Controlling Genes in Eukaryotes: Chromatin, Transcription Factors and RNA

Same DNA, different cells

A nerve cell and a skin cell look and act completely differently, yet nearly every cell in your body has the same genome. The difference is which genes each cell expresses. A liver cell makes albumin and liver enzymes; a developing red blood cell makes huge amounts of hemoglobin; neither makes the other's proteins.

In the last lesson you saw that bacteria control genes mostly with operons. Eukaryotic control is more complex, because eukaryotes have bigger genomes packed into chromatin, a nucleus that separates transcription from translation, many cell types, and the need to respond to signals from other cells, such as hormones. This lesson completes expectation D3.3.

Six places to turn a dial

A eukaryotic cell can regulate a gene at almost every step on the way from DNA to working protein. The main levels are:

1. Chromatin structure: is the DNA accessible?
2. Transcription: do transcription factors start RNA polymerase II on this gene?
3. RNA processing: which exons are included (alternative splicing)?
4. mRNA lifetime: how long does the mRNA survive in the cytoplasm?
5. Translation: is the mRNA translated?
6. Protein activity and lifetime: is the protein activated, and how fast is it destroyed?

Level 1: chromatin and epigenetics

Tightly packed DNA (heterochromatin) is hard for RNA polymerase to reach, so genes there are mostly silent. Loosely packed euchromatin can be transcribed. Cells change the packing in two main ways:

• Histone acetylation. Enzymes add acetyl groups to the positively charged tails of histones. This reduces the histones' positive charge, so they hold DNA's negative backbone less tightly; the chromatin opens and genes can be expressed. Removing acetyl groups closes it again.
• DNA methylation. Enzymes add methyl groups to cytosines in DNA, usually where C is followed by G. Heavily methylated promoters are usually silent. After replication, an enzyme copies the methylation pattern onto the new strand, so the pattern is inherited when the cell divides.

Changes like these, passed from a cell to its daughter cells without changing the DNA sequence, are called epigenetic ("on top of genetics"). They help a skin cell stay a skin cell through many divisions. Identical twins have the same DNA sequence, but their methylation patterns become more different as they age, which may help explain some differences between them.

A dramatic example: in female mammals, one of the two X chromosomes in each body cell is packed into tight heterochromatin early in development and almost all its genes are silenced (X inactivation). Which X is silenced is random in each early cell, and all of that cell's descendants keep the same choice.

Level 2: transcription factors (the most important level)

In eukaryotes, RNA polymerase II needs general transcription factors at the promoter (such as the protein that binds the TATA box) just to start. On their own, they give only a low rate of transcription. The rate for each gene is set by specific transcription factors:

• Activators bind DNA sequences called enhancers and increase transcription.
• Repressors bind silencers and decrease it.

Enhancers can be thousands of base pairs away from the gene, upstream, downstream or even inside an intron. The DNA loops so the activator can contact the transcription machinery through a large protein complex called the mediator. Activators also recruit enzymes that acetylate histones, linking level 2 back to level 1.

Combinatorial control. Each gene has several enhancers, and each cell type has its own mix of transcription factors. A gene is strongly expressed only in cells that have the right combination of activators. With a limited number of transcription factors, cells can produce a huge variety of patterns.

Signals from outside. Many transcription factors are switched on by signals. For example, steroid hormones such as estrogen, testosterone and cortisol pass through the cell membrane and bind receptor proteins inside the cell; the hormone-receptor complex then acts as a transcription factor and turns specific genes on. You will see these hormones in the Homeostasis unit.

Levels 3 to 6: after transcription

RNA processing. Alternative splicing (from the RNA processing lesson) lets a cell choose which version of a protein to make.

mRNA lifetime. Some mRNAs last minutes; others last days. The length of the poly-A tail and sequences in the 3′ UTR affect how fast an mRNA is broken down. A short-lived mRNA gives a quick on-off response.

MicroRNAs and RNA interference. Cells make microRNAs (miRNAs), about 22 nucleotides long, that do not code for proteins. A miRNA, held in a protein complex, base-pairs with matching sequences (usually in the 3′ UTR) of target mRNAs and either blocks their translation or causes them to be destroyed. Humans have hundreds of miRNAs, and each can regulate many mRNAs. Victor Ambros and Gary Ruvkun shared the 2024 Nobel Prize in Physiology or Medicine for discovering microRNA, first in a tiny roundworm (C. elegans) in 1993. A related process, RNA interference (RNAi), using double-stranded RNA to silence genes, earned Andrew Fire and Craig Mello the 2006 prize, and scientists now use it as a tool to switch off chosen genes.

Translation. Cells can block the start of translation for particular mRNAs, or for all mRNAs at once (for example, during stress). An unfertilized egg stores many mRNAs that are only translated after fertilization.

Protein activity and breakdown. Many proteins are made inactive and activated later: insulin is cut from proinsulin, and many enzymes are switched on or off by adding or removing phosphate groups. Proteins that are no longer needed are tagged with a small protein called ubiquitin and broken down by a proteasome.