Histone marks are reversible through the activity of “chromatin erasers.” Other proteins function as “chromatin readers,” binding histones that bear particular marks and thereby regulating gene expression.
The mechanisms involved in the cell-specific epigenetic regulation of genomic organization and gene expression are undeniably complex. Despite the intricacies, learning to manipulate these processes will likely bear significant therapeutic benefits because many diseases are associated with inherited or acquired epigenetic alterations, and dysregulation of the “epigenome” has a central role in the genesis of benign and malignant neoplasms (Chapter 6). Moreover—unlike genetic changes—epigenetic alterations (e.g., histone acetylation and DNA methylation) are readily reversible and are therefore amenable to intervention; indeed, HDAC inhibitors and DNA methylation inhibitors are already being used in the treatment of various forms of cancer.
Another mechanism of gene regulation depends on the functions of noncoding RNAs. As the name implies, these are encoded by genes that are transcribed but not translated. Although many distinct families of noncoding RNAs exist, only two examples are discussed here: small RNA molecules called microRNAs and long noncoding RNAs >200 nucleotides in length.
• Micro-RNAs (miRNAs) are relatively short RNAs (22 nucleotides on average) that function primarily to modulate the translation of target mRNAs into their corresponding proteins. Posttranscriptional silencing of gene expression by miRNA is a fundamental and evolutionarily conserved mechanism of gene regulation present in all eukaryotes (plants and animals).
Even bacteria have a primitive version of the same general machinery that they use to protect themselves against foreign DNA (e.g., from phages and viruses).
The human genome contains almost 6000 miRNA genes, only 3.5-fold less than the number of protein-coding genes. Moreover, individual miRNAs appear to regulate multiple protein-coding genes, allowing each miRNA to coregulate entire programs of gene expression. Transcription of miRNA genes produces a primary transcript (pri-miRNA) that is processed into progressively smaller segments, including trimming by the enzyme Dicer. This generates mature single-stranded miRNAs of 21 to 30 nucleotides that associate with a multiprotein aggregate called RNA-induced silencing complex (RISC;
Fig. 1.3 ). Subsequent base pairing between the miRNA strand and its target mRNA directs the RISC to either induce mRNA cleavage or to repress its translation. In this way, the target mRNA is posttranscriptionally silenced.
Taking advantage of the same pathway, small interfering RNAs (siRNAs) are short RNA sequences that can be introduced into cells. These serve as substrates for Dicer and interact with the RISC complex in a manner analogous to endogenous miRNAs. Synthetic siRNAs that can target specific mRNA species are therefore powerful laboratory tools to study gene function (so-called knockdown technology); they also are promising as therapeutic agents to silence pathogenic genes, e.g., oncogenes involved in neoplastic transformation.
Long noncoding RNA (lncRNA). The human genome also contains a very large number of lncRNAs—at least 30,000, with the total number potentially exceeding coding mRNAs by 10-to 20-fold. lncRNAs modulate gene expression in many ways (