Download Eukaryotic Genome and its Expression Chapter 14

Eukaryotic Gene Expression
The “More Complex” Genome
genome characteristics differ
dramatically
Table 14.1
E. coli and yeast, the “eukaryotic E. coli”
Table 14.2
Table 14.3
Table 14.4
The Eukaryotic Genome
• prokaryotic and eukaryotic genomes encode
many of the same functions
• eukaryotes encode additional functions
associated with organelles
• genomes of multicellular eukaryotes encode
additional functions
• each eukaryotic kingdom encodes specialized
products
– so, eukaryotic genomes are larger
– but why so much?
Genomes Vary in Size
Organism
Genome Size (bp)
Genes
E. coli
4,460,000 (h)
4,300
Yeast
24,136,000
6,200
Nematode
97,000,000
19,099
Fruit fly
180,000,000
13,600
Puffer fish
365,000,000
~30,000
6,200,000,000
22,000
Arabidopsis
119,000,000
15,000 (26,000)
Rice
389,000,000
37,544
Lily
600,000,000,000
??????????????
Human
Table 14.5
The Eukaryotic Genome
• Genomics
– analyzes and compares entire genomes of
different organisms
– sequences of many genomes are complete
• Proteomics
– analyzes and compares the functions of the
proteins in an cells, tissues, organs,
organisms
The Eukaryotic Genome
• repetitive DNA sequences
– highly repetitive sequences (103 - 106 each)
• tandemly repeated satellites (5-50 bp)
–mainly at centromeres
• minisatellites (12-100 bp)
–Variable Number Tandem Repeats
• microsatellites (1-5 bp x 10-50)
–small, scattered clusters
• untranslated
Figure 11.18
rRNA genes are tandemly repeated
Figure 14.2
The Eukaryotic Genome
• repetitive DNA sequences
– moderately repetitive sequences
• telomeres (~2500 x TTAGGG per
chromosome end - human)
• clustered tRNA, rRNA genes (~280 rRNA
coding units on 5 chromosomes - human)
• transposable elements (transposons)
The Eukaryotic Genome
• transposable elements (transposons)
– SINES: transcribed elements ~500 bp long
– LINES: elements ~7000 bp long; some are
expressed
• >100,000 copies
• retrotransposition
– retrotransposons: like retroviral genomes
– DNA transposons: translocating DNAs
Figure 14.3
gene
expression
in
eukaryotes
Figure 14.1
The Eukaryotic Genome
• Gene expression
– protein-coding genes
• contain non-coding sequences
–promoter
–terminator
–introns interrupt the coding sequence
found in exons
• the primary transcript is processed to
produce an mRNA
eukaryotic genes contain non-coding regions
Figure 14.4
Figure 14.5
DNA-mRNA
hybrids
revealed
the
presence
of
introns
Figure 14.6
the ends of primary transcripts
are processed
Figure 14.9
capping
tailing
The Eukaryotic Genome
• Gene expression
– protein-coding genes
• primary transcripts are processed to
produce mRNAs primary transcripts are
processed to produce mRNAs
–the 5’ end is capped with reversed GTP
–the 3’ end is given a “poly (A)” tail at
the polyadenylation site, AAUAAA
–introns are removed during splicing by
snRNPs of the spliceosome
introns
are
removed
from
primary
transcripts
by
spliceosomes
Figure 14.10
regulation
of
eukaryotic
gene expression
may occur
at many
different
points
Figure 14.11
transcription
factors
assist
RNA polymerase
to bind
to the
promoter
Figure 14.12
The Eukaryotic Genome
• expression of eukaryotic genes is highly
regulated
– three different RNA polymerases transcribe
different classes of genes
– each RNA polymerase binds to a different
class of promoters
– RNA polymerases require transcription
factors in order to bind to their promoters
– transcriptional activators may bind far from
the promoter
DNA elements are binding sites for proteins
of the transcription machinery
Figure 14.13
DNA looping can bring distant protein factors
into contact with the promoter complex
Figure 14.13
The Eukaryotic Genome
• expression of eukaryotic genes is highly
regulated
– eukaryotes do not group genes with related
functions together in operons
– genes that are coordinately expressed share
DNA elements that bind the same
transcriptional regulator proteins
common response
elements enable
coordinated
expression of
independent
genes
Figure 14.14
gene regulators bind to DNA elements
• common motifs are found among gene
regulators
Figure 14.15
The Eukaryotic Genome
• many genes are present in single copies
– some genes are present in a few similar
copies in “gene families”
• one or more expressed, functional genes
• non-functional pseudogenes
human globin genes are found in
two gene families
Figure 14.7
nonfunctional pseudogenes
changes in expression of
alternate globin genes
Figure 14.8
transcription
factors
remodel
chromatin
to bind
promoters
Figure 14.16
The Eukaryotic Genome
• DNA is packaged as chromatin in the nucleus
– transcription factors remodel chromatin to
bind promoters
• condensed DNA can “turn off” entire
regions of chromosomes
The Eukaryotic Genome
• one gene can encode more than one
polypeptide
– some primary transcripts undergo
alternative splicing
alternate splicing: multiple polypeptides from
single genes
Figure 14.20
The Eukaryotic Genome
• proteins are ultimately removed, degraded and
replaced
– the proteasome degrades proteins that are
tagged for degradation
the proteasome recognizes
ubiquitin-bound polypeptides
Figure 14.22