Lecture 5. Transcriptional Regulation Flashcards
Why is transcriptional regulation needed?
Allows development of different tissues
Transition from childhood to adult
Deregulation can result in uncontrolled growth cancers
Allows reaction to environmental cues
And so on
What is an example of transcriptional regulation?
The transition from foetal to adult haemoglobins – changes in protein subunits expressed and therefore changes in functions, all co-ordinated with birth
What determines how/when/why genes are transcribed?
Chromatin structure
RNA polymerase (and general TF) binding specificity
Additional binding and activation factors
How are expressed genes found in the chromatin?
Expressed genes are found in the ‘open’ conformation
What genes within chromatin are not usually expressed?
Genes within highly packed heterochromatin
What does methylation at position 9 on histone 3 (H3K9me) result in?
Heterochromatin formation - Gene silencing
What does methylation at position 27 on histone 3 (H3K27me) result in?
Inactivation of HOX genes (developmental genes that are arranged int he same order as the segments of the body). X chromosome inactivation
Two X chromosomes could cause gene overdose so one of them is inactivated randomly in all cells
What does H3S10p H3K14ac and H3K4me H3K9ac result in (acetylation)?
Relaxes chromatin allowing gene expression
Both open up the chromatin (methylation at position 4 says to stay open in H3K4me H3K9ac)
Why is methylation at position 4 on histone 3 important?
Important for the structure of the centromere that needs an open confromation at all times
What is the structure of an interphase chromosome?
30nm fibre is compacted into loops held together by scaffold proteins
Scaffold proteins are rich in topoisomerases that regulate torsional changes caused by packing/unpacking (implies a lot of unwinding and rewinding)
Loops can extend when we need to express them (loops are mobile)
How does an interphase chromosome turn on a gene?
The loop that bears the gene that needs to be turned on opens up and relaxes
The loop moves into an area where all the requirements for transcription are concentrated
How does an interphase chromosome turn off a gene?
The gene is moved towards the nuclear periphery and allowing enzymes associeted with the nuclear lamin to turn the gene off
What are the two major types of heterochromatin?
Facultative heterochromatin and Constitutive heterochromatin
What is facultative heterochromatin?
Cell-type-specific, can switch into euchromatin following developmental cues (turns gene back on). Characterised by a specific histone code mark: H3K27me3 that binds ‘polycomb’ proteins (important in development)
What is constitutive heterochromatin?
Regions that are consistently silenced in all cell types of an organism - centromeres, telomeres, some transposons and some gene-poor regions of the genome. Characterised by H3K9me3, a modification carried out by the histone methyltransferases (HMT). These HMTs propagate heterochromatin by recognising H3K9me3 and methylating adjacent nucleosomes. HMTs copy signals and pass it on to neighbours
What is centric chromatin?
Flanked on each edge by pericentirc chromatin (normal H3K4me2)
Long highly repetitive chromatin structures (centromere specific H3)
How do centromeres remain open?
The centromeric histone force an open structure
Double methylation at position 4 also forces open structure
Because centromeres remain open, what does this allow access to?
Kinetochore proteins which then associate with the centromere and acts as the focal points for the microtubules that will eventually pull the centromere apart
What is the structure of telomeres?
Telomeres are repetitive structures
Vary in length and repeated DNA sequence (constant repeating of same sequence)
What are examples of telomere repeats?
GGGTTG in the ciliate Tetrahymena (unicellular organism)
GGGTTA in vertebrates
G1–3A in Saccharomyces cerevisiae
What is the telomere problem/how do telomeres shorten?
- Because DNA synthesis can only proceed 5’ to 3’ there is continuous synthesis on the leading strand and discontinuous synthesis on the lagging strand: synthesis requires RNA primers
- The lagging strand template can be primed near the telomere (and then extended)
- The DNA polymerase complex disengages (two Okazaki fragments, each with RNA primer)
- The RNA primers are erased leaving two gaps
- The gap on the leading strand is filled by a DNA polymerase and repaired by a DNA ligase. The gap on the lagging strand cannot be filled by a DNA polymerase as there is no primer, so there is no 3’-OH for extension (telomere shortened)
What is the consequence of both the 5’ to 3’ synthesis of DNA and the erasure of RNA primers?
Telomeres shrink
What is the Hayflick limit?
The number of times a normal somatic, differentiated human cell population will divide before cell division stops (between 40 and 60 divisions): the cell becomes senescent (cell will die). It is an inbuilt ageing mechanism
How does the compensatory mechanism for telomere shortening function?
Telomerase binds the single-stranded G-overhang: a ribonucleoprotein (RNP) enzyme made of the telomerase RNA (TER) and telomerase reverse transcriptase protein (TERT)
It extends the 3’ end of the parental strand using its own RNA subunit as a template
And so on resulting in RNA-templated DNA synthesis that extends the telomeres