Chapter Introduction

22: The Posttranscriptional Regulation of Gene Expression in Eukaryotes

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  • 22.1 Posttranscriptional Control inside the Nucleus

  • 22.2 Translational Control in the Cytoplasm

  • 22.3 The Large-Scale Regulation of Groups of Genes

  • 22.4 RNA Interference

  • 22.5 Putting It All Together: Gene Regulation in Development

  • 22.6 Finale: Molecular Biology, Developmental Biology, and Evolution

MOMENT OF DISCOVERY

Judith Kimble

One of the more thrilling moments in my career happened when our lab uncovered a previously unknown mechanism of gene control. I have long been interested in how stem cells are maintained and how they manage to generate different cell types. To get at the molecular identity of stem cell regulators, our lab started genetically and screened for mutations that would help find them. For these studies, we chose the worm C. elegans, because we could easily select for regulatory mutations. One particularly exciting group of mutations fell in a single gene and transformed cells beautifully from one fate to another, depending only on incubation temperature. Julie Ahringer, a student in my lab at the time, began to sequence the gene mutants, but found no molecular changes in the gene’s open reading frame! This was really puzzling, but she pushed on into noncoding regions and discovered a single base-pair change in the part of the gene corresponding to the 3′UTR of the mRNA.

When Julie tested the effect of introducing wild-type or mutant 3′UTRs back into the worm, she confirmed the effect of that single base-pair change. She soon sequenced the same region in nine independently isolated mutations of the same class, and they all carried 3′UTR mutations falling within a five base-pair region.

This was a truly exhilarating discovery, because at the time, no one expected the noncoding bits of an mRNA to be so important for cell-fate regulation. That breakthrough paved the way for many subsequent studies of 3′UTR regulation, which we now know is a fundamental and conserved mechanism of gene control.

—Judith Kimble, on the discovery that noncoding regions of mRNA regulate cell fate

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One of the most complex and fascinating processes in molecular biology is how different cell types arise during the development of a multicellular organism. For example, the adult human body contains about 50 trillion (50 × 1012) cells that originated from a single fertilized egg cell. Almost all these cells contain the same DNA, yet the cells of each organ, and even those within an organ, have vastly different shapes and functions. The differences must reflect gene regulation.

In eukaryotic cells, gene transcription and pre-mRNA processing—splicing, 5′ capping, and 3′ polyadenylation—occur in the nucleus. Only after export to the cytoplasm are mature mRNAs recognized by ribosomes for translation into proteins. This physical and temporal separation of transcription and translation, distinct from the situation in bacterial cells, requires additional steps in the information pathways of eukaryotes. Although these extra steps take time (which is not always available), they provide unique opportunities to impose control.

The early research on eukaryotic gene regulation focused on transcription, particularly transcription initiation. It made practical sense that cells would control gene expression by regulating the first step, avoiding energy expenditure on unneeded transcripts. However, the experimental data have increasingly pointed to an abundance of regulatory mechanisms that occur after transcription. In humans and other multicellular organisms, for many genes, transcripts and even proteins are routinely produced that are not immediately used. Instead, the mRNAs and proteins are stored and used later, bypassing the time-consuming transcription and transport steps and thus allowing a more rapid response to cellular needs or metabolic signals.

To a large degree, the importance of posttranscriptional regulation parallels the complexity of the cellular processes that are regulated. Signal transmission in the brain, color patterns in flower petals, and that most complex of all biological processes, the development of a multicellular organism, are all governed by regulatory processes that take place after transcription. In this chapter, we discuss some of the predominant ways in which cells select which mRNAs are to be translated into protein and how much protein is to be made.

We begin with overviews of mechanisms that provide exquisite posttranscriptional control of gene expression levels in the nucleus and in the cytoplasm. We then turn to pathways for regulating groups of genes, including a discussion of the exciting and eminently exploitable discovery of small interfering RNAs (siRNAs) that alter gene expression through a process commonly called RNA interference (RNAi). Next, we discuss embryonic development, a process in which almost all the transcriptional and posttranscriptional regulatory mechanisms described in the last several chapters come together. Most of the regulatory mechanisms that guide development are highly conserved in eukaryotes, from nematodes to humans. In addition to exemplifying mechanisms of gene regulation, elucidation of developmental pathways has taught us much about evolution and how it generates alterations in function and appearance in organisms. Thus, we end the book where we started—with a discussion of molecular biology from the perspective of evolution.