Gene Expression 1

Homeodomain

(helix-turn-helix) -hox genes -based on their DNA binding domain

Describe combinatorial control as a mechanism for controlling gene expression.

***Answer from wikispaces Combinatorial control refers to the fact that SSDBPs can dimerize, making possible a wide variety of possible DNA binding sequences. --Note that this is always within classes of SSDBPs (e.g. zinc-finger with zinc-finger) --For example: SSDBP can dimerize into homodimers and heterdimers, the combination of these proteins leads to many different transcription factors. If you have 4 monomers that can mix and match into dimers you have 2^4 transcription factors. Larger complexes, trimers and tetramers, are also possible. --- With 1,000s of TF genes you can have 10,000s of TFs (Not 2^1000 - not all TFs can form heterodimers with each other).

Describe a particular human disorder that arises from a mutation in a sequence specific DNA binding protein, explaining how the mutation leads to the disorder: MSX2 and Craniosynostosis

-Boston type is due to autosomal-dominant segregates with a proline to histidine substitution within the MSX2 homeodomain -1/3,000 live birth -sutures in the skull prematurely fuse resulting in malformed skull -serious problems for growth of the brain, craniofacial abnormalities -Not a loss of function, but a gain of function

Describe a disease that arises from a mutation in a DNA control element, and how the mutation leads to the disease state: Hemophilia B-leyden

-Clotting disorder -Mutation in DNA control element -Mutation in Factor IX, where the transcription factor can't bind to the promoter site, make only 1% of factor 9, so they can't clot. -When kids hit puberty, testosterone can activate and they can then make about 60% of clotting factor 9. -X linked disorder

Co-Factors

-Do not bind directly to the DNA elements but rather bind to sequence-specific DNA binding proteins and affect transcription through this contact

Dimerization or Combinatorial Control

-Many sequence specific DNA binding factors bind DNA as homo or heterodimers -The Zinc finger, bZIP, and bHLH can all form heterodimers. -If each monomer of the heterodimer has a different DNA binding specificity, the formation of heterodimers will increase the number of potential sequences to which that family of sequence specific transcription factors can bind.

Describe a disease that arises from a mutation in a DNA control element, and how the mutation leads to the disease state: Fragile-X Syndrome

-Mental retardation -Effects upstream, gene FMR (brain synapses) -Number of repeats -Gets for methylation, and the methylation silences and makes it no longer repressed and the less the gene gets made -CPG island gets expanded, so people get more and more repeats and becomes site for lots of methylation, which leads to Fragile X syndrome.

Describe the role of transcriptional activators and repressors

-Multiple activators stimulate the transcription from proximal and distal site -Multi-protein complexes form on enhancers and activate transcription at a distance: the B-interferon enhancer -Not linear, looping out

Describe a particular human disorder that arises from a mutation in a sequence specific DNA binding protein, explaining how the mutation leads to the disorder: Androgen Insensitivity Syndrome

-Mutations in AR DNA binding domain or ligand binding domain leading to a decreased response to androgens -Can have partial or complete AIS, depending on degree to which mutation disrupts activity -Zinc Finger

Heterodimerization

-Same DNA sequence will lead to different responses depending on the repertoire of txn factors present in a particular cell at a particular time -factors that recognize different DNA sequences allow recognition of new DNA sites

Describe a disease that arises from a mutation in a DNA control element, and how the mutation leads to the disease state: Thalassemia

-anemia, RBCs cannot take up O2 like normal -Splicing mutations in the genes -Normally a mild thalassemia, so it can be made, but won't be as effective as normal

Sequence-specific DNA binding proteins

-bind to promoter or enhancer elements (DNA control elements) in their target genes to regulate transcription. -Usually bind DNA by inserting their α-helices into the major groove of DNA, making contacts between the amino acid side chains of the protein and the bases in the DNA

Enhancer

-contain multiple control elements -Upstream or downstream -Farther away from promoter or on last exon of gene or located within an intron -Has multiple binding sites for proteins in it and work together -Often work in cell specific way

TATA box/initiator (promoter)

-determines the site of transcription initiation and directs binding of RNA Poly II -Where basal txn factors will bind.

Basic Leucine Zipper (bZIP)

-every 7 amino acid, they have leucine, which forms domain that is important for dimerization as well as DNA binding -Have to bind the DNA as dimers

DNA binding domains

-highly structured and evolutionarily conserved -folded so that they can "read" the DNA sequence and bind to their specific target DNA.

Activation Domains

-mediate protein-protein interactions that recruit the general transcription machinery and/or coactivators that modify chromatin -specificity is commonly determined by non-covalent interactions between atoms in an alpha helix in the DNA binding domain atoms on the edges of the base within a major groove in the DNA -not highly conserved and are very unstructured until they bind co-factors or general transcription factors

Promoter Proximal element

-upstream of start site -Helps regulate transcription, can be cell type specific -proteins (i.e. transcription factors) bind here that can regulate transcription

2 major domains of transcriptional activators

1. DNA binding domains 2. Activation Domains

four major families of sequence specific DNA binding proteins

1. Homeodomain (helix-turn-helix) 2. Zinc Finger 3. Basic Leucine Zipper (bZIP) 4. Helix-Loop-Helix

Two classes of Activators and Repressors

1. Sequence-specific DNA binding proteins 2. Co-factors

Describe a particular human disorder that arises from a mutation in a sequence specific DNA binding protein, explaining how the mutation leads to the disorder: Waardenburg Syndrome Type II

15% of cases results from mutation in MITF gene (encodes a BHLH (basic helix-loop-helix) DNA binding protein) o Mutation MITF nonfunctional—affects transcription of genes important in pigmentation and in hearing. o White hair

_______________ of factors that recognize the same sequence allows new combinations of activation domains to be brought together

Heterodimerization

________________ are modular proteins composed of distinct functional domains

Transcriptional activators

Zinc Finger

cysteine residue causes fingers to form in hairpin turns

Helix-Loop-Helix

have domains that are required for dimerization, but has a loop in it

DNA binding domain is

how DNA binding proteins recognize a specific DNA sequence and will be different for specific proteins

DNA controlled elements

part of the DNA sequence that acts locally (cis)

Transcriptional activators/repressors

proteins encoded by one gene that act on other genes to regulate their transcription. Diffuse around nucleus bind to DNA control element to influence transcription (trans)