Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

436 Chapter 7: Control of Gene Expression
and RNA sequences (Figure 7–79B). This behavior is similar to that of snoRNAs
(see Figure 6–41), crRNAs (see Figure 7–78), and miRNAs (see Figure 7–75), all of
which act in this way to guide protein enzymes to specific nucleic acid sequences.
In some cases, lncRNAs work simply by base-pairing, without bringing in
enzymes or other proteins. For example, a number of lncRNA genes are embedded
in protein-coding genes, but they are transcribed in the “wrong direction.”
These antisense RNAs can form complementary base pairs with the mRNA (transcribed
in the “correct” direction) and block its translation into protein (see Figure
7–66D). Other antisense lncRNAs base-pair with pre-mRNAs as they are synthesized
and change the pattern of RNA splicing by masking splice-site sequences.
Still others act as “sponges,” base-pairing with miRNAs and thereby reducing their
effects.
Finally, we note that some lncRNAs can act only in cis; that is, they affect only
the chromosome from which they are transcribed. This readily occurs when the
transcribed RNA has not yet been released from RNA polymerases (Figure 7–79C).
Many lncRNAs, however, diffuse from their site of synthesis and act in trans.
Although the best understood lncRNAs work in the nucleus, many are found in the
cytosol. The functions—if any—of the great majority of these cytosolic lncRNAs
remain undiscovered.
Summary
RNA molecules have many uses in the cell besides carrying the information needed
to specify the order of amino acids during protein synthesis. Although we have
encountered noncoding RNAs in other chapters (tRNAs, rRNAs, snoRNAs, for example),
the sheer number of noncoding RNAs produced by cells has surprised scientists.
One well understood use of noncoding RNAs occurs in RNA interference, where
guide RNAs (miRNAs, siRNAs, piRNAs) base-pair with mRNAs. RNA interference
can cause mRNAs to be either destroyed or translationally repressed. It can also
cause specific genes to be packaged into heterochromatin suppressing their transcription.
In bacteria and archaebacteria, RNA interference is used as an adaptive
immune response to destroy viruses that infect them. A large family of large noncoding
RNAs (lncRNAs) has recently been discovered. Although the function of most of
these RNAs is unknown, some serve as RNA scaffolds to bring specific proteins and
RNA molecules together to speed up needed reactions.
What we don’t know
• How is the final rate of transcription
of a gene specified by the hundreds of
proteins that assemble on its control
regions? Will we ever be able to predict
this rate from inspection of the DNA
sequences of control regions?
• How does the collection of cisregulatory
sequences embedded in a
genome orchestrate the developmental
program of a multicellular organism?
• How much of the human genome
sequence is functional, and why is the
remainder retained?
• Which of the thousands of unstudied
noncoding RNAs have functions in the
cell, and what are these functions?
• Were introns present in early cells
(and subsequently lost in some
organisms), or did they arise at later
times?
Problems
Which statements are true? Explain why or why not.
7–1 In terms of the way it interacts with DNA, the
helix–loop–helix motif is more closely related to the leucine
zipper motif than it is to the helix–turn–helix motif.
7–2 Once cells have differentiated to their final specialized
forms, they never again alter expression of their
genes.
7–3 CG islands are thought to have arisen during evolution
because they were associated with portions of the
genome that remained unmethylated in the germ line.
7–4 In most differentiated tissues, daughter cells retain
a memory of gene expression patterns that were present
in the parent cell through mechanisms that do not involve
changes in the sequence of their genomic DNA.
Discuss the following problems.
7–5 A small portion of a two-dimensional display
of proteins from human brain is shown in Figure Q7–1.
These proteins were separated on the basis of size in one
dimension and electrical charge (isoelectric point) in the
other. Not all protein spots on such displays are products
Figure Q7–1 Twodimensional
separation of
proteins from the human
brain (Problem 7–5). The
proteins were displayed
using two-dimensional
gel electrophoresis. Only
a small portion of the
protein spectrum is shown.
(Courtesy of Tim Myers and
Leigh Anderson, Large Scale
Biology Corporation.)
larger
smaller
acidic
basic