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 SizeOrganism 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

Human 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 ??????????????

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 expressi

on 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 regionsFigure 14.4

Figure 14.5

DNA-mRNA hybrids revealedthe

presence of

intronsFigure 14.6

capping tailing

the ends of primary transcripts are processedFigure 14.9

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

byspliceosomesFigure 14.10

regulation of

eukaryotic gene

expression may occur at many different points

Figure 14.11

transcriptionfactorsassist 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 independentgenesFigure 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

nonfunctional pseudogenes

human globin genes are found in

two gene familiesFigure 14.7

changes in expression of alternate globin genes

Figure 14.8

transcription factors remodel chromatin to bind promotersFigure 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