1. Lecture 6 Supplementary notes

2. level 1: Regulation at the chromatin level Histones are proteins that surround and “protect” DNA and form chromatin While the histones conceal the DsDNA so no RNA/DNA polymerase can bind to it. Chromatin modification can be considered to be the first step of gene regulation: – Prerequisite for some gene(s) transcription – Simultaneous with others [dna exposed and then transcribed] Forms the basis of the field of epi-genetics: modification of the phenotype with any change to the genotype or DNA sequences.

3. level 2: An eukaryotic promoter sequence The Core promoters regions : Just upstream of where RNA polymerase binds and transcription starts [transcription start site] initiating low level transcription; Contains TATA and/or CAAT boxes and/or CG rich

4. level 2: Expression Ctrl at the transcription level Enhances: – DNA sequences that can be located at some distance on either side of the gene or within it – Required to achieve maximum level of expression – There position is not fixed and they seem to be generic to an extent (an enhancer need not be gene specific ([1] p 322) – They can also be inside the gene they regulate; Ig heavy chain enhancer. – Can enhance more than one gene; e.g. β and ε globins in chickens (ref [1] p. 322) – Time and tissue specific (play a part in organism development.

5. level 2: Expression Ctrl at the transcription level Silencers : – Cis-acting transcription regulatory element – Acts upon the gene to repress the level of transcription that was initiated by the corresponding promoter. – Are tissue specific and temporoal-specific – E.g. found in gene that produces a hormone involved in thyroid production/stimulation. This hormone is only produced in pituitary cells. Expression only occurs in these cells because of a silencer that binds a cellular factor which repress transcription. However, in cells that are required to produce the hormone the effect of the silencer is itself neutralised by an enhancer located 1.2 kb upstream of the promoter of the gene and is only “activated” in the cells [thyrotrophs] that must produce this hormone

6. AS regulation[2] Normal regulation Cis-acting splicing disorder Indirect Trans-acting splicing disorder

7. Examples of abnormal A.S. regulation [2] Cis-acting disorder: – Found in neurological disease such as spinal muscular atrophy Indirect transacting-acting disorder: – Found in Prader Willi syndrome; ocd, autism Direct trans-acting disorder. – Cases of epilepsy and mental retardation.

8. Level 5: Regulation via RNA degradation Small fragments of RNA strands called Micro RNA (miRNA) (22 nucleotides in length). Can regulated gene expression in a number of ways: – Degrade the target (mature) mRNA – Prevent the early stages on translation by ribosome “drop off” – Affect chromatin Remodelling by causing histones to bind more tightly to the DNA and so prevent pre- translation expression. This process can hace a significant affect as it can “knock out” large segments of the DNA (100 to 1000s of genes An aside: It seems that the origins of the process was protecting cells from viral infection.