Other cases of imprinting involve long noncoding RNAs, which are defined as RNA molecules over 200 nucleotides in length that do not code for proteins. We discuss lncRNAs broadly at the end of this chapter; here, we focus on the role of a specific lncRNA in imprinting. In the case of the Kcnq1 gene, which codes for a voltage-gated calcium channel needed for proper heart function, the lncRNA is made from the paternal allele (which is unmethylated) but it is not released by the RNA polymerase, remaining instead at its site of synthesis on the DNA template. This RNA in turn recruits histone-modifying and DNA-methylating enzymes that direct the formation of repressive chromatin, which silences the protein-coding gene associated on the paternally derived chromosome (Figure 7–49B). The maternally derived gene, on the other hand, is immune to these effects because the specific methylation present from imprinting blocks the synthesis of the lncRNA but allows transcription of the protein-coding gene. Like Igf 2, the specificity of Kcnq1 imprinting arises from the inherited methylation patterns; the difference lies in the way these patterns bring about differential expression of the imprinted gene.
Why imprinting should exist at all is a mystery. In vertebrates, it is restricted to placental mammals, and many of the imprinted genes are involved in fetal development. One idea is that imprinting reflects a middle ground in the evolutionary struggle between males to produce larger offspring and females to limit offspring size. Whatever its purpose might be, imprinting provides startling evidence that features of DNA other than its sequence of nucleotides can be inherited.
We have seen that DNA methylation and certain types of chromatin structure can be heritable, preserving patterns of gene expression across cell generations. Perhaps the most striking example of this effect occurs in mammals, in which an alteration in the chromatin structure of an entire chromosome can modulate the levels of expression of most genes on that chromosome.
Figure 7–49 Mechanisms of imprinting.
On chromosomes inherited from the female, a protein called CtCf binds to an insulator (see figure 7–24), blocking communication between cis-regulatory sequences (green) and the Igf2 gene (orange). Igf2 is therefore not expressed from the maternally inherited chromosome. Because of imprinting, the insulator on the male-derived chromosome is methylated (red circles); this inactivates the insulator by blocking the binding of the CtCf protein, and allows the cis-regulatory sequences to activate transcription of the Igf2 gene. in other examples of imprinting, methylation simply blocks gene expression by interfering with the binding of proteins required for a gene’s transcription.
imprinting of the mouse Kcnq1 gene. On the maternally derived chromosome, synthesis of the lncrnA is blocked by methylation of the DnA (red circles), and the Kcnq1 gene is expressed. On the paternally derived chromosome, the lncrnA is synthesized, remains in place, and by directing alterations in chromatin structure blocks expression of the Kcnq1 gene. Although shown as directly binding to lncrnA, the histone-modifying enzymes are likely to be recruited indirectly, through additional proteins.
Males and females differ in their sex chromosomes. Females have two X chromosomes, whereas males have one X and one Y chromosome. As a result, female cells contain twice as many copies of X-chromosome genes as do male cells. In mammals, the X and Y sex chromosomes differ radically in gene content: the X chromosome is large and contains more than a thousand genes, whereas the Y chromosome is small and contains less than 100 genes. Mammals have evolved a dosage compensation mechanism to equalize the dosage of X-chromosome gene products between males and females. The correct ratio of X chromosome to auto-some (non-sex chromosome) gene products is carefully controlled, and mutations that interfere with this dosage compensation are generally lethal.