Transcription Regulation of Eukaryotic Gene Expression II

My last post was called Transcription Regulation of Eukaryotic Gene Expression I... well, this one is imaginatively called Transcription Regulation of Eukaryotic Gene Expression II!

Describe coordinated and combinatorial control of eukaryotic gene expression, and give examples.

I've mentioned combinatorial control of eukaryotic gene expression in my previous post. Essentially, the presence of different combinations of gene regulatory proteins may affect transcription. Which proteins are present or absent may depend on the cell and the stage of development. As well as multiple proteins controlling the expression of a gene, individual proteins may also contribute to the expression of several different genes. For example, the glucocorticoid receptor (which is actually a transcription factor) can bind to several different genes and play roles in their activation.

Describe the functions and structures of RNA polymerase I, II and III.

Yup, I'm finally going to talk about RNA polymerases I and III. Time to give them some love. (RNA Polymerase II is still the star of the show though. Just because. Okay, well, their roles in transcribing mRNAs which end up as proteins is pretty damn important, I suppose.)

First, a word on their functions. RNA polymerase I is mainly responsible for transcribing most pre r-RNA ("pre" refers to RNA that hasn't undergone post-transcriptional processing yet). RNA polymerase II, as I just alluded to, transcribes mRNAs, as well as snRNAs (small nuclear RNAs) and miRNAs (micro RNAs). (According to one of my previous posts, snRNAs process RNA transcripts while miRNAs cause degradation or block translation of RNA. Finally, RNA Polymerase III transcribes tRNAs and other small RNAs that aren't transcribed by the other two.

Now for the structures! All three RNA polymerases have 5 subunits, just like how prokaryotic RNA polymerase has 5 subunits. RNA Polymerase II's alpha-like subunits are quite different to those of the other two, however. It also has a C-terminal domain (CTD) on one of its beta-like subunits. I've written about the C-terminal domain in an earlier post. Essentially, it contains almost perfect repeats of seven highly conserved amino acids, some of which can be phosphorylated, allowing capping proteins and so forth to "dock" and do their job.

Describe the factors and assembly of RNA polymerase I and III transcription initiation complexes.

RNA Polymerase I, like II, is attracted to particular regulatory sequences. These consist of a core element and an upstream element which stimulates transcription. I'm not sure how much detail we need to know about this, however, as there is plenty of detail on the slide but I don't think it was covered in such great detail in the lecture. The gist of it though is that upstream activating factor (UAF), core factor (CF) and so forth assemble on the upstream element and/or the core element, positioning RNA polymerase I and allowing it to do its job.

RNA polymerase III's promoter regions are a bit different in that they are located inside the sequences that are to be transcribed. These regions are known as A, B and C boxes. A and B boxes are located in all tRNA genes, whereas the C box is located in the 5S-rRNA gene. (5S-rRNA is one of those rRNAs that is made by pol III and not pol I. I'm just going to call them "pols" from now on because I'm sick of typing out "polymerase.") Just like the other two RNA pols, pol III has transcription factors, such as TFIIIA, TFIIIB and TFIIIC. (Wow, how imaginative.) TFIIIA is only found in the 5S-rRNA gene, whereas TFIIIB and TFIIIC are found in all tRNA and 5S-rRNA genes. TFIIIB is the one that has the TATA-binding protein (TBP)- yes, apparently pol III needs a TBP as well.

Describe the structure and function of mitochondrial and chloroplastic RNA polymerases, and their transcription initiation complexes.

As you should know by now, mitochondria and chloroplasts were probably originally bacteria that moved into their eukaryotic hosts. As such, they have circular genomes, like bacteria. They also have their own polymerases.

Human (and probably other eukaryotic) mitochondrial DNA (mtDNA) has two strands: a heavy strand and a light strand. Most genes are located on the heavy strand. The two strands are transcribed in opposite directions by mitochondrial RNA polymerase, a.k.a. POLRMT. POLRMT is a bacteriophage-type RNA polymerase (whatever that means). Main point to know about this one is that POLRMT is actually made outside of the mitochondria: its gene is transcribed in the nucleus and translated in the cytoplasm, just like most other proteins. It is then imported into the mitochondria.

POLRMT is placed at the promoters by the transcription initiation factors TFAM and TFB2M. (Just looked up what they stand for- TFB2M stands for Transcription Factor B2, Mitochondrial, so I assume TFAM stands for Transcription Factor A, Mitochondrial.) The promoters also have names: the light strand promoter is LSP, whereas the heavy strand promoter is HSP1. (Not sure if there's an HSP2.)

Chloroplasts, like mitochondria, have circular genomes with strands transcribed in opposite directions. However, transcription occurs in blocks, each with a different promoter, as opposed to mtDNA where the entire strand is just translated in one go. Chloroplasts have two types of RNA polymerases: NEP (nuclear-encoded polymerase) which is encoded in the nucleus, and PEP (plasmid/chloroplast-encoded polymerase), which is encoded in the chloroplast. NEP is required for transcription of 3 of the 4 core subunits of PEP. NEP and PEP transcribe different genes.