CH. 11 : CH. 11 : Transcriptional Transcriptional Control of Gene Control of Gene

ExpressionExpression

Jennifer BrownJennifer Brown

INTRODUCTIONINTRODUCTION

Gene expression: the entire process Gene expression: the entire process whereby the information in a particular whereby the information in a particular gene gene is decoded into a particular is decoded into a particular protein.protein.

RNA polymerase is required to initiate RNA polymerase is required to initiate transcriptiontranscription

mRNA is then synthesized at a certain site, mRNA is then synthesized at a certain site, transported from the nucleus to cytoplasm, transported from the nucleus to cytoplasm, then translated into proteinthen translated into protein

Ribosomes, tRNA, and translation factors all Ribosomes, tRNA, and translation factors all aid in this processaid in this process

Control of Transcription Control of Transcription InitiationInitiation

This is the first step and most important This is the first step and most important mechanism for determining whether genes are mechanism for determining whether genes are expressed and how much of encoded mRNAs expressed and how much of encoded mRNAs (proteins) are produced(proteins) are produced

Gene control allows for the correct expression Gene control allows for the correct expression of the correct genes during developmentof the correct genes during development

Regulation of transcription initiation is most Regulation of transcription initiation is most widespread form of gene controlwidespread form of gene control

Transcription PromotersTranscription Promoters

The promoter is the DNA sequence that The promoter is the DNA sequence that specifies where transcription beginsspecifies where transcription begins

Transcription factors may bind upstream Transcription factors may bind upstream or downstream from the promoteror downstream from the promoter

This allows for complex control of gene This allows for complex control of gene expressionexpression

RNA PolymerasesRNA Polymerases

Eukaryotic cells contain three different RNA Eukaryotic cells contain three different RNA polymerases which contain 2 large and 3 small polymerases which contain 2 large and 3 small core subunitscore subunits

RNA polymerase I is located in the nucleolus RNA polymerase I is located in the nucleolus and transcribes genes encoding pre-rRNA and transcribes genes encoding pre-rRNA which is processed into 28S, 5.8S, and 18S which is processed into 28S, 5.8S, and 18S rRNAsrRNAs

RNA polymerase III transcribes genes RNA polymerase III transcribes genes encoding tRNA, 5S rRNA, and other small encoding tRNA, 5S rRNA, and other small stable RNAsstable RNAs

RNA Polymerase IIRNA Polymerase II

Transcribes ALL protein-coding genes and Transcribes ALL protein-coding genes and function in production of mRNAsfunction in production of mRNAs

Contains a carboxyl-terminal domain which the Contains a carboxyl-terminal domain which the other two do not haveother two do not have

Carboxyl end of largest subunit contains a Carboxyl end of largest subunit contains a stretch of 7 amino acidsstretch of 7 amino acids

This sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser is This sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser is repeated multiple timesrepeated multiple times

Also initiates transcription of genes at the DNA Also initiates transcription of genes at the DNA sequence encoding the capped 5’ end of the sequence encoding the capped 5’ end of the mRNAmRNA

Transcription-Control Transcription-Control RegionsRegions

Protein-binding DNA sequences that Protein-binding DNA sequences that regulate protein-coding genesregulate protein-coding genes

Promoter: control elements plus TATA-Promoter: control elements plus TATA-box or initiator box or initiator

Enhancers: long distance transcriptional-Enhancers: long distance transcriptional-control elements which can occur control elements which can occur upstream or downstream from a upstream or downstream from a promoter and are cell-type specificpromoter and are cell-type specific

Types of Promoter Types of Promoter Sequences in Eukaryotic Sequences in Eukaryotic

DNADNA 3 Types3 Types TATA box: this is the most common type found TATA box: this is the most common type found

upstream from start site and rapidly transcribes upstream from start site and rapidly transcribes genesgenes

Initiators: these have cytosine at -1 position Initiators: these have cytosine at -1 position and adenine at start site (+1)and adenine at start site (+1)

CpG Islands: located upstream from start site CpG Islands: located upstream from start site and have low rate of transcribed genesand have low rate of transcribed genes

TATA BOX TATA BOX

Transcription FactorsTranscription Factors

Activate or repress expression of protein-Activate or repress expression of protein-coding genescoding genes Example is GAL4 which is composed of a N-Example is GAL4 which is composed of a N-

terminus DNA-binding domain and a C-terminus DNA-binding domain and a C-terminus activation domainterminus activation domain

Transcription repressors are functionally Transcription repressors are functionally converse of activatorsconverse of activators

Classes of DNA Binding Classes of DNA Binding ProteinsProteins

Homeodomain Proteins: contain conserved 60-Homeodomain Proteins: contain conserved 60-residue DNA-binding motifresidue DNA-binding motif

Zinc-Finger Proteins: regions fold around a Zinc-Finger Proteins: regions fold around a central Zinc ion and produce compact domain central Zinc ion and produce compact domain from short polypeptide chainfrom short polypeptide chain

Leucine-Zipper Proteins: contain the amino Leucine-Zipper Proteins: contain the amino acid Leucine at every 7acid Leucine at every 7thth position and bind to position and bind to DNA as dimersDNA as dimers

Basic Helix-Loop-Helix Proteins: similar in Basic Helix-Loop-Helix Proteins: similar in structure to basic-zipper motifstructure to basic-zipper motif

DNA-BINDING PROTEINSDNA-BINDING PROTEINS

Heterodimeric Heterodimeric Transcription FactorsTranscription Factors

Allow activation domains of each Allow activation domains of each monomer to be placed together in monomer to be placed together in different combinationsdifferent combinations

Each monomer with different DNA-Each monomer with different DNA-binding specificity increases number of binding specificity increases number of DNA sequences the family of DNA sequences the family of transcription factors can bindtranscription factors can bind

Allows for combinatorial complexityAllows for combinatorial complexity

Transcription Initiation Transcription Initiation by RNA Polymerase IIby RNA Polymerase II

General Transcription Factors: initiation General Transcription Factors: initiation factors that place polymerase molecules factors that place polymerase molecules at transcription start sites and help at transcription start sites and help template strand enter active site template strand enter active site Example in Polymerase II: TFIIA, TFIIB, etc.Example in Polymerase II: TFIIA, TFIIB, etc.

Required for synthesis of RNA from most Required for synthesis of RNA from most genesgenes

TRANSCRIPTION TRANSCRIPTION FACTORSFACTORS

Regulatory ProteinsRegulatory Proteins

Act in concert with other proteins to Act in concert with other proteins to modulate chromatin structure modulate chromatin structure This influences ability of transcription factors This influences ability of transcription factors

to bind to promotersto bind to promoters Also interact with large multiprotein Also interact with large multiprotein

complex = mediatorcomplex = mediator This binds with Pol II and directly regulates This binds with Pol II and directly regulates

assembly of transcription preinitiation assembly of transcription preinitiation complexescomplexes

Regulation of Transcription-Regulation of Transcription-Factor ActivityFactor Activity

Expression of transcription factor by a Expression of transcription factor by a cell is regulatedcell is regulated

Activities of those factors expressed are Activities of those factors expressed are also controlled indirectlyalso controlled indirectly

This is done by interaction between This is done by interaction between proteins on surface of cell and by proteins on surface of cell and by external hormones and growth factorsexternal hormones and growth factors

Nuclear ReceptorsNuclear Receptors

All have unique N-terminal regionAll have unique N-terminal region Response elements bind several nuclear Response elements bind several nuclear

receptors and can be:receptors and can be: InvertedInverted Direct repeatsDirect repeats Heterodimeric:located exclusively in nucleusHeterodimeric:located exclusively in nucleus Homodimeric: found in cytoplasm in Homodimeric: found in cytoplasm in

absence of ligansabsence of ligans

Mechanisms for Mechanisms for Terminating Terminating TranscriptionTranscription

Differ for each of 3 RNA PolymerasesDiffer for each of 3 RNA Polymerases RNA Polymerase I: termination requires RNA Polymerase I: termination requires

polymerase-specific termination factorpolymerase-specific termination factor RNA Polymerase II: terminates after RNA Polymerase II: terminates after

polymerizing a series of U residuespolymerizing a series of U residues RNA Polymerase III: doesn’t terminate until RNA Polymerase III: doesn’t terminate until

after a sequence is transcribed that directs after a sequence is transcribed that directs cleavage and polyadenylation of RNAcleavage and polyadenylation of RNA

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