Mechanisms of Human Health and Disease

2012

Mechanisms of Human Health and Disease

Regulation of Gene Expression

Joe Schultz

[email protected]

D4

RoGE : Mysteries

• How are such massive quantities of DNA packaged and maintained? • How do gene products production rates get turned up or down? • What is a protein party? http://www.nsls.bnl.gov/newsroom/science/2006/images/02-Stock-figure1.jpg

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Mechanisms of Human Health and Disease

2012

RoGE : Table of Contents

• Genes – Packaging – Structure

• Transcription Factors • Chromatin Structure • Epigenetic Regulation – Histone modification – DNA methylation http://www.nsls.bnl.gov/newsroom/science/2006/images/02-Stock-figure1.jpg

Structural Genetics : Storing, Packaging, and Protection

http://nanobiologynotes.blogspot.com/

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Mechanisms of Human Health and Disease

2012

RoGE: Chromatin Structure

• Heterochromatin: tightly packed • Euchromatin: loosely packed (usually under transcription)

http://nanobiologynotes.blogspot.com/

RoGE : Chromatin Structure*

• Nucleosome – Fundamental packaging unit for chromatin – Histone Core: • • • •

2 H2A 2 H2B 2 H3 2 H4

• Histones – Have a head and a tail structurally exposed capable of modification http://content.answers.com/main/content/wp/en/8/8a/Nucleosome_structure.png

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Mechanisms of Human Health and Disease

2012

RoGE : Chromatin Structure*

• Nucleosome – Fundamental packaging unit for chromatin – Histone Core: • • • •

2 H2A 2 H2B 2 H3 2 H4

http://bioweb.wku.edu/courses/biol566/Images/NucleosomeF09-30A.JPG

• Histones – Have a head and a tail structurally exposed capable of modification

http://www.cellbiol.ru/REVIEW/Chromosome/dnapacking/nucleosome2.jpg

RoGE : Gene Structure

http://www.nsls.bnl.gov/newsroom/science/2006/images/02-Stock-figure1.jpg

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Mechanisms of Human Health and Disease

2012

RoGE : Gene Structure

• Gene expression – Does every cell have a complete set of DNA? – What makes a liver cell different from a brain cell? – How many copies of a gene does one have?

• External and Internal signalling events – Regulate which genes are on and off – Create signaling cascades to spread the message quickly http://www.nsls.bnl.gov/newsroom/science/2006/images/02-Stock-figure1.jpg

RoGE : Gene Structure

http://www.wellesley.edu/Chemistry/chem227/nucleicfunction/transcription/lac%20operon/06eukaryotes.jpg

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Mechanisms of Human Health and Disease

2012

RoGE : Gene Expression Analogy

• Gene product modulation – Stereo • On vs. off • Up vs. down

– Gene • • • •

On/activated turned up/upregulated suppressed / downregulated off/silenced

RoGE : Gene Expression Analogy

• Gene regulation – ON: Presence of transcription factors – OFF: Lack of transcription factors, or regulatory “block” (siRNA, inhibitory proteins) – UP: Increased # of transcription factors and / or tight binding affinities and stabilized complexes – DOWN: Decreased # of transcription factors

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Mechanisms of Human Health and Disease

2012

RoGE : Transcription Factors

• Transcription factors – proteins that bind to gene promoters and regulate transcription

http://scienceblogs.com/pharyngula/2006/07/transcription_factors_and_morp.php

RoGE : Transcription Factors

• Transcription factors – Use structural domains and motifs to attach to specific sequences of DNA. • Specific… structure yields fxn

– Thus the DNA sequence has a structural element that is specific for a factor • DNA ladder external electronic environment that attracts the transcription factors

• http://www.dnai.org/lesson/go/22964/ – Transcription factors binding to DNA, 3D animation with no audio (2 min)

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Mechanisms of Human Health and Disease

2012

RoGE : Transcription Factors

Transcription Factors = Protein Parties

RoGE : Transcription Factors

• Protein Parties – Create a stable environment to hold proteins over the area of DNA to • “turn on” a gene • Begin mRNA transcription • Hold on to the promoter area of the gene to continue transcription

– The more stable the complex is, the tighter it binds, the longer the DNA is transcribed, and the more mRNA is made.

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Mechanisms of Human Health and Disease

2012

RoGE : Regulation of Gene Transcription

• Follow: – http://www.dnai.org/lesso n/go/22964/

• Lecture: Regulation of Gene Transcription – Slide 1: Transcription factors binding to DNA, 3D animation with no audio – Slide 2: DNA packaging, 3D animation with basic narration

RoGE : Common DNA Binding Structural Domains/motifs

Helix turn Helix (HTH)

http://www.swbic.org/education/comp-bio/images/CentromereBindingProtein.jpg

Helix loop Helix (HLH)

Leucine Zipper

http://www3.interscience.wiley.com:8100/legacy/college/boyer/0471661791/structure/protein_dna/LZS.gif

Zinc-finger

http://chemistry.umeche.maine.edu/CHY431/Helix-loop-helix.jpg http://www.snv.jussieu.fr/vie/dossiers/therapie_genique/Zinc_finger.png

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Mechanisms of Human Health and Disease

2012

RoGE : Zinc Finger domain* •

Structure – The structure of each individual finger is highly conserved and consists of about 30 amino acid residues, constructed as a ββα fold and held together by the zinc ion. The α-helix occurs at the C-terminal part of the finger, while the β-sheet occurs at the N-terminal part. – The consensus sequence of a single finger is: Cys-X2-4-Cys-X3-Phe-X5Leu-X2-His-X3-His (wikipedia)

•

DNA Binding – Occurs where the alpha helix lies in the major grove of DNA and hydrogen bonds with specific base pairs

RoGE : Transcription Factor Examples*

AP-1

•

•

The transcription factor AP1 is a heterodimer formed by c-jun and c-fos. The association between c-jun and c-fos is required for binding to DNA and involves a structural motif known as a leucine zipper. Hydrophobic interactions between leucines located every 7th amino acid in an alpha-helix region of each subunit hold the two sub-units together . AP1 binds to DNA sequences (TRE's - transcription response elements) in the promotor region of many genes which are involved in regulating cell proliferation. Ionic interactions between clusters of argenines (basic amino acids with positively charged side-groups) located at one end of each of the sub-units are involved in the interaction with DNA (with its negatively charged phosphates).

http://www.yeric.com/ap1.jpg

http://biopro1.step.in-systeme.net/imperia/md/images/artikelgebunden/freiburg/arndt_coiled_coils_kl.jpg

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Mechanisms of Human Health and Disease

2012

RoGE : Epigenetic Regulation

• Epigenetics – Defined: Refers to the inheritable information that is encoded by modifications of the genome and chromatin components. – It is NOT a change in the DNA sequence – Accounts for differential gene expression in different cell types – Can be acquired or inherited

RoGE : Epigenetic Regulation

• Histone Modification – Acetylation, methylation, phosphorylation, ubiquitination

• Acetylation – HATs – HDACs

• Acetyl group

http://www.oup.com/uk/orc/bin/9780199264728/image/c03f06.jpg

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Mechanisms of Human Health and Disease

2012

RoGE : Epigenetic Regulation* • Methylation – CH3 groups are added to the 5C on Cytosine – CpG islands located in 50% of promoter regions of human genes are not methylated – Cyt-CH3s are often found in promoter regions of repressed genes (Xchromosome, and some tissue specific genes) – Cyt-CH3s often deaminate and turn into Thymine http://www.epiontis.com/graphics/images/5bases.jpg

RoGE : Epigenetic regulation and cancer • Hypermethylation – When CpG islands for genes that are normally not methylated become over methylated and are silenced. – Silencing of tumor suppressors would promote neoplasia.

• Hypomethylation – When genes that are normally silenced are under methylated and turned on.

http://www.jacobs-university.de/imperia/md/images/schools/ses/facultypages/ajeltsch/6.jpg

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Mechanisms of Human Health and Disease

2012

RoGE : Mechanisms of Human Health and Disease

• Gene expression is regulated by activators and repressors of transcription operating on noncoding regulatory elements within a given gene. • Several further levels of control have been described – – – –

Chromatin modications Post-translational modification of mRNA Stability and processing of mRNA siRNAs

• Patterns of DNA Methylation can silence (hyper) or activate (hypo) genes • Some cancers are found to be epigenetically unstable with epigenetic silencing of CpG islands.

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