DNA MODIFICATIONS AND LONG-TERMPATTERNS OF GENE EXPRESSION

EPIGENETICSPART 1

Feb 19, 2015

The Wikipedia article is useful, howeveryou will have to research each topiccarefully, the article is provides summaries,but is short on detail.

http://en.wikipedia.org/wiki/Epigenetic

The metaphase chromosome on the upper left is DNA thatis condensed and packed together. Levels of RNA transcriptionfrom this DNA will be very low.

In women, the dormant X-chromosome (Barr body) showsvery little transcriptional activity. Portions of every chromosomeare like the Barr body, and essentially dormant.

ADDING A METHYL GROUP TO THECYTOSINE BASE LEADS TOWARDGENE SILENCING.

THIS IS A FUNDAMENTAL ANDIMPORTANT MECHANISM IN THEREGULATION OF GENE ACTIVITY.

CH3

Methylation onBOTH strands:

Notice that ithappens onCG PAIRS!

ACTTGGCGCGATACGGGCGATCGATCC

TGAACCGCGCTATGCCCGCTAGCTACC

Transcriptionstart site

SEQUENCE IN PROMOTER OF A GENE WHICH IS BEING ACTIVELY TRANSCRIBED INTO RNA

ACTTGGCGCGATACGGGCGATCGATCC

TGAACCGCGCTATGCCCGCTAGCTACC

Transcriptionstart site

SEQUENCE IN PROMOTER OF A GENE WHICH IS IN A DORMANT STATE: NOT TRANSCRIBED

The RED cytosines (part of a CG pair) have been methylated

If you sequenced through this promoter, you would seethe difference.

ACTTGGCGCGATACGGGCGATCGATCC

TGAACCGCGCTATGCCCGCTAGCTACC

The human genome has about 30,000,000 methylcytosines.

There are about 3 billion base pairs, and about 1.2 billionC-G base pairs (40% of total), so methyl-cytosine that common,about 1.5% of all cytosine.

Cytosine ACTIVELYdemethylated

Methylation MAINTAINEDby enzyme Dnmt1

MECHANISMS OPERATE TO MAINTAINMETHYLATION DURING REPLICATIONOF DNA: SOME PATTERNS ARE STABLE.

1) Methyl binding domain (MBD)(part of Methyl-CpG-binding protein-2)binds to methyl-cytosine.

2) The transcription repressiondomain (TRD) recruits other proteins.

3) These proteins work together to convertDNA into condensed chromatin.

ACTIONS OF MeCP2

METHYLATION PATTERNS CAN BE CONTROLLED BY GENDER.IN THE MOUSE, THE MATERNAL GENE FOR INSULIN-LIKE GROWTH FACTOR (IGF-1) IS METHYLATED AT THE PROMOTER, AND DORMANT.THE PATERNAL COPY IS ACTIVE, AND THE ONLY GENE THAT CANPROVIDE THIS PROTEIN TO THE GROWING MOUSE.

THERE ARE PERHAPS 20 GENES IN HUMANS THAT ARE LIKE THIS.

WHAT CAN HAPPEN IF THERE IS A MUTATION IN THE AMINO-ACID SEQUENCE OF THE IGF-1 GENE FROM THE PATERNAL DNA?

DNA-methyl-transferase(DNMT) puts methylgroups on cytosinesnext to guanines

Methyl-binding-domainproteins (MBD) complexwith those sites

Histone-methyl-tranferases(HMT) add methyl groupsto SELECTED lysine chainsof histone proteins

The gene CONDENSES to becomeheterochromatin, and the gene becomesLARGELY dormant.

Histone deacetylase removesacetyl group from SELECTEDlysines of histrone protein

Histones, like most proteins, have side-chain lysines, that mighthave a positive charge (NH3+). But since DNA phosphate groupsgive DNA a negative charge, histones are strongly-associated withDNA and cover up the nucleotides.

What if the lysine is ACETYLATED? What happens to the positivecharge on the histone? Will it bind more/less strongly to DNA?

Acetylated histones, octameric proteins that organize chromatin into nucleosomes and ultimately higher order structures, represent a type of epigenetic tag within chromatin.[4] Acetylation removes the positive charge on the histones, thereby decreasing the interaction of the N termini of histones with the negatively charged phosphate groups of DNA. As a consequence, the condensed chromatin is transformed into a more relaxed structure that is associated with greater levels of gene transcription.

Phosphorylation (histone kinase) also makes histones more NEGATIVE, which moves histone AWAY from DNA and makes the DNA more open for transcription.

WITH ALL THE CHANGES SEEN IN THE LOWER PART OF THEFIGURE, DNA IS EFFECTIVELY MOVED TO A DORMANT STATE.