There are many more genes in a eukaryote, and most are not organized into operons. A huge number of repressors would be needed at all times if negative regulation predominated. Eukaryotic DNA is packaged into chromatin, which effectively silences most genes, and special mechanisms are needed to open up the chromatin when a gene must be expressed. Chromatin is not present in bacteria.

Eukaryotes often use multiple regulatory proteins to activate transcription of a single gene. Given the large size of eukaryotic genomes, the chance of nonspecific binding of a given regulator to DNA sequences unrelated to that particular gene is too great for the cell to rely on a single regulatory protein.

HATs generally modify Lys residues in the C-terminal tails of histones. Histone acetylation reduces the affinity of nucleosomes for DNA and can increase the transcriptional activity of a chromosomal region. The acetyl groups are removed by histone deacetylases (HDACs).

Gal4p is a transcription factor that largely functions as a transcription activator of the GAL genes. Gal11p is probably involved in regulation of a much larger set of genes. (In fact, Gal11p is part of the yeast Mediator coactivator complex.)

(a) Phosphorylated. (b) Phosphorylated. (c) Unphosphorylated. (d) Unphosphorylated.

First, most genes are regulated by multiple transcription factors (activators), and different (often unique) combinations of factors are used at different genes. Second, families of activators form heterodimers, such that a family of four related proteins can make a total of 10 different dimeric species that can recognize 10 different DNA sequences.

CTCF is a key component of the gene insulator system in eukaryotes; it binds to sequences that prevent inappropriate activation of certain genes during development and in the mature organism. Its loss would be lethal.

HMG proteins bind DNA and facilitate DNA bending. The presence of HMG protein–binding sites in the DNA that interacts with an enhanceosome may reflect HMG-mediated facilitation of DNA wrapping around the enhanceosome structure.

Gene expression is generally silenced in regions of heterochromatin. If the gene were essential, as most housekeeping genes are, moving it into heterochromatin would be lethal for the cell.

In mammalian females, one X chromosome is inactivated by condensation into a structure called a Barr body. Condensation begins at the X inactivation center, near the center of the X chromosome.

(a) With elimination of the nuclear import signal, the receptor could bind the hormone in the cytoplasm, but the complex would not be imported into the nucleus to activate gene expression. (b) With elimination of the interaction with Hsp70, most of the receptor molecules would be in the nucleus, where they would not have access to the hormone signal.

(a) A nuclease-hypersensitive site is a region of uncondensed (or less condensed) chromatin where the DNA is accessible to nuclease action. The decondensed state signals a site for the binding of proteins that function in genome maintenance and/or gene regulation. (b) The LCR triggers chromatin remodeling on both sides and can help activate transcription of genes on both sides. (c) The constructs are integrated at random locations in the chromosome. Some may accidentally be integrated near an LCR that could activate transcription from a site on the 5′ side. (d) Yes. Many more colonies are observed when the λ DNA is flanking the neomycin-resistance gene than when the chicken hypersensitive site is flanking this gene. (e) Because the constructs were integrated at random locations in the genome, they might have been subjected to the differential effects of sequences on either side of the integration sites that could affect expression of the neomycin-resistance gene. Sometimes, multiple copies of the constructs could have been integrated. If these effects were present, the hygromycin-resistance gene provided a way to normalize the results. (f) No. The effect could be at the level of posttranscriptional modification or translation. (g) To show that the effect was at the level of transcription, researchers would have to directly measure the production of mRNA from the genes in stably transfected cell lines (which the authors did).