cell specialization in multicellular organisms results ... · d. cell specialization: regulation of...
TRANSCRIPT
D. Cell Specialization: Regulation of Transcription
Cell specialization in multicellular organisms results from differential gene expression
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D. CELL SPECIALIZATION: Regulation of Transcription
1. Chromosome, Gene and RNA Architecture
2. Cell-Specific Regulation of Chromosome Structure
3. Cell-Specific Regulation of Transcription Activation
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1. Review of Chromosome, Gene and RNA Architecture
a. Review of Chromatin Structure
b. Chromosomal Gene Arrangement
c. Single Gene Components
d. Nuclear RNA, mRNA and Protein
e. Other RNA Molecules
f. Fast review of Transcription
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a. Review of Chromatin Structure
• Chromatin is a complex of DNA and protein in the eukaryotic nucleus
• Loosely packed chromatin is called euchromatin
• Dense packing of the heterochromatin makes it difficult for the cell to express genetic information coded in these regions
• Histones are proteins that are responsible for the first level of DNA packing in chromatin
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DNA double helix (2 nm in diameter)
Nucleosome(10 nm in diameter)
Histones Histone tailH1
DNA, the double helix Histones Nucleosomes, or “beads on a string” (10-nm fiber)
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Figure 4-65 Molecular Biology of the Cell (© Garland Science 2008)
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Figure 4-11 Molecular Biology of the Cell (© Garland Science 2008)
b. Chromosomal Gene Arrangement
Humans:23 chromosome pairs3 billion bases~24,000 genes
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Figure 4-15 Molecular Biology of the Cell (© Garland Science 2008)
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Figure 6-14 Molecular Biology of the Cell (© Garland Science 2008)
Genes can reside on either strand
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c. Single Gene Components
Anatomy of a gene
Exon means sequence that exits the nucleusIntron means sequence that stays inside the nucleus
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d. Nuclear RNA, mRNA and Protein
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Figure 6-21 Molecular Biology of the Cell (© Garland Science 2008)
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e. Other RNA Molecules
1. The Translational Apparatus
2. Nuclear Effectors
3. Cytosolic Effectors
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Table 6-1 Molecular Biology of the Cell (© Garland Science 2008)
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DNAmolecule Gene 1
Gene 2
Gene 3
DNAtemplatestrand
TRANSCRIPTION
TRANSLATION
mRNA
Protein
Codon
Amino acid
Transcription:“To transcribe”to copy in the same language
Translation:“To translate”to copy into a new language
Templated Polymerization
f. Fast review of transcription
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Figure 6-8a Molecular Biology of the Cell (© Garland Science 2008)
RNA Polymerase II Complex Does it All
12 Protein Subunits in Human
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• As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at a time
• Transcription progresses at a rate of 40 nucleotides per second in eukaryotes
• The large subunit of RNA Pol II caps and polyadenylates the nascent nRNA
• The same large subunit of RNA also links to the splicosome to facilitate subsequent processing
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings
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Figure 6-9 Molecular Biology of the Cell (© Garland Science 2008)
Multiple RNA Pol II molecules can read DNA simultaneously
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• So, how do individual cells regulate which of the genes in their genome they will express?
• Remember from Intro Bio that prokaryotes regulate expression through repressors/activators
• Eukaryotes have more complex regulatory mechanisms
• Histone modification regulates chromatin structure
• DNA modification regulates promoter accessibility
• Epigenetic modification can be copied and inherited
• Transcription factors regulate promoter activation
• Specialized transcriptional activities
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2. Nucleosome and Histone Modification Regulates of Chromatin Structure
• Chromatin is a complex of DNA and protein in the eukaryotic nucleus
• Loosely packed chromatin is called euchromatin
• Dense packing of the heterochromatin makes it difficult for the cell to express genetic information coded in these regions
• Histones are proteins that are responsible for the first level of DNA packing in chromatin
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Cell-specific control of chromosome structure
Eukaryoticcells can systematicallycontrol whichgenes areavailable forexpression.
Our DNA iscomplexed50:50 withproteins andis very highly regulated byenzymaticalterations ofwhat is openand closed.
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Figure 4-28 Molecular Biology of the Cell (© Garland Science 2008)
Spontaneousnucleosomeunwrapping
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Figure 4-29 Molecular Biology of the Cell (© Garland Science 2008)
ATP-dependentnucleosomeunwrapping
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Histones are covalently modified to control gene accessibility
• The methylation and/or acetylation of either histones or the DNA itself determines what promoters are exposed.
• Different cell types have different enzymes and, thus, different areas of protein and DNA are targeted for alteration
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Cell-specific control of chromosome structure
3 Stages of Transcription1. Initiation2. Elongation3. Termination
Acetylation promotes Initiation Methylation can go either way
(lysine amino acid residues)
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3. The “Histone Code” Hypothesis
• Combinations of covalent modifications have specific information for the cell
– This DNA is newly replicated
– This DNA is damaged and needs repair
– Express this DNA
– Put this DNA into heterochromatin storage
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Figure 4-43 Molecular Biology of the Cell (© Garland Science 2008)
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Figure 4-45 Molecular Biology of the Cell (© Garland Science 2008)
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Figure 4-46a Molecular Biology of the Cell (© Garland Science 2008)
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b. Direct covalent modifications of DNA can also control expression from genes in the euchromatin
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Methylation of globin genes in human embryonic blood cells
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c. Heritability: Epigenetic Memory
OK. So a cell differentiates to become a blood vessel smooth muscle cell or fibroblast ......
• How come all of its mitotic descendents don’t have to go through differentiation?
– Trithorax proteins bind to open nucleosomes and keep them open.
– Polycomb proteins methylate uneeded nucleosomes and then bind to them to keep them tight.
– These effects can then be directly passed through mitotic cell division to the offspring.
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Two DNA methyltransferases are important in modifying DNA
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d. Transcription factors regulate promoter activation
– Core promoter made up of TATAbox and CpG islands
• Site of RNA Pol II recruitment and activation
• TF II family transcription factors bind RNA Pol II to core
– Tissue-specific TF are true transcriptional determinant for the cell type
• Bind to core promoter elements and distal enhancers
• Create binding sites for TF II family TF and stabilize Transcription Initiation Complex
• TS-TF also recruit histone acetyltransferases to expose DNA
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Tissue-Specific Transcription Factor Families
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Fig. 17-8
3�
Promoter
TATA box Start point
Template
TemplateDNA strand
5�3�5�
GeneralTranscriptionfactors
5�5�3�3�
RNA polymerase IICell-Specific Transcription factors
5�5� 5�3�
3�
RNA transcript
Transcription initiation complex
The TranscriptionInitiation Complexforms on every genethat gets expressed.Its presence there isreally determined bythe tissue specifictranscription factorsthat bind to enhancercis-elements.
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RNA polymerase is stabilized on the promoter site of the DNA by transcription factors recruited by promoters and enhancers
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Fig. 17-7b
Elongation
RNApolymerase
Nontemplatestrand of DNA
RNA nucleotides
3� end
Direction oftranscription(“downstream”) Template
strand of DNANewly madeRNA
3’
5’
5�
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Figure 6-3 Molecular Biology of the Cell (© Garland Science 2008)
The stability of the initiation complexdetermines how many transcripts
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Tissue-specific transcription factors may bind different enhancers
The pax-6 gene hasfour enhancers and isexpressed exclusivelyin those four tissue types.
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TS TFs can even control differentiation stability
A really important idea in cell differentiation is that there must be a molecular mechanism that keeps a cell differentiated.
– The pax-6 gene has a Pax-6 site in its enhancer
– When it is present the transcription rate is maximal
– This mechanism is repeated in several cell types
– A rare positive feedback loop
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e. Specialized transcriptional activities
• Only about 3-5% of RNA in a cell is mRNA
• Up to 80% of RNA is ribosomal RNA
– As many as 10 million ribosomes per cell
– humans have 400 rRNA gene copies on 5 chromosome pairs (frogs have 1200)
– 4 eukaryotic subunits: 18S, 5.8S, 28S, 5S
– First 3 from one gene with RNA Pol I
– 5S is from a separate gene with RNA Pol III
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Figure 6-42 Molecular Biology of the Cell (© Garland Science 2008)
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Table 6-1 Molecular Biology of the Cell (© Garland Science 2008)
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RNA Molecules and their RNA Polymerases
• Most snRNA and miRNA: Pol II
• tRNA, shRNA, snRNA 6, miRNA: Pol III
• snoRNA often encoded in introns: Pol II
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