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C H A P T E R 4

REGULATION OF GENE EXPRESSION, TRANSCRIPTION, SPLICING,

AND RNA METABOLISM

Christopher R. Cogle

exons are separated from each other by intervening, noncoding
INTRODUCTION TO GENE REGULATION IN HEMATOLOGY sequences known as introns. Genes also have other noncoding DNA,
typically short sequences near or within genes that function as regula-
The function of a cell is governed by the sum of the specific proteins tory sequences critical for controlling gene expression. Together these
expressed. Protein expression is most commonly regulated at the level regulatory sequences determine in which cell, at what time, and in
of gene transcription into RNA, which is then processed and trans- what amount the gene is converted into the corresponding protein.
lated. The life of a cell is the life of its RNA. Therefore, to understand In order for transcription to begin, RNA polymerase must attach
how a cell behaves, one must understand the expression of a gene to a specific DNA region at the beginning of a gene. These regions,
through RNA. known as promoters, contain specific nucleotide sequences and
Transcription of DNA into RNA controls cellular differentiation, response elements. These provide a secure initial binding site on the
proliferation, and apoptosis in all differentiating cell systems, but gene for RNA polymerase. RNA polymerase often requires other
especially in hematopoiesis. For example, through regulation of proteins called transcription factors for proper recruitment to a given
transcription, hematopoietic stem cells maintain a balance between gene. Not all transcription factors are activating; some may inhibit
quiescence and differentiation to mature blood cell types. Regulation RNA polymerase, and repress gene expression by attaching to specific
of transcription is also necessary for erythroid progenitors to produce promoters and blocking binding of RNA polymerase. Promoters can
vast quantities of hemoglobin, for myeloid cells to generate granules additionally function together with other more distant regulatory
of immune responses, for lymphocytes to control immunoglobulin DNA regions (termed enhancers, silencers, boundary elements, or
levels, and for platelets to regulate levels of thrombotic receptors. insulators) to direct the level of transcription of a given gene. Unlike
Aberrant gene expression can result in hematologic disorders RNA polymerase, transcription factors are not limited to the pro-
such as lymphomas, leukemias, and myelodysplastic and myelopro- moter region, but can be directed by these other regulatory DNA
liferative syndromes, as will be discussed later. Understanding the sequences to either promote or repress transcription. The minimum
process behind RNA synthesis is also crucial for the diagnosis and essential transcription factors needed for transcription to occur are
treatment of hematologic disorders. Converting genetic information termed basal transcription factors and include transcription factor (TF)
contained in the DNA sequence of a gene into a finished protein IIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH. These ubiquitous
product is a complex process consisting of several steps, with each proteins bind to the recognition sequence in the promoter, forming
step involving distinct regulatory mechanisms. Beginning with the a transcription initiation complex that recruits the RNA polymerase.
basics of gene structure, this chapter will present the foundation Basal transcription factors cannot by themselves increase or decrease
necessary to understand the process of gene expression through RNA the rate of transcription but may be linked to activators by coactivator
synthesis and processing, including transcription, splicing, posttran- proteins that can.
scriptional modification, and nuclear export. Subsequent chapters The promoter is a regulatory sequence located near the start of
will present regulation of protein translation and posttranslational the gene, to provide the exact start site recognized by the transcription
modifications. machinery where conversion of the DNA template into intermediary
The first step of gene expression is transcription, where RNA molecules begins. The promoter contains the consensus sequence to
polymerases decode the DNA using specific start and stop signals to bind the transcription factors and then the RNA polymerase needed
synthesize RNA. In the subsequent step, splicing removes portions to initiate transcription. The best known example of this sequence is
of the RNA that do not code for protein. Next, the spliced RNA is the TATA box sequence, TATAAA, which binds RNA polymerase
modified for export out of the nucleus and into the cytoplasm, where and associated transcription factors. However, more than 80% of
ribosomes translate the RNA into protein products. mammalian protein-coding genes are driven by TATA-less promoters,
which contain different recognition sequences—often GC boxes. The
GC promoters are repeats of guanine and cytosine nucleotides, fre-
HOW GENES ARE ORGANIZED IN DNA quently have multiple transcriptional start sites, and require alterna-
tive transcription factors, like Specificity Protein 1 (Sp1).
The gene is the fundamental unit for storage and expression of Genes can have more than one promoter. This results in different-
genetic information. Genes are made up of nucleotide sequences of sized mRNAs, depending on how far the promoter is from the 5′ end
DNA, and are transferred to daughter cells during mitosis (and of the gene. The binding strength between a promoter and the
meiosis in gametes) via semi-conservative replication. Each cell in the transcription factors determines the avidity of RNA polymerase
human body contains about 25,000 genes, which are distributed binding, and subsequently of transcription. Some genetic diseases are
unevenly across the 46 individual chromosomes found within the associated with mutations in promoters, such as β-thalassemia, which
nucleus. Chromosomes are dense DNA–protein complexes that are can involve single nucleotide substitutions, small deletions, or inser-
made up of individual linear DNA helices packed tightly together by tions in the β-globin promoter sequence. The promoter mutations
specific protein repeats. Unwound completely and stretched out, the in β-thalassemias result in decreased RNA polymerase binding to
largest chromosome is about 1 m in length, demonstrating that the the transcriptional start site, and thereby reduce β-globin gene
cell, to even exist, must be an expert at packaging. expression.
Only 1% to 2% of human DNA actually serves as genes, which Globin gene expression in erythroid cells is also dependent on
are the templates for protein production. Most genes are broken another regulatory unit: the enhancer. Unlike promoters, which are
down into separated coding sections known as exons (Fig. 4.1). These situated close to the start site of the gene, enhancers can be positioned

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