Eukaryotic Gene Regulation

Question 1

describe cis regulatory elemtns

Answer 1

• DNA binding sites
  
  • transcription factor binding site or enhancer binding site
• ON THE DNA ITSELF

Question 2

describe trans regulatory elements

Answer 2

• Modify the expression of genes distant from the gene that was originally transcribed to create them
• These are typically proteins such as TFs/enhancer binding proteins
• can have positive or negative effects

Question 3

name cis elements

Answer 3

• Basal promoter sequence
  
  • bind the general transcription factor proteins which are associated with RNA pol
• Proximal control regions
  
  • these bind TF proteins and are found near promoter
• Enhancer sequence
  
  • found far away from the promoter (usually 5’ upstream)

Question 4

describe the basal promoter region

Answer 4

• includes TATA and CAAT box
• not much regulation involved
  
  • responsible for interaction with the general TFs which directly recruit RNA pol II to promoter
  • termed the basal transcription apparatus

Question 5

name 3 trans elements (transcription factors)

Answer 5

• DNA binding domain
  
  • TFs have DNA binding domains that only bind to certain DNA sequences
• Dimerization domain (Glucocorticoid, HIF1α and HIF1B)
  
  • 2 TFs bind together to form a functional DNA binding unit called a dimer. Formation of a dimer adds an extra element of complexity and versatility
• Activation/repression domain (myc/max)
  
  • binds to enhancer binding proteins or other TF factors and modulates their function

Question 6

describe “competition” of repressor proteins

Answer 6

• competition for enhancer sequence: binding between activator and repressor proteins
• Binding of repressor to enhancer sequence competes for the DNA binding site (cis-element) of the activator
• Repressor proteins may reduce transcription levels through competition

Question 7

describe “quenching” of repressor proteins

Answer 7

• Quenching occurs when a repressor protein binds to and interferes with the DNA-binding domain of an activator protein
  
  • now the activator cannot bind to enhancer sequence
• repressor proteins may reduce transcription through quenching

Question 8

describe “blocking” by repressor proteins

Answer 8

• blocking occurs when the repressor protein binds to the activation domain of an activator protein and prevents it from interacting with the basal transcriptional machinery
• repressor proteins may reduce transcription levels through blocking

Question 9

describe response elements

Answer 9

• response elements are short sequences of DNA within a gene promoter region that are able to bind a specific transcription factor and regulate transcription of genes
  
  • all genes that contain a specific response element will be regulated in a similar fashion

Question 10

describe the hypoxia inducible factor

Answer 10

• most, if not all, oxygen-breathing species express the highly-conserved transcriptional Hif-1
  
  • heterodimer
• Hif-1 allows a coordinated cellular response to low oxygen tension

Question 11

describe the hypoxia response elements

Answer 11

• HIF1α and HIF1ß transcription factors must dimerize, then bind DNA sequences to regulate expression of many different genes
  
  • 5’ TACGTG 3’

Question 12

describe HIF1α

Answer 12

• HIGH O2: HIF1α is hydroxylated and degraded by proteasome
• Low/No O2: HIF1α stabilized, moves to the nucleus and dimerizes with HIF1ß to activate multiple genes that enhance O2 delivery to tissues and/or energy supply via glycolysis

Question 13

what is the hypoxia event sequence an example of?

Answer 13

• Induction of expression of a family of genes by transcription factor binding to a common enhancer sequence of many different genes

Question 14

HIF as a therapeutic target?

Answer 14

• Solid cancers are quick growing and hungry–they are often hypoxic
  
  • learning how to inhibit HIF1α/HIF1B mediated gene expression may provide a way of selectively killing tumors

Question 15

describe the glucocorticoid receptor

Answer 15

• the glucocorticoid receptor (GR) is a zinc-finger type TF
• the activated GR complex up-regulates the expression of anti-inflammatory genes in the nucleus and represses the expression of pro-inflammatory proteins in the cytosol

Question 16

describe the events of cortisol binding to GR

Answer 16

• When glucocorticoid (cortisol) binds to GR, it dissociates from regulatory complex
• the GR dimerizes
• the GR moves to the nucleus
• in the nucleus, GR may induce or repress target genes
• GR binds response element DNA in the promoter regions of glucocorticoid-responsive genes

Question 17

describe the myc/max system

Answer 17

• myc/max system is a regulatory mechanism for switching between gene activation or repression
• Myc has a transcriptional regulation domain, but it may not bind to DNA unless it dimerizes
• Myc regulates expression of many genes involved in cell cycle progression

Question 18

absence of myc?

Answer 18

• in the absence of Myc, Max forms a homodimer, binds to enhancer DNA and it represses gene transcription
• in non-proliferative cells:
  
  • max expressed
  • myc not expressed

Question 19

in the presence of myc?

Answer 19

• in the presence of myc, a myc/max heterodimer is formed, binds to the enhancer activation and activates gene expression

Question 20

summarize gene expression by control of dimerization

Answer 20

• gene activation occurs when Myc and Max are made in the cell at the same time
  
  • max prefers myc as a partner
  • max will always heterodimerize with myc, if possible
• gene repression results when only the max protein is made in the cell
  
  • homodimers of max will form if myc is not available

Question 21

what are the 2 types of regulation by RNAi

Answer 21

1. inhibition of translation on the ribosome
2. degradation of the target mRNA

Question 22

name the 2 types of naturally-forming interfering RNAs

Answer 22

• miRNA - micro RNA
  
  • derived from specific ds-pre-miRNA species
  • regulated expression by repressing mRNA translation
• siRNA - short interfering RNA
  
  • derived from long dsRNAs and “random” processing
  • regulates expression by mRNA degradation

Question 23

describe synthesis of miRNA

Answer 23

• long prI-miRNAs are processed to prE miRNAs hairpin structures by Drosha
• Pre-miRNA transported to cytoplasm by Exportin 5
• Dicer further processes them to ss RNA and initiates the formation of the RNA-induced silencing complex (RISC)

Question 24

describe the mechanism of translational regulation by miRNA

Answer 24

• microRNAs regulate gene expression by binding to sequence elements in the 3’UTR of a specific mRNA and imperfect base pairing with it
  
  • prevents: interaction of the translational machinery with the 5’ cap
• Example of gene regulation by preventing an mRNA from getting translated

Question 25

mechanism of mRNA degradation by siRNA

Answer 25

* siRNAs regulate gene expression by perfectly binding to sequence elements in the 3'UTR of a specific mRNA and base pairing with it * perfect pairing of siRNA with mRNA within the RISC complex will activate RISC endonuclease activity * **this is an example of gene regulation by destroying mRNA transcript**