Chapter 11: Transcription in Eukaryotes

What is eukaryotic gene regulation involved in?

• DNA-protein interaction

• protein-protein interactions

• chromatin structure 

• nuclear architecture

• cellular compartmentalization

In eukaryotes where does transcription take place?

nucleus

In eukaryotes where does translation take place?

cytoplasm

How long does transcription and translation take place in eukaryotes?

take hours or months for developmentally regulated genes

How is transcription mediated?

• transcription factors

• RNA pol II transcription machinery

• coactivators and corepressors

• elongation factors

chromosome painting

each chromosome occupies its own distinct territory in the nucleus

What does transcription do to chromatin territories?

it decondenses them

What are transcription factories associated with?

the DNA loops that form in decondensed regions

What is associated with the nuclear pore complex?

transcriptionally active genes

What genes does RNA polymerase transcribe?

all bacteria genes

What genes does RNA pol I transcribe?

rRNA genes

What genes does RNA pol II transcribe?

mRNA, snoRNA, some snRNA, miRNA

What genes does RNA pol III transcribe?

tRNA, 5S rRNA, some snRNA

What genes does RNA pol IV and V transcribe?

siRNA directed DNA methylation and gene silencing

transcription factor

interpret the info present in gene promoters and regulatory elements

What does the transcription factor do? 

transmit a response to the RNA pol II

How does a particular gene turn into a particular cell?

the unique combo of regulatory elements and transcription factors

gene regulatory elements

specific cis-acting DNA elements that recognize trans-acting transcription factors

categories of cis-acting regulatory elements

promoter elements and long-range regulatory elements

unicellular eukaryotes

only composed of short sequences located adjacent to the core promoter

multicellular eukaryotes

scattered over an average distance of 10 kb of genomic DNA

What is the variation of regulatory elements?

• presence or absence of an element

• number of distinct elements

• orientation relative to start site

• distance between them

gene promoter

the collection of cis-regulatory elements

What is a gene promoter required for?

initiation of transcription

What does the gene promoter increase as it gets closer to the start site?

the frequency of initiation

core promoter elements

the recognition site for RNA pol II and general transcription factors

Which core promoter is not recognized by TFIID?

BRE

TATA box

first core promoter element identifed

What did Chambon demonstrate with the TATA box?

it is necessary and sufficient for specific initiation of transcription by RNA pol II

What is the percentage of TATA boxes of potential core promoters?

32%

promoter proximal elements

regulation of TFIID binding to the core promoter depending on an upstream activating sequence

What two types of promoter proximal elements do multicellular elements contain?

CAAT box and GC box

What can promoter proximal elements also serve as?

tethering elements, they do not directly activate or repress transcription

enhancer and silencers

increase or repress gene promoter activity

How far away are enhancers and silencers

700 to 1000 bp away

How many binding sites de enhancers and silencers contain?

10 bindng sites for several different transcription factors

insulators

chromatin boundary markers that block enhancer and silencer activity

locus control region

organize and maintain a functional domain of active chromatin

What is B-globin gene LCR required for?

high level transcription

matrix attachement regions

organize the genome into loop domains

Where is the matrix attachement region located?

near enhancers in 5’ to 3’ flanking sequences

What is the matrix attachment region attached to?

nuclear matrix

nuclear matrix

branched meshwork of insoluble proteins that remains after digestion with high salt nucleases and detergents

What does the nuclear matrix do?

serves as a structural organizer within the cell nucleus

What does interactions with matrix attachment region do with the nucleus?

organizes chromatin into loop domains and maintain chromosomal territories

What is not involved in eukaryotic transcription?

operators

What is the difference between an enhancer and proximal promoter?

enhancers are a distance from the core promoter and proximal promoters are closer

insulator

marks the border between regions of heterochromatin and euchromatin

What regulatory sequences must maintain their orientation to the start site to function?

promoter and locus control region

What is the key property of DNase I that makes it useful for DNase I footprinting assay?

digests DNA not associated with proteins

What makes one cell different from another?

contain different sets of transcription factors

What does a multicellular eukaryotic gene promoter region comprised of?

core promoter and proximal promoter elements