during the lifecycle of a cell. Chromatin is in its most condensed or coiled form during
mitosis, when it forms a metaphase chromosome (700 nm in diameter). Regulation of
gene expression, as detailed below, involves nucleosome uncoiling and this change in
DNA conformation is termedchromatin remodeling. So, chromatin not only is necessary
for packaging DNA to conveniently fit within the nucleus of a cell but also plays an import-
ant role in gene expression.
6.3 Transcription
6.3.1 Transcription of DNA to Produce Messenger RNA (mRNA)
How does the information contained in a protein-coding gene on a chromosome within the
nucleus lead to the formation of a polypeptide in the cytoplasm? The key is that the DNA of
a gene does not directly participate in the synthesis of a polypeptide. The gene’s infor-
mation or message is faithfully carried by another molecule out of the nucleus and into
the cytoplasm. The first step in this information flow from DNA to polypeptide is to syn-
thesize this “messenger” from the gene in a process calledtranscription. The transcribed
messenger molecule, also referred to as atranscript, is another polynucleotide aptly
namedmessenger ribonucleic acid(mRNA). Like DNA, mRNA is composed of nucleo-
tides that are assembled in a 5^0! 30 direction; however, mRNA is made up ofribonucleo-
tides, because its sugar is aribose. Messenger RNA also differs from DNA in that it is a
single-stranded molecule and, in place of T, it has another base, uracil (U), which can
form a complementary base pair with A. Only one DNA strand of a gene is used as a “tem-
plate” during transcription to create the mRNA. The order or linear sequence of bases in this
DNAtemplatestrand (3^0! 50 ) determines the sequence of the mRNA (5^0! 30 ) because
transcription works through complementary base pairing. Consequently, the mRNA
made is a complement of the DNA template strand of the gene and an exact copy of the
other DNA strand of the gene (the codingstrand) except for having a U where a T
would be located (Fig. 6.4).
Transcription is carried out by the enzymeRNA polymerase II(RNAP II) in eukaryotes
such as plants. RNAP II does not act alone. Its binding and activity are controlled by both
DNA sequences located within the gene (cis-regulatory region) and by proteins (trans-
acting factors) calledtranscription factors, which can be general in helping transcribe
many genes or specific to one or a few genes. Gaining a better understanding of the
roles thatcis-regulatory regions and transcription factors play in gene regulation is an
active area of current research. Thegeneral transcription factors(GTFs) are necessary
for RNAP II to transcribe DNA. The specific transcription factors affect the efficiency or
the rate of RNAP II transcription for specific genes.
Thecis-regulatory region controlling transcription by RNAP II, called thepromoter,is
located at a gene’s 5^0 end (using the coding strand as a reference). The promoter is com-
posed of a core promoter plus other promoter elements that help define when and where
a gene is transcribed. The core promoter element is where RNAP II and the GTFs bind
to begin transcription. Thetranscription start site(the gene location where the first ribonu-
cleotide of the RNA being synthesized will base-pair) is designated as theþ1 site (i.e., the
first base in the transcript), so the gene promoter is therefore located upstream of (or before)
theþ1 site and its nucleotides are given negative numbers, whereas all nucleotides after the
þ1 site are positive sequential numbers (Fig. 6.5). As will be detailed below, the actual
140 MOLECULAR GENETICS OF GENE EXPRESSION