription activation.

A
  1. general TFs bind to the promotor region
  2. General TFs facilitate binding of RNA polymerase to the promotor (pre-initiation complex)
  3. activator TFs bind to proximal and enhancer sequences
  4. activators bound to the enhancer region work with mediator proteins to initiate transcription
33
Q

Describe modulation of transcription

A
  • activator proteins bound to DNA at an upstream enhancer
  • attract proteins to promotor region
  • these proteins activate RNA polymerase and thus transcription
  • DNA can loop around on itself to cause interaction between activator proteins/ proteins that mediate RNA polymerase activity
34
Q

What is a mediator

A
  • large multiprotein complex, required for transcription by RNA polymerase II
  • functions as a transcriptional coactivator
  • regulates various steps transcriptional activation
  • main function: transduce signals from enhancer-bound TFs to the components of the preinitiation complex
35
Q

What is an enhanceosome

A
  • higher-order protein complex assembled at the enhancer and regulates expression of a target gene
36
Q

Humans have a low number or protein-coding genes. Where does our complexity come from?

A
  • human complexity depends on combinatorial control of gene expression
  • in other words, how those genes are regulated in used
37
Q

What is the effect our complex system of multiple regulators?

A
  • the same gene can be transcribed in multiple ways
  • depends on combination, presence or absence of various transcriptional regulator proteins
38
Q

What is combinatorial regulation?

A
  • a specific combination of TFs are needed to turn the gene on
39
Q

Describe the many results from an interplay between combinatorial regulation?

A
  • different enhancer regions (modules) can be used by different TFs to activate same gene
  • expression of different genes can be coordinated by a single TF
  • different roles may be fulfilled by the same TF
  • different combinations of a few TFs can generate many different results
  • many TFs work together as a committee, combining their effects to determine final transcription rate
40
Q

What are alternative promotors?

A
  • promotors that are active and allow for independent regulation in different situations
41
Q

What are 3 ways to identify and study regulatory sequences

A
  1. mutation analysis
  2. identify conserved non-coding sequences across species
  3. evaluate gene expression with reporter genes
42
Q

How to evaluate gene expression with reporter genes?

A
  • promotor and enhancer analysis
  • regulation by micro RNAs and lincRNAs
  • temportal and spatial expression
43
Q

What is a mutation analysis?

A
  • create a gene mutation and observe the consequences in order to uncover the function of a gene
  • mutations that result in lower transcription indicate nucleotides that are important for transcription
44
Q

What does it mean to identify conserved non-coding sequences across a species?

A
  • align sequences to determine identities (look for similarities among the sequences)
45
Q

How can you study the strength of a regulatory region when you cant easily assay them for the gene product?

A
  • substitute the gene with a reporter gene, one that encodes a product that you can easily assay
46
Q

What is the purpose of a reporter gene plasmid?

A
  • sequences of interest are cloned into reporter gene plasmids
  • contains reporter gene and other gene s necessary for plasmid maintainance/gene expression
47
Q

Reporter plasmids may be used to study:

A
  • promotor and enhancer analysis
  • regulation by micro-RNAs and lincRNAs
  • temporal and spatial expression
48
Q

Regions cloned into the reporter plasmid/vector depend on whether one wants to study the:

A
  • promotor regions 5’ to the gene of interest
  • regulatory regions in the 3’ UTR
49
Q

transcriptional fusions can be used to study:

A
  • promotor and enhancer analysis for regulatory regions
  • regulation by micro rnas and linc rnas
  • spatial location: cell types, tissue types
  • temporal location of gene expression
  • subcellular localization
50
Q

describe pair-rule genes

A
  • pair-rule genes are expressed in alternate parasegments during development of segmented insects

ex: expression of the pair-rule genes even-skipped (eve) and fushi tarazu (ftz) in alternating bands in drosophilia early embryo… each band corresponds to one parasegment

51
Q

What are the three examples of differential gene transcription?

A
  • expression of beta-globin genes
  • expression of Sonic Hedgehog
  • regulation of yeast GAL regulon
52
Q

Describe the expression of beta-globin genes (1st example of differential gene transcription)

A
  • regulation in response to a developmental program
  • six closely related globin genes form beta-globin complex
  • each gene produces distinct beta-glovin polypeptide with unique oxygen-carrying capacity
53
Q

What is a locus control region

A
  • highly specialized enhancer
  • regulates transcription of multiple genes packed into complexes of closely related genes
54
Q

Describe the graph showing developmental expression of beta-globin-complex genes

A
  • two beta-globin polypeptides join with two copies of alpha-globin to form hemoglobin
  • at bird, hemoglobin molecule is made of 2 alpha chain and 2 gamma chains.
  • gamma chains gradually replaced by. beta chains as infant grows
    (gestation = gamma + alpha dominate)
    (birth = beta dominate)
55
Q

Describe expression of Sonic Hedghog (2nd example of differential gene transcription)

A
  • regulation for tissue-specific expression
  • due to the action of two different enhancers
  • one combo of regulatory proteins binds brain enhancer in brain tissue, a different combo binds limb enhancer in developing limbs
56
Q

Describe regulation of the the yeast GAL regulon? (3rd example of differential gene transcription)

A
  • regulation in response to changing conditions
57
Q

What is a regulon?

A
  • group of genes regulated as a unit, controlled by same regulatory gene that expresses a protein acting as repressor/activator
58
Q

Eukaryotic version of lactose?

A

Galactose

59
Q

Cellular response to high [glucose]

A
  • represses genes for alt C-source use (galactose operon)
  • induce genes for efficient glucose use
60
Q

Cellular response to low [glucose]

A
  • represses genes for glucose uptake
  • induces genes for gluconeogenesis, genes fot alt C-source use (galactose)
61
Q

Describe GAL regulation

A
  • defined by Gal4 which regulated over 22 galactose-related genes, using structural and regulatory GAL genes
62
Q

What is GAL4

A
  • DNA -binding transcription factor
  • responds to galactose
  • binds to the UAS of GAL genes activating the GAL genes (UAS = upstream activating sequence)
63
Q

Describe transcriptional activation by GAL4 when GALACTOSE is ABSENT

A
  • Gal4 recognizes 17 gp seq. (UAS)
  • binds to UAS as a dimer
  • inactive when bound to Gal80 (Gal80 acts as a repressor, cannot activate transcription
64
Q

Describe transcriptional activation when GALACTOSE is PRESENT (glucose absent)

A
  • Gal3 binds to galactose, then to Gal80
  • bind of Gal3-Galactose to Gal80 induces conformational change in protein, Gal80 leaves from Gal4
  • release of gal80 from gal4 = gal4 is active, transcription can activate
65
Q

What is SAGA?

A
  • recruited by an activated Gal4
  • transcriptional co-activator complex
  • histone modification
  • allows chromatin to relax in order for the promotor to open
66
Q

What are the sequences of events in the activaton of Gal4- regulated genes

A
  • Gal 3 moves gal80 to cytoplasm, gal4 is now active
  • gal4 recruits SAGA
  • gal4 recruits mediator and SWI/SNF
  • SWI/SNF along with SAGA remove nucleosomes from promotor
  • SAGA and mediator recruit GTFs and RNA poly II, forms pre-initiaion complex

Cell biology III (18 decks)

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