Gene Regulation, Part 2
Lecture 15 (cont.)
Fall 2008
Eukaryotic Gene Expression
• Regulation occurs at many levels
Fig. 18.6
1
Chromatin Packing
• Chromatin
– Complex of DNA and proteins
• Histones
– Small proteins
– Positive charged so bind with DNA
• Nucleosomes (10 nm fiber)
– DNA wound twice around 8 histones
– Linker DNA: DNA between the nucleosomes
– Histones release from DNA during DNA replication and gene
expression
Fig. 16.21
2
Chromatin Packing
• 30 nm fiber
– Interactions between histone tails and linker DNA
• Looped domains (300 nm fiber)
– Loops form around a protein scaffold
• Metaphase
chromosome (700
nm)
– Further compaction
occurs
– Packing steps highly
specific
Fig. 16.21
3
Chromatin Packing
• Chromatin much less condensed in Interphase
– Nucleosomes, 30 nm and some loops (but no
scaffolding
• Loops attached to nuclear lamina
– May help organize regions of chromatin where genes
active
• Heterochromatin
– Areas of highly condensed chromatin during
interphase
• E.g., centromeres, telomeres
• Euchromatin
– Less condensed regions
• Read Fig. 16.22 Inquiry
4
Chromatin Packing & Gene Regulation
5
• Transcription affected by:
– Where promoter located in
relation to nucleosomes
– Genes within heterochrome
typically not transcribed
– Chemical modifications to
histones and DNA
• E.g., X chromosome inactivation
Fig. 15.8
Chromatin Packing & Gene Regulation
6
• Histone acetylation
– Addition of acetyl group (-COCH3) to histone tail
– Neutralizes positive charge of tail
• No binding to neighboring nucleosomes
• Genes available for transcription
– Requires enzymes
• May be part of transcription factors binding to promoter
• Deacetylation
Fig. 18.7
7
Chromatin Packing & Gene Regulation
• Histone methylation
– Adds methyl group (-CH3) to histone tails
– Promotes chromatin condensation
• Histone phosphorylation
– Promotes unfolding of chromatin
• Many signals may work together
Fig. 18.7
8
Chromatin Packing & Gene Regulation
• DNA methylation
– Addition of methyl group to base (~cytosine)
• Inactivated X chromosome highly
methylated
• Long term inactivation of genes
• Multiple mechanisms may work together
– Certain proteins binding to methyl groups
recruit histone deacetylation enzymes
• Both act to increase condensation of
chromatin
Chromatin Packing & Gene Regulation
• Methylation patterns passed on in cell division
– Genomic imprinting
• Variations in phenotype depending on whether an allele is
inherited from the male or female parent
– One allele “silenced” via methylation
Fig. 15.18
9
Chromatin Packing & Gene Regulation
• Epigenetic inheritance
– Modifications to chromatin that do not involve
a change in DNA sequence
– Inherited
– Can be reversed
10
Regulation of Transcription Initiation
• Control elements
– Segments of noncoding DNA that help
regulate transcription by binding certain
proteins
Fig. 18.8
11
Regulation of Transcription Initiation
• Transcription Factors
– Mediate binding of
RNA polymerase to
promoter & initiation
(eukaryotes)
– One TF binds to
TATA box
• Transcription initiation
complex
– Complex of RNA
polymerase and
transcription factors
Fig. 17.8
12
Regulation of Transcription Initiation
• General transcription factors
– Essential for the transcription of all protein-coding
genes
– Most transcription factors bind to other proteins
– Formation of transcription initiation complex allows for
initiation and transcription
• Rate of transcription low
13
Regulation of Transcription Initiation
• Specific transcription factors
– Control elements that control transcription of specific
genes
• Increase or decrease rate of gene expression
– Proximal control elements
– Close to promoter
– Distal control elements (Enhancers)
• More distant from promoter
• May be multiple enhancers per gene
Fig. 18.8
14
Regulation of Transcription Initiation
• Activators or repressors
can bind to enhancers
• Activators bind to
enhancers
• DNA bent to bring distal
control element closer to
promoter
– DNA bending protein
Fig. 18.9
15
16
Regulation of Transcription Initiation
• Activators interact with
mediator proteins
• Mediator proteins
interact with general
transcription factors
• Allows RNA
polymerase to bind
and promotes
increased transcription
Fig. 18.9
17
Regulation of Transcription Initiation
• Repressors can inhibit gene expression
– Block enhancer and prevent activator from
binding
– Block activator from binding with DNA
– Recruit proteins that deacetylate histones
Regulation of Transcription Initiation
• Enhancers ~ 10 control
elements
– Control elements bind to
only 1 or 2 specific
transcription factors
• Combination of control
elements important for
differential gene
expression
• Transcription activated
only when particular
combination of activator
proteins available
Fig. 18.10
18
Post-Transcriptional Regulation
• Alternative RNA splicing
– Different RNA molecules produced from same
primary transcript
– Regulatory proteins control intron-exon
choices
Fig. 18.11
19
Post-Transcriptional Regulation
• mRNA degradation
– Enzymes degrade mRNA after translation
• Bacterial mRNA – quick (few minutes)
• Eukaryote mRNA varies (hours to weeks)
– Poly-A tail shortened by enzymes
– Triggers removal of 5’ cap
– Nuclease enzymes degrade mRNA
20
21
Post-Transcriptional Regulation
Initiation of Translation
• Regulatory proteins bind to
untranslated regions (UTR) and block
binding of mRNA to ribosome
• Size of poly-A tail may prevent
translation
– Addition of adenine prompts translation
• “Global” activation of translation
– Activates translation in egg after
fertilization
– Trigger of activation of translation initiation
factors
– E.g., light triggers in plants
Fig. 17.17
Fig. 17.9
Post-Transcriptional Regulation
• Protein processing
– Cleavage, phosphorylation, addition of sugars
• Protein degradation
– Ubiquitin
• Marks protein for degradation
– Proteasome
• Protein complex that unfolds & degrades proteins
Fig. 18.12
22
23
Noncoding RNA & Gene Regulation
• ~ 1.5% of DNA codes for proteins
• Small portion of genome codes for small RNAs
– E.g. tRNA, rRNA
• Large amount of genome transcribed into nonprotein-coding RNA
Noncoding RNA & Gene Regulation
microRNA (miRNA)
• Small, single stranded RNA
– ~20 nucleotides long
• Bind to complementary
sequence in mRNA
• Degrades or blocks
translation of target mRNA
Fig. 18.13
24
25
Noncoding RNA & Gene Regulation
• Small interfering RNAs (siRNAs)
– Similar effect as microRNAs
– Involved in formation of heterochromatin at
centromeres