Honors Biology 298 - Week 3

 

Transcriptional Regulation in Eukaryotes

 

general transcription

 

an organisms DNA encodes

 

all RNA molecules are made by RNA polymerase

 

 

 

eukaryotes differ from prokaryotes in 2 other ways

 

 

 

 

 

 

So how do the 100,000 or so genes get turned on and off?

 

most cells retain full complement

 

originally thought cells

 

some type of regulation determines

 

 

regulation provides cells with a mechanism for determining

 

 

underlies the development and maintenance of complex organisms

 

 

 

 

 

Molecular basis of transcription is not completely understood

 

not simple

 

many regulatory proteins act together

 

 

significant area of research

 

 

Mention a few characteristics of regulatory proteins and how they control gene expression

 

1)      to activate or repress transcription

 

 

 

2)      regulatory proteins act by universal mechanisms

 

 

 

 

3)      eukaryotic regulatory factors are composed of modular components

 

 

 

 

 

 

4)      almost all regulatory proteins are phosphorylated

 

 

 

 

 

5)      other ways to regulate activity of proteins

 

 

 

 

 

 

 

6)      transcription factors and other regulatory proteins bind to promoters and enhancers

                        generic structure

 

 

 

 

 

 

 

 

 

 

 

important elements

            a) multimeric complex

 

            b) TATA box in promoter

 

 

            c) CAAT sequences in enhancers

 

 

            d) CG boxes

 

 

            e) separated by large distances

 

 

 

 

Overall….

 

 

another example of how elements interact

 

GAL4/GAL80 system

 

 

 

 

 

 

 

 

 

 

a)      binding of GAL4 to enhancer

b)      interaction of enhancer

c)      transcription starts

d)      repressor protein GAL80 binds

e)      when galactose is present

 

 

7)      gene expression is controlled by the cooperative regulation of multiple proteins

 

small number of proteins regulate large number of genes

 

 

avoids the need for so many proteins

part of complex that activates and represses

 

 

 

 

 

 

ex: control of serum albumin gene

 

 

 

 

 

 

 

 

in most eukaryotes, gene control requires both widely distributed and

 

 

 

 

8)      controlled in networks

 

 

 

a) steroid hormone receptors

 

 

 

 

 

 

b) homeotic genes

 

 

 

 

 

 

c) heat shock genes

 

 

 

 

 

 

What about mechanisms that modify transcription in general, rather than particular genes

 

DNA is not a linear molecule

 

not possible because if all DNA is stretched

 

 

DNA is packaged

 

 

 

packaging of DNA by proteins and other modifications play a major role in gene regulation

 

 

Chromatin structure and the control of gene expression

 

 

 

 

 

 

 

problem presented by folding and activation of transcription?

 

 

certain mechanisms must be used to place a gene(s) in a transcriptionally-ready state

 

 

modifications to DNA and other proteins can repress gene activation

 

 

General mechanisms which control transcription

 

1)      primary DNA modification is methylation

 

            CH3 groups

 

 

            gene inactivation by the binding of

 

 

            certain regulatory proteins bind methylated DNA

 

 

            inactive genes are highly methylated in CG islands

            1 of 2 X chromosomes in female cells are almost completely inactivated

 

            methylation patterns of globin genes

 

 

 

 

 

 

2)      chemical modifications of histones by acetylation and phosphorylation

 

 

 

 

 

 

 

 

            core histones are acetylated in regions that interact with DNA

 

 

 

 

 

 

 

            may be complete unfolding/partial unfolding of nucleosomes

 

 

 

 

 

phosphorylation of H1

 

 

conclusions:

1)

 

 

 

 

 

2)

 

 

 

Chromosomes and Chromatin

 

how a chromosome is organized and what regulates its cycle of condensation and decondensation during cell division

 

 

 

 

 

 

Within this cramped environment, chromosomes replicate, carry out gene expression, undergo division, etc. and chromosome structure is important for these cellular processes.

 

In recent years, a combination of biochemical and microscopic techniques have been used to gather a wealth of information about

 

 

 

Of central importance is the finding that a single molecule of DNA is complexed with proteins to form a structure called

 

            there are two types of proteins associated with chromatin:

                        1) histones –

 

 

                        2) nonhistones –

 

 

 

There are successive levels of DNA folding that package DNA to give a final compaction on the order of 10,000 fold:

 

1) nucleosomes –

 

 

 

 

2) chromatin fiber –

 

 

 

 

3) higher order structures –

 

 

4) chromosomes –

 

 

 

Other Chromatin Facts

 

chromatin fibers can be distributed in the nucleus as:

1) euchromatin – \

 

 

 

2) heterochromatin –

 

 

 

 

What about maintaining chromatin in position inside the nucleus?

 

            : Chromatin fibers are attached to the nuclear matrix (skeleton)

 

            : This matrix is thought to help organize the chromatin

 

 

 

 

            : Proteins forming the matrix have yet to be identified (is it an artifact?)

 

What about maintaining chromatin in a chromosome?

 

            : Chromosomes also have a scaffold