Mr. Anderson to the Rescue!

This is a video in which Mr. Anderson goes over gene regulation. He explains from the beginning, mentioning how E. coli is in our intestines and breaks down what we eat. He goes over and defines regulatory genes, regulatory sequences, promoters, lac operon, trp operon, transcription factors, and activators and repressors. He then carries out scenarios through diagrams so we can see how things like repressors and activators work. If you are having trouble grasping this concept, I highly recommend you watch this video!

Circadian Clock Without DNA

This article talks about two recent articles that were released recently. It goes into depth about both of the articles that have been causing quite the controversy. In both papers, both of the researchers' laboratory models were eukaryotic cells and neither had any DNA transcription or RNA translation going on inside the cell.
The results of both papers demonstrated that transcription of DNA and translation of RNA is not needed for the generation of circadian rhythms in two different types of eukaryotic cells belonging to evolutionarily very distant relatives – protists and mammals.

In the case of red blood cells, the result is lucid – there is no DNA or RNA in these cells. Thus, leaving the circadian rhythms in these cells, to be generated in the cytoplasm.

In the case of O.tauri, the picture result was a little bit more complex: the cells had a nucleus which had DNA. There was a clock driven by transcription and translation of recognized "clock genes." However, when this mechanism was supressed, by constant darkness or by chemicals, the cells still exhibited circadian rhythms generated by the molecules residing in the cytoplasm (and some of those molecules may have been strands of RNA transcribed earlier).

This is exactly what they discovered in both cases – there was a clear circadian rhythm of peroxiredoxins state-switching both in cultured red blood cells and in the cultured Ostreococcus tauri .

In sum, the phase at which the DNA-centered clock starts its cycle is determined by the phase of the cytoplasmic clock, not the other way round, i.e., the cytoplasmic clock is dominant over the nuclear clock.

Regulation of Transcription in Eukaryotes

This article talks about regulating transcription in eukaryotes. Controlling gene expression is far more complex in eukaryotes than it is in bacteria; but, they have the same basics. Eukaryotic gene expression is controlled at initiation of transcription. In bacteria, proteins control transcription. They bind to specific regulatory sequences and modulate the activity of RNA polymerase. The same thing happens in eukaryotes. The complex task of regulating gene expression in the many differentiated cell types of multicellular organisms is accomplished primarily by the synergy of multiple different transcriptional regulatory proteins. Packaging DNA into chromatin and modifying it by the process of methylation, transmit further levels of complexity to the control of eukaryotic gene expression.

This is a picture of a transcriptional activator. It has two independent domains.

This is a picture of a eukaryotic repressor. Some repressors block the binding of activators to regulatory sequences. While, others have active repression domains that inhibit transcription by interacting with general transcription factors. 

Gene expression in eukaryotes is regulated by transcriptional activators and repressors. Activators bind to regulatory DNA sequences and stimulate transcription. They appear to be modular proteins. So, the DNA binds and activates domains of different factors and thereby these factors can frequently be interchanged using different DNA techniques. Repressors on the other hand, bind to specific DNA sequences. I like to think of them as inhibitors. In most cases, eukaryotic repressors interfere with the binding of other transcription factors to DNA. For example, when a repressor binds near the transcription start site, it can block the interaction of RNA polymerase (or general transcription factors) with the promoter. Other repressors compete with activators for binding to specific regulatory sequences.