9 TRANSCRIPTION (Full Edition)
1 Introduction
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- The coding strand (Sense strand)
of DNA has the same sequence as the mRNA and is related by the genetic code to the
protein sequence that it represents.
- The antisense strand (Template strand)
of DNA is complementary to the sense strand, and is the one that acts as the template
for synthesis of mRNA.
- RNA polymerases are enzymes that
synthesize RNA using a DNA template (formally described as DNA-dependent RNA polymerases).
- A promoter is a region of DNA where RNA polymerase
binds to initiate transcription.
- Startpoint refers (Startsite)
to the position on DNA corresponding to the first base incorporated into RNA.
- A terminator is a sequence of DNA that causes
RNA polymerase to terminate transcription.
- A transcription unit is the sequence between sites
of initiation and termination by RNA polymerase; may include more than one gene.
- Upstream identifies sequences in the opposite
direction from expression; for example, the bacterial promoter is upstream of the
transcription unit, the initiation codon is upstream of the coding region.
- Downstream identifies sequences proceeding farther
in the direction of expression; for example, the coding region is downstream of
the initiation codon.
- A primary transcript is the original unmodified
RNA product corresponding to a transcription unit.
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Figure 9.1
The function of RNA polymerase is to copy one strand of duplex DNA into RNA.
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Transcription involves synthesis of an RNA chain representing one strand of a DNA
duplex. By "representing" we mean that the RNA is identical in sequence
with one strand of the DNA, which is called the coding strand. It is complementary
to the other strand, which provides the template strand for its synthesis. Figure
9.1 recapitulates the relationship between double-stranded DNA and its single-stranded
RNA transcript.
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Figure 9.2
A transcription unit is a sequence of DNA transcribed into a single RNA, starting
at the promoter and ending at the terminator.
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RNA synthesis is catalyzed by the enzyme RNA polymerase. Transcription starts when
RNA polymerase binds to a special region, the promoter, at the start of the gene.
The promoter surrounds the first base pair that is transcribed into RNA, the startpoint.
From this point, RNA polymerase moves along the template, synthesizing RNA, until
it reaches a terminator sequence. This action defines a transcription unit that
extends from the promoter to the terminator. The critical feature of the transcription
unit, depicted in Figure 9.2, is that it constitutes a stretch of DNA expressed
via the production of a single RNA molecule. A transcription unit may include
more than one gene.
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Sequences prior to the startpoint are described as upstream of it; those after the
startpoint (within the transcribed sequence) are downstream of it. Sequences are
conventionally written so that transcription proceeds from left (upstream) to right
(downstream). This corresponds to writing the mRNA in the usual 5′→
3′ direction.
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Often the DNA sequence is written to show only the coding strand, which has the
same sequence as the RNA. Base positions are numbered in both directions away from
the startpoint, which is assigned the value +1; numbers are increased going downstream.
The base before the startpoint is numbered – 1, and the negative numbers increase
going upstream. (There is no base assigned the number 0.)
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The immediate product of transcription is called the primary transcript. It would
consist of an RNA extending from the promoter to the terminator, possessing the
original 5′ and 3′ ends. However, the primary transcript is almost always
unstable. In prokaryotes, it is rapidly degraded (mRNA) or cleaved to give mature
products (rRNA and tRNA). In eukaryotes, it is modified at the ends (mRNA) and/or
cleaved to give mature products (all RNA).
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Transcription is the first stage in gene expression, and the principal step at which
it is controlled. Regulatory proteins determine whether a particular gene is available
to be transcribed by RNA polymerase. The initial (and often the only) step in regulation
is the decision on whether or not to transcribe a gene. Most regulatory events occur
at the initiation of transcription, although subsequent stages in transcription
(or other stages of gene expression) are sometimes regulated.
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Within this context, there are two basic questions in gene expression:
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- How does RNA polymerase find promoters
on DNA? This is a particular example of a more general question: how do proteins
distinguish their specific binding sites in DNA from other sequences?
- How do regulatory proteins interact
with RNA polymerase (and with one another) to activate or to repress specific steps
in the initiation, elongation, or termination of transcription?
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In this chapter, we analyze the interactions of bacterial RNA polymerase with DNA,
from its initial contact with a gene, through the act of transcription, culminating
in its release when the transcript has been completed. The operon discusses
the various means by which regulatory proteins can assist or prevent bacterial RNA
polymerase from recognizing a particular gene for transcription. Regulatory circuits
discusses other means of regulation, including the use of small RNAs, and considers
how these interactions can be connected into larger regulatory networks. In Phage
strategies we consider how individual regulatory interactions can be connected
into more complex networks. In Promoters and enhancers and Activating transcription,
we consider the analogous reactions between eukaryotic RNA polymerases and their
templates.
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©Jones and Bartlett Publishers (2007)
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