Expression of Human Genes Chapter 8 Expression of Human Genes Regulation of gene expression occurs at three levels: A. At the transcriptional level B. Post-transcriptional C. Epigenetic and long range control

A. Control of gene expression by binding of trans-acting protein factors to cis-acting regulatory sequences in DNA and RNA: Control by DNA-binding proteins Control by RNA-binding proteins

1. Ubiquitous transcription factors are required for transcription by RNA polymerase I and III Requirements for transcription by RNA polymerase I (18S, 5.8S and 28S RNA) Requirements for transcription by RNA polymerase III (tRNA and 5S RNA)

2. Transcription of polypetide-coding genes require a set of cis-acting elements and tissue- and developmental-specific transcription factors RNA polymerase II is responsible for transcribing protein-coding genes and certain snRNA genes.

3. Transcription factors contain conserved structural motifs that permit DNA binding: Transcription factors for humans have two distinct functions An activation domain A DNA-binding domain

Four types of transcription factors: 1. The leucine zipper motif 2. The helix-loop-helix motif 3. The helix-turn-helix motif 4. The zinc finger motif

4. Several mechanisms permit transcriptional regulation of gene expression in reponse to external stimuli: (a) Ligand-inducible transcription factors (for small hydrophobic hormones such as steroid which diffuse through plasma membrane) Transcription factors (often known as hormone nuclear receptors) are activated by binding to a ligand then bind to a response element located in the promoter regions of about 50-100 target genes and activates their transcription. The hormone nuclear receptors are characterized by two conserved domains: - a DNA binding domain (68 amino acid long). It contains zinc fingers and binds to DNA as a dimer. - a ligand binding domain (240 amino acid)

(b) Activation of transcription factors by signal transduction For hydrophilic signaling molecules that cannot diffuse through plasma membrane. Instead they bind to a specific receptor. Two genral mechanisms permit transmission of signals from cell-surface receptors to the nucleus: -i- Protein kinases are activated then translocated from the cytoplasm to the nucleus where they phosphorylate target transcription factors. E.g. hormonal signaling through cyclic AMP pathway -ii- Inactive transcription factors stored in the cytoplasm are activated by phosphorylation and translocated into the nucleus. E.g. activation of NF-kB via protein kinase C signaling

5. Translational control of gene expression can involve specific recognition by RNA-binding proteins of regulatory sequences within the untranslated sequences of RNA: Several cis-acting regulatory elements, mostly are bound by trans-acting RNA-binding proteins and regulate at the translational level in three ways: -i- intracellular RNA localization -ii- translational control of gene expression in response to external stimuli. E.g. The IRE-binding protein regulates the production of ferritin heavy chain and transferrin receptor by binding to iron-response elements (IREs) in the 5’- or 3’-untranslated regions. -iii- translational control of gene expression of gene expression during early development. Upon fertilization no new mRNA is transcribed until the 4-8 cell stage and regulation occurs at the translational level for maternal mRNA synthesized during oogenesis.

B. Alternative transcription and processing of individual genes 1. Transcription of a single human gene can be initiated from a variety of alternative promoters and can result in a variety of tissue-specific isoforms. This results in Tissue-specificity e.g. dystrophin gene Developmental stage-specificity e.g. the insulin-like growth factor II gene Differential subcellular localization e.g. soluble and mebrane-bound isoforms Differential functional capacity e.g. the progesterone receptor Sex-specific gene regulation the Dnmt1 methyltransferase gene

2. Human genes often encode more than one product as a result of alternative splicing and alternative polyadenylation events. E.g. -i- Differential splicing in the WT1 Wilm’s tumor gene -ii- Alternative polyadenylation of the calcitonin gene results in tissue-specific products

3. RNA editing is a rare form of post-transcriptional processing whereby base-specific changes are enzymatically introduced at the RNA level. Types of RNA editing in humans: (i) C---> U, occurs in humans by a specific cytosine deaminase e.g. The expression of the human apolipoprotein B gene in the intestine involves tissue-specific RNA editing (ii) A ---> I, the amino group in in carbon 6 of adenine is replaced by a carbonyl group. I then acts as a G. Occurs in some ligand-gated ion channels. (iii) U ---> C, in mRNA of the WT1 Wilms’ tumor gene (iv) U ---> A, in alpha-galactosidase mRNA