What does the word Promoter mean? It is the place at which RNA Pol II binds. But the word is...
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What does the word Promoter mean?
It is the place at which RNA Pol II binds.But the word is incorrectly used to describeEnhancers plus Promoter.
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Initiation by RNA Polymerase II
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TFIID recognition site is TATAA
How often is this site found in the genome? 1/45
Once every 1000 nucleotides 109 nucleotides or 106 times
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More CellsBut on a per cellBasis expression levels of -gal is about the same
Transient transfection
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Stable transfection
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Recruitment Model
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Chapter 6Genome
Sequences andGene Numbers
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6.1 Introduction
Figure 06.01: The minimum gene number required for any type of organism increases with its complexity.
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6.2 Prokaryotic Gene Numbers Range Over an Order of Magnitude
• The minimum number of genes for a parasitic prokaryote is about 500; for a free-living nonparasitic prokaryote it is about 1500.
Figure 06.02: Genome sizes and gene numbers are known from complete sequences for
several organisms.
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Figure 06.03: The number of genes in bacterial and archaeal genomes is proportional to genome size.
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6.2 Prokaryotic Gene Numbers Range Over an Order of Magnitude
• pathogenicity islands – DNA segments that are present in pathogenic bacterial genomes but absent in their nonpathogenic relatives.
• horizontal transfer – The transfer of DNA from one cell to another by a process other than cell division, such as bacterial conjugation.
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6.3 Total Gene Number Is Known for Several Eukaryotes
• There are 6000 genes in yeast; 21,700 in a nematode worm; 17,000 in a fly; 25,000 in the small plant Arabidopsis; and probably 20,000 to 25,000 in mice and humans.
Figure 06.04: The number of genes in a eukaryote varies from 6000-
40,000 but does not correlate with genome size or the organism
complexity.
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Figure 06.05: The S. cerevisiae genome of 13.5 Mb has 6000 genes, almost all uninterrupted.
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6.3 Total Gene Number Is Known for Several Eukaryotes
• monocistronic mRNA – mRNA that encodes one polypeptide.
• polycistronic mRNA – mRNA that includes coding regions representing more than one gene.
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6.3 Total Gene Number Is Known for Several Eukaryotes
Figure 06.06: Functions of Drosophila genes based on comparative genomics of twelve species.
Adapted from Drosophila 12 Genomes Consortium, “Evolution of genes and genomes on the Drosophila phylogeny,” Nature 450 (2007): 203–218.
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6.4 How Many Different Types of Genes Are There?
• The sum of the number of unique genes and the number of gene families is an estimate of the number of types of genes.
Figure 06.07: Many genes are duplicated,
and as a result the number of different
gene families is much less than the total number of genes.
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6.4 How Many Different Types of Genes Are There?
• orthologous genes (orthologs) – Related genes in different species.
• The minimum size of the proteome can be estimated from the number of types of genes.
Figure 06.09: Fruit fly genome can be divided into genes present in all eukaryotes, genes present in all multicell eukaryotes, genes specific to flies.
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6.5 The Human Genome Has Fewer Genes Than Originally Expected
• Only 1% of the human genome consists of exons.• The exons comprise ~5% of each gene, so genes (exons
plus introns) comprise ~25% of the genome.• The human genome has 20,000 to 25,000 genes.
Figure 06.11: Genes occupy 25% of the human genome, but protein-coding sequences are only a
small part of this fraction.
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6.5 The Human Genome Has Fewer Genes Than Originally Expected
Figure 06.12: The average human gene is 27 kb long and has nine exons, usually comprising two longer exons at each end and seven internal exons.
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6.5 The Human Genome Has Fewer Genes Than Originally Expected
• ~60% of human genes are alternatively spliced.
• Up to 80% of the alternative splices change protein sequence, so the proteome has ~50,000 to 60,000 members.
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6.6 How Are Genes and Other Sequences Distributed in the Genome?
• Repeated sequences (present in more than one copy) account for >50% of the human genome.
• The great bulk of repeated sequences consists of copies of nonfunctional transposons.
• There are many duplications
of large chromosome regions.
Figure 06.14: The largest component of the human genome consists of transposons.
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6.7 The Y Chromosome Has Several Male-Specific Genes
• The Y chromosome has ~60 genes that are expressed specifically in the testis.
• The male-specific genes are present in multiple copies in repeated chromosomal segments.
• Gene conversion between multiple copies allows the active genes to be maintained during evolution.
Figure 06.15: The Y chromosome consists of X-transposed regions,
X-degenerate regions, and amplicons.
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6.8 How Many Genes Are Essential?
• Not all genes are essential. In yeast and flies, deletions of <50% of the genes have detectable effects.
• When two or more genes are redundant, a mutation in any one of them may not have detectable effects.
Figure 06.16: Essential yeast genes are found in all classes.
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6.8 How Many Genes Are Essential?
• We do not fully understand the persistence of genes that are apparently dispensable in the genome.
Figure 06.17: A systematic analysis of loss of function
for 86% of worm genes shows that only 10% have detectable effects on the
phenotype.
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6.8 How Many Genes Are Essential?
• synthetic lethal – Two mutations that are viable by themselves but cause lethality when combined.
• synthetic genetic array analysis (SGA) – An automated technique in budding yeast whereby a mutant is crossed to an array of approximately 5000 deletion mutants to determine if the mutations interact to cause a synthetic lethal phenotype.
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6.8 How Many Genes Are Essential?
Figure 06.19: The chart shows how many lethal interacting genes there are for each test gene.
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6.9 About 10,000 Genes Are Expressed at Widely Differing Levels in a Eukaryotic Cell
• In any particular cell, most genes are expressed at a low level.
• scarce (complex) mRNA – mRNA that consists of a large number of individual mRNA species, each present in very few copies per cell.– This accounts for most of the sequence complexity in
RNA.
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6.9 About 10,000 Genes Are Expressed at Widely Differing Levels in a Eukaryotic Cell
• Only a small number of genes, whose products are specialized for the cell type, are highly expressed.– abundance – The average number of mRNA
molecules per cell.
– abundant mRNA – Consists of a small number of individual species, each present in a large number of copies per cell.
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6.9 About 10,000 Genes Are Expressed at Widely Differing Levels in a Eukaryotic Cell
Figure 06.20: Hybridization between excess mRNA and cDNA
identifies components in chick oviduct cells, characterized by the
Rot1/2 of reaction.
Figure 06.21: The abundances of yeast mRNAs vary from <1 per cell to >100 per cell.
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6.9 About 10,000 Genes Are Expressed at Widely Differing Levels in a Eukaryotic Cell
• mRNAs expressed at low levels overlap extensively when different cell types are compared.– housekeeping gene – A gene that is (theoretically)
expressed in all cells because it provides basic functions needed for sustenance of all cell types.
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6.9 About 10,000 Genes Are Expressed at Widely Differing Levels in a Eukaryotic Cell
• The abundantly expressed mRNAs are usually specific for the cell type.– luxury gene – A gene encoding a specialized
function, (usually) synthesized in large amounts in particular cell types.
• ~10,000 expressed genes may be common to most cell types of a multicellular eukaryote.
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6.10 Expressed Gene Number Can Be Measured En Masse
• DNA microarray technology allows a snapshot to be taken of the expression of the entire genome in a yeast cell.
• ~75% (~4500 genes) of the yeast genome is expressed under normal growth conditions.
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6.10 Expressed Gene Number Can Be Measured En Masse
• DNA microarray technology allows detailed comparisons of related animal cells to determine (for example) the differences in expression between a normal cell and a cancer cell.
Figure 06.22: Heat map of 59 invasive breast tumors from women who breastfed ≥6 months (red lines) or who never breastfed (blue lines).
Image courtesy of Rachel E. Ellsworth, Clinical Breast Care Project, Windber Research Institute.