Eukaryotic Transcription

What is the most highly regulated step of transcription?

Transcription initiation

What is Rett Syndrome?

genetic neurological disorder that primarily affects girls, causing progressive loss of motor skills and language, with symptoms typically appearing between 6 and 18 months of age. It is caused by a mutation in the MECP2 gene on the X chromosome, leading to a range of physical, social, and behavioral challenges.

What is chromatin?

Eukaryotic chromosomal material composed of DNA, protein, and RNA

Structural changes in chromatin is called

chromatin remodeling

What is heterochromatin?

The more condensed form of chromatin that is transcriptionally inactive

Constitutive heterochromatin is

always heterochromatin in every cell

Facultative heterochromatin is

heterochromatin sometimes or in certain cell types

What is euchromatin?

less-condensed form of chromatin where transcription can occur

Nucleosome is

the basic unit of chromatin

Nucleosome contains

8 histone proteins that make up the histone core

In euchromatin, nucleosomes look like “beads on a string” which is called

10nm fiber (diameter of a nucleosome)

Histones are

positively charged proteins that are tightly associated with chromatin and function to package and order the DNA

DNA-histone core contacts are

sequence independent, but not random

Histones form electrostatic interactions and h-bonds with

negatively charged backbone of DNA

Histone core made up of eight histone molecules:

2 copies of each: H2A, H2B, H3, H4

Function of Histone H1

locks DNA to the nucleosome

Chromatin structure is a product of the combined action of:

• epigenetic marks (e.g. histone modifications and DNA methylation)

• trans-acting transcription factors that bind to epigenetic marks or to DNA

Histone acetylation is found in areas of

open chromatin

Histone acetyltransferases (HAT) acetylates

lysine in the histone tails

Histone deacetylase (HDAC) removes acetyl groups from

the histone tails

Hypermethylation is often associated with

closed chromatin

Histone methyltransferase (HMT) methylation ___________ and ___________ in the histone tails

lysine and arginine

Effect of acetylation by HAT on transcription

Turns transcription on

Effect of methylation by HMT on transcription

Turns transcription off

Histone code hypothesis states

DNA transcription is largely regulated by post-translational modifications to histone proteins

How to designate a modification

1. histone protein that is modified

2. one letter code of the amino acid

3. # position of the amino acid beginning at N-terminus

4. covalent modification

Cytosine in the sequence CG is called a

CpG

CpG can by methylated by

DNA methyltransferase (DNMT)

CpG island are

promoter proximal regions have many CG’s in the sequence

Hypermethylation of a CpG island can ____ the promoter

silence

Mammalian genes have promoter-proximal elements like:

• transcription start site (+1)

• promoter proximal elements

Transcription start site (+1) lies within the

promoter region

Do eukaryotes have multiple or single promoters and terminators?

multiple

Promoter proximal elements are located

upstream of promoter (-40 to -200)

Enhancers are located at

promoter distal positions

Enhancers house clusters of binding sites for

transcription factors

Cis-acting regulators of eukaryotes

• transcriptional start site (+1)

• promoter proximal elements

• enhancers

Activators have what domains

a sequence-specific DNA-binding domain (DBD), a flexible hinge, and an activation domain (AD)

DBD recognition helix interacts with

major groove forming chemical bonds with the base pairs

DBD recognition helix has one of two zinc finger motifs:

• classical zinc finger

• nuclear receptor zing finger

DBD recognition helix has one of two extended dimerization domain motifs

• leucine zipper proteins

• helix-loop-helix proteins

Chromatin remodeling to yield transcriptionally active genes involves…

• repositioning nucleosides (chromatin remodeling complexes)

• covalent modifications of nucleosides (acetylation, HATS)

What are the function of SWI/SNF complexes?

Remodel chromatin so that nucleosomes are ejected near transcription start sites

SWI/SNF complexes are involved in a cycle that

Replaces nucleosomes with transcription factors

Architectural regulators facilitate

DNA looping

High mobility group (HMG) proteins bend

DNA

Eukaryotic transcription requires what kind of regulation

Positive regulation

Co-activators facilitate

Communication between activators and the complex of Pol II and general transcription factors

Mediator complex is

A major eukaryotic coactivator for pol II

General transcription factors forms

RNA pol II complex at promoter

RNA polymerase II synthesizes

mRNA and ncRNA

RNA polymerases have a similar subunit to

prokaryotic core enzyme

Transcription factors for RNA Pol II are

array of proteins that work with Pol II to form the active transcription complex

General transcription factors

those required at every RNA Pol II promoter

TFIID is a complex made up of

TBP and many TAF proteins

TATA Binding Protein (TBP) locates and binds to

TATA boxes in eukaryotic promoters

TBP is an example of a ________ groove DNA binding protein

minor

TBP-associated factors (TAFs) function in

the recognition of other sequence elements

TFIIF/RNA Pol II joints the complex by binding to

TFIIB

______ and _______ enter the complex in succession in locating promoters for RNA Pol II

TFIEE and TFIIH

TFIIH has ______________ unwinds DNA to create an open complex and requires ATP

DNA helicase

TFIIH also has ____ activity that…

kinase; phosphorylates Pol II at the CTD

CTD phosphorylation causes a conformational change which initiates

transcription

Corepressor action is

repressor binds to activator to prevent interaction with mediator

Repressors can inhibit transcription by providing a docking site for an

HDAC

Condensation of heterochromatin depends on the actions of

HMTs and chromatin a

H3K9me3 provides a docking site for

heterochromatin protein (HP1)

HP1 to HP1 protein protein interaction does what to the chromatin

compact

HP1 recruits more ____ which spreads the heterochromatin

HMT

What is combinatorial control

a mechanism involving mixing and matching of protein family variants in dimeric transcription factors