White: Control of gene expression 1&2 Flashcards
Gene regulation requires
Recognition sites for DNA binding proteins-TATA
Gene regulatory proteins-TFs
Recognition sequences can be proximal or distal to first exon: T or F
True- they can be either proximal or distal
Transcription factor modules and which of these are required
DNA-binding module–required
Activation module–required
Dimerization module– not required
Regulatory module– not required
Helix-turn-helix
Simplest most common DNA binding motif
Two alpha-helices
Longer helix= recognition module–DNA binding module fits into its major groove
Zinc finger domain
DNA binding motif includes Zn domain
Binds to major groove of DNA
Found in tandem clusters
Stabilizes interaction with DNA, multiple contact points
Leucine zipper motif I
Two alpha-helical DNA binding domain
Grabs DNA like clothespin
Activation domain overlaps dimer domain
Interaction b/w hydrophobic AA side chains (leucines)
Leucine Zipper motif II
Dimerizes through leucine zipper region
Interactions b/w hydrophobic AA side chains (leucines)
Leucine residue every 7 AAs down one side of a-helix, forms zipper structure
Helix-loop-helix domain
Consists of short Alpha-chain connected to longer alpha chain
Can be Homo or Heterodimers
3 modules- DNA binding domain, Dimerization domain, Activation domain
Hereditary spherocytosis and zinc finger domain
HS can be caused by mutation in Zinc finger protein gene Klf1
Mutation is Glu to Asp in exon 3
HS KLF1 binds to opposite strand as the wildtype protein, which will NOT allow transcription to start
Identification of transcription factors
Describe one way TFs are identified
Gene control region
DNA region involved in regulating and initiating transcription of a gene
Gene control region includes
Promotor- TFs and RNA poly II assemble here
Regulatory sequences for binding of regulatory proteins which control rate of assembly process at the promoter
Activation of transciption
DNA looping and a mediator complex allow the gene regulatory proteins to interact with the proteins at the promoter
The mediator serves as an intermediary between gene regulatory proteins and RNA polymerase II
Transcription factors bind to DNA in _______,
Fact about affinity in this process
Nucleosomes
Transcription regulators bind to DNA in nucleosomes with lower affinity than naked DNA because surface of nucleotide recognition sequence may be facing inward when attached to nucleosome
Ways to overcome affinity problem w/nucleosomes
Nucleosome remodeling
Nucleosome removal
Histone replacement
Histone acetylation
Gene repressors inhibit transcription in what ways
Competitive DNA binding
Masking of the activation surface
Direct interaction with TF- repressor binds DNA and blocks assembly of TFs
Recruitment of chromatin remodeling complexes
Recruitment of histone deacetylases
Recruitment of histone methyl transferase
Proteins can be either activating or repressing depending on
The composition of complexes at gene regulatory sites
7 ways gene regulatory proteins are controlled
Synthesis Ligand binding Covalent modification-phosphorylation Addition of subunit Unmasking Nuclear entry Proteolysis Must be able to describe two of these
Negative vs positive control of alternative splicing
Negative control- Repressor molecule prevents splicing machinery access to splice site
Positive control- Activator recruits and helps directs splicing machinery
Spatial localization of mRNAs
mRNA leave nucleus through pores
They travel to destination using cytoskeletal motors
Randomly move and can be trapped by special proteins
Non trapped RNA is degraded
Regulation by RNA stability
Poly-A tail– once reduced to 25 nucleotides, two pathways converge to degrade mRNA
- Decapping- mRNA degraded from 5’ end
- mRNA degraded from 3’ end through poly-A tail
IREs IRAs
IRE- Iron responsive elements- recognition sites for binding
IRP- Iron responsive regulatory protein- Aconitase
IRP binds IRE
Effect when IRP binds IRE at 5’ ferritin mRNA vs binding IRE at 3’ transferrin receptor mRNA
Iron starvation
IRP binds IRE at 5’ ferritin mRNA- no ferritin- translation is blocked
IRP binds IRE at 3’ transferrin receptor mRNA- Transferrin receptor made- mRNA stable
What would happen with excess iron?
Remember with excess iron, the iron binds IRP which releases IRP from binding sites
microRNAs
Regulatory RNAs that regulate mRNA
Silence expression of specific mRNA targets
Bind to complementary sequences in the 3’ UT end of mRNA and degrade or block translation (depending on strength of complementary binding)
Formation of miRNAs
Precursor miRNA Cropped in nucleus Forms double stranded loop Further cleaved by Dicer Joins with Argonaute and others to form RISC complex Base pairs with mRNA Cleaves RNA, shuts down expression
Are changes in microRNA expression causative of disease or responsive to disease
Both
Causative miRNA disease
Tourettes syndrome
Change in recognition sequence on target SLITRK1 mRNA–> increased miRNA binding–> decreased SLITRK1 expression–> tourettes syndrome
3 ways to activate degredation signal
Phosphorylation by kinase
Unmasking by protein dissociation
Creation of destabilizing N-terminus
Proteasome therapy
Proteasome inhibitors used to treat multiple myelomas
Proteasome inhibition may prevent degradation of pro-apoptotic factors for cell suicide
-leads to cell apoptosis of cancer cells
Coordinated gene expression
Expression of critical regulatory protein can trigger battery of downstream genes
Example- glococorticoid hormone causes gene expression
Decision for specialization
Different options for products of differentiation at each step
Example is Hematopoietic stem cells
DNA methylation
Silences genes
Can be inherited
Genomic imprinting is based on ____, Genomic imprinting definition
Based on DNA methylation
-Differential expression of genetic material depending on the parent of origin
Epigenetics definition
Regulation of expression of gene activity without altering gene expression (e.g., methylation)
X-chromosome inactivation
One X chromosome is inactivated in females by Heterochromatin- Barr Body
