BIO 138 Chapter 6.

Mechanisms of Gene Regulation in Eukaryotes Page |1

VI. MECHANISMS OF GENE REGULATION IN EUKARYOTES

I. GENES THEMSELVES ARE ALTERED

A. GENE LOSS
o total loss of a gene or chromosome (whole or part)
o prominent in protozoa, insects and crustaceans
o except in cell destined to produce germ cells
 with complete DNA complement

1. Chromosome diminution in gall midges (an insect) and Parascaris aequorum (a roundworm)
 during early development (16-cell stage)
 whole or part of chromosome eliminated in all cells
 32 out of 40 chromosomes in gall midges are cells
 certain parts of 4 chromosomes in Parascaris are fragmented
 except in two cells that become germ cells
 with complete genome

2. macronucleus formation in Oxytrichia (a protozoan)

 formed from macronucleus
 via DNA cleavage and loss of some gene fragments
 possibly via restriction endonucleases

 ciliated protozoans
 macronucleus
 polyploid; somatic
 controls transcription during vegetative growth and asexual reproduction
 micronucleus
 haploid; germline
 How?

B. GENE AMPLIFICATION
o selective reproduction of multiple copies of a given gene without proportional increase in the copy of other
genes
o a small region of the genome is replicated many times

1. development of follicle cells in Drosophila

 chorion genes (X chromosome) amplified
 ~16-fold at stage 9 of egg chamber development
 chorion proteins form the hard coat or chorion
 in response to special needs during a specific stage of development

2. Amplification of the metallothionein gene in tissue cultured cells

 this gene codes for a protective metal-binding proteins
 in response to toxic dose of cadmium (an environmental stress)

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3. development of oocytes in Xenopus laevis
 gene for rRNA amplified ~4000 fold
 to produce large amounts of ribosomes (due to increased protein synthesis during cleavage)
 each unit of the rRNA consists of 18s and 28s separated by spacers of varying size

4. amplification of the myc gene (a protooncogene) in lung cancer cells

C. GENE REARRANGEMENT
o reorganization of particular sequences
o for switching expression form one pre-existing gene to another
 e.g. gene expression in mating type switching
o may create new genes, needed for expression in particular circumstances
 e.g. Ig gene

1. Mating Type switching in Yeast

o involves gene conversion in the MAT gene in chromosome 3
o 2 mating types of yeast
 a - with MATa allele --> a-factor pheromone
 α - with MATα allele --> α-factor pheromone
o two additional MAT-like genes (also in chromosome 3)
 HMRa (like a MATa sequence)
 HMRα (like a MATα sequence)
 silent mating type cassettes
 not transcribed
 upstream is a silencer which represses initiation of their transcription

Possible Mechanism for Gene Conversion

o one of the 3' ends produced by HO endonuclease -->
o extended through DNA synthesis using either silent mating type cassette (HMLα in this case)-->
o newly synthesized DNA subsequently replaces DNA currently at the MAT locus

2.Trypanosome antigen variation

o The major component of it s surface coat:
 VSG = variable surface glycoprotein
 VSG protein is constantly changing
 The trypanosome evades immune surveillance and perpetuates itself indefinitely
 Coded by VSG genes
 VSG genes: basic copy vs ELC
 Basic copy VSG genes
 ~1000 VSG genes
 Internal (not telomeric)
 Not transcribed (silent)
 Collection of DVDs on the rack
 ELC (expression-linked copy) VSG gene
 A VSG gene located at an expression site at the telomere
 The single VSG gene that is transcribed in a trypanosome at a given time
 Playing a DVD; DVD player: expression site
 The ELC can be changed by substituting the ELC with any one of the basic copy genes through
transposition

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Generation of Immunoglobulin Diversity
o Immunoglobulin (Ig)
 Antibodies
 Proteins that specifically recognize and help combat viruses, bacteria and antigens
 Very diverse (millions of different Igs)
 A genetic problem
 How could such a large number of proteins be coded without requiring an unreasonably large
number of genes?
 Somatic mutation
 Gene rearrangement
 The Ig structure (see handout)

D. DNA METHYLATION
o Cytosine--> 5-methylcytosine
o Methyl transferases
o Gene-specific and genome-wide
o Proper methylation patterns must be established and maintained specially during development
o In eukaryotes:
 Lower eukaryotes: rare
 Vertebrate: 10% of Cs
 Plants: 30% of Cs
o Methylation pattern is not random
 Limited to C in some copies of the sequences
 5"---CG---3' (or 5'---CNG---3' in plants)
 CpG s _______
o Methylation represses gene activity
o 2 types of DNA methylation activities
 maintenance methylation
 after genome replication
 methylated new strand at positions methylated sites in the parent strand
 the two daughter DNA retain methylation pattern of parent DNA
 daughter cells in a differentiated tissue inherit the methylation pattern and therefore, the pattern
of expression
 de novo methylation
 at totally new positions
 changes the methylation pattern in a localized region of the genome
o active genes are in unmethylated regions
o housekeeping genes - CpG unmethylated
o tissues specific genes - CpG unmethylated only in specific tissues
o How? (see handout)

II. EXPRESSION OF GENES IS MODULATED

A. TRANSCRIPTIONAL CONTROL
1. changes on the chromatin
 accessibility of a gene to TFs
 histone modifications
 --> gene activation
2. histone acetylation
 --> gene activation
 HATs (histone acetyl transferases
 acetylates histones and even general TFs (e.g. TFIIE and TFIIF)
 vs. HDAC (histone deacetylases)
3. Histone phosphorylation of H3 and H4
 --> gene activation
4. histone methylation of H3
 if at Lys 9 --> inactivation
 if at Lys 4 --> activation
5. Nucleosome remodeling
 repositioning of the nucleosomes within a short region
 DNA binding proteins can access their binding sites

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EPBQuebral 2009-39772 Cell and Molecular Biology