1. DNA MODIFICATIONS AND LONG-TERM PATTERNS OF GENE EXPRESSION EPIGENETICS PART 1 Feb 19, 2015

2. The Wikipedia article is useful, however you will have to research each topic carefully, the article is provides summaries, but is short on detail. http://en.wikipedia.org/wiki/Epigenetic

3. The metaphase chromosome on the upper left is DNA that is condensed and packed together. Levels of RNA transcription from this DNA will be very low. In women, the dormant X-chromosome (Barr body) shows very little transcriptional activity. Portions of every chromosome are like the Barr body, and essentially dormant.

4. ADDING A METHYL GROUP TO THE CYTOSINE BASE LEADS TOWARD GENE SILENCING. THIS IS A FUNDAMENTAL AND IMPORTANT MECHANISM IN THE REGULATION OF GENE ACTIVITY.

5. CH 3 Methylation on BOTH strands: Notice that it happens on CG PAIRS!

6. ACTTGGCGCGATACGGGCGATCGATCC TGAACCGCGCTATGCCCGCTAGCTACC Transcription start site SEQUENCE IN PROMOTER OF A GENE WHICH IS BEING ACTIVELY TRANSCRIBED INTO RNA ACTTGGCGCGATACGGGCGATCGATCC TGAACCGCGCTATGCCCGCTAGCTACC Transcription start 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 see the difference.

7. ACTTGGCGCGATACGGGCGATCGATCC TGAACCGCGCTATGCCCGCTAGCTACC The human genome has about 30,000,000 methylcytosines. There are about 3 billion base pairs, and about 1.2 billion C-G base pairs (40% of total), so methyl-cytosine that common, about 1.5% of all cytosine.

8. Cytosine ACTIVELY demethylated Methylation MAINTAINED by enzyme Dnmt1 MECHANISMS OPERATE TO MAINTAIN METHYLATION DURING REPLICATION OF DNA: SOME PATTERNS ARE STABLE.

9. 1)Methyl binding domain (MBD) (part of Methyl-CpG-binding protein-2) binds to methyl-cytosine. 2)The transcription repression domain (TRD) recruits other proteins. 3)These proteins work together to convert DNA into condensed chromatin. ACTIONS OF MeCP2

10. 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 CAN PROVIDE 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?

11. DNA-methyl-transferase (DNMT) puts methyl groups on cytosines next to guanines Methyl-binding-domain proteins (MBD) complex with those sites Histone-methyl-tranferases (HMT) add methyl groups to SELECTED lysine chains of histone proteins The gene CONDENSES to become heterochromatin, and the gene becomes LARGELY dormant. Histone deacetylase removes acetyl group from SELECTED lysines of histrone protein

14. Histones, like most proteins, have side-chain lysines, that might have a positive charge (NH3+). But since DNA phosphate groups give DNA a negative charge, histones are strongly-associated with DNA and cover up the nucleotides. What if the lysine is ACETYLATED? What happens to the positive charge on the histone? Will it bind more/less strongly to DNA?

15. 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.histonesnucleosomesepigenetic chromatin[4]DNAtranscription Phosphorylation (histone kinase) also makes histones more NEGATIVE, which moves histone AWAY from DNA and makes the DNA more open for transcription.

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