Switching genes on and silencing them

Chromatin-remodeling complexes and histone tags are tools, and activators put them to work to switch genes on. Cells also have ways to keep genes firmly off: tagging the DNA itself and packing whole regions into heterochromatin.

Nucleosome-free regions

Many eukaryotic genes share a common layout of nucleosomes. In genes that are active, or ready to be activated, the core promoter lies in a nucleosome-free region (NFR), a stretch of about 150 base pairs where the histones have been evicted.

• The NFR is flanked by two nucleosomes, the −1 nucleosome upstream and the +1 nucleosome downstream. These often contain histone variants that promote transcription.
• The end of many genes is followed by a second NFR, which may help transcription terminate.
• An NFR is needed for transcription but isn’t enough by itself. At any moment, many genes with an NFR aren’t being transcribed.

How an activator switches a gene on

Besides working through TFIID and mediator, activators open up the chromatin around a gene. They do it by recruiting chromatin-remodeling complexes and histone-modifying enzymes to the promoter. The order of recruitment differs from one activator to another, but the overall sequence runs like this:

Check yourselfA nucleosome in the middle of a gene can’t be moved or loosened, but the core promoter sits in a nucleosome-free region. How far does transcription get?

It starts but stalls at that nucleosome. The preinitiation complex can form at the open promoter, but RNA polymerase II can’t read DNA tightly wrapped in a nucleosome.

DNA methylation

The DNA itself can be tagged too. An enzyme called DNA methyltransferase attaches methyl groups to cytosine bases. This DNA methylation usually silences genes, especially when it happens near a promoter. It’s common in vertebrates and plants but rare or absent in some other eukaryotes.

Methylation targets a cytosine that is followed by a guanine on the same strand, a site called CpG (the “p” is the phosphodiester linkage between them). Near the promoters of many genes in vertebrates and flowering plants lie CpG islands, clusters of many CpG sites. Unmethylated CpG islands go with active genes, and methylated ones go with silenced genes.

Methylation shuts genes off in two ways:

• It can stop an activator from binding its enhancer, so transcription never gets started.
• Proteins that recognize methylated sites bind there and recruit other proteins that inhibit transcription, for example by packing the chromatin more tightly.

Facultative heterochromatin

Chapter 11 contrasted loosely packed euchromatin with tightly packed heterochromatin, which is too compact to transcribe. Some heterochromatin is the same in every cell type. Other regions differ between cell types, and these make up facultative heterochromatin. A stretch of DNA can be packed into facultative heterochromatin in a muscle cell, silencing its genes, but stay open as euchromatin in a neuron, where those genes can be expressed.

These regions are chosen during embryonic development. Particular histone modifications and methylation of CpG islands mark them, and the chromatin compacts. Once formed, the pattern is copied through cell division: every cell descended from that embryonic cell keeps the same regions packed and the same genes silenced. That is how facultative heterochromatin silences genes in a tissue-specific way.

Check yourselfA drug blocks DNA methyltransferase, and a gene that’s normally silent in those cells switches on. Explain.

Methylation near its promoter normally keeps the gene silent. With the enzyme blocked, the gene stays unmethylated and can be transcribed.