The interphase nucleus is a highly structured organelle with chromosome territories, interchromatin compartments, and transcription factories. In cultured human cells, researchers have identified approximately 8000 transcription factories per cell, each containing an average of eight tightly associated RNAP II molecules actively transcribing RNA. If each RNAP II molecule is transcribing a different gene, how might such a transcription factory appear? Provide a simple diagram that shows eight different genes being transcribed in a transcription factory and include the promoters, structural genes, and nascent transcripts in your presentation.

Research indicates that promoters may fall into one of two classes: focused or dispersed. How do these classes differ, and which genes tend to be associated with each?

Explain the features of the Initiator (Inr) elements, BREs, DPEs, and MTEs of focused promoters.

Many transcriptional activators are proteins with a DNA-binding domain (DBD) and an activation domain (AD). Explain how each domain contributes to transcriptional initiation. Would you expect repressors to also have each of these domains?

How do the ENCODE data vastly help determine which enhancers regulate which genes?

The accompanying illustration shows a portion of a gene undergoing transcription. The template and coding strands for the gene are labeled, and a segment of DNA sequence is given.

For this gene segment, write the polarity and sequence [TIP 1] of the RNA transcript from the DNA sequence given.

The accompanying illustration shows a portion of a gene undergoing transcription. The template and coding strands for the gene are labeled, and a segment of DNA sequence is given.

For this gene segment indicate the direction in which RNA polymerase moves as it transcribes this gene.

The accompanying illustration shows a portion of a gene undergoing transcription. The template and coding strands for the gene are labeled, and a segment of DNA sequence is given.

For this gene segment, superimpose a drawing of RNA polymerase as it nears the end of transcription of the DNA sequence.

Elysia chlorotica is a sea slug that acquires chloroplasts by consuming an algal food source, Vaucheria litorea. The ingested chloroplasts are sequestered in the sea slug's digestive epithelium, where they actively photosynthesize for months after ingestion. In the algae, the algal nuclear genome encodes more than 90% but not all of the proteins required for chloroplast metabolism. Thus it is suspected that the sea slug actively maintains ingested chloroplasts, supplying them with photosynthetic proteins encoded in the sea slug genome. How would you determine whether the sea slug has acquired photosynthetic genes by horizontal gene transfer from its algal food source? Discuss the steps required for heritable endosymbiosis to eventuate, and their plausibility.