Genotype to Phenotype: Noncoding DNA
Genotype to Phenotype: Noncoding DNA
Learning Objectives
Describe the two types of information in the genome.
Explain how gene regulatory switches and transcriptional regulatory proteins function to cause structural and functional differences between cell types in the same organism and different phenotypes between individuals.
Explain how transcriptional regulation can cause the same individual to have different phenotypes at different stages of development.
Introduction
Genetics explains biodiversity.
Genetic differences occur in:
Protein-coding DNA sequences
Non-coding DNA sequences
Differences between alleles in non-coding sequences explain phenotype differences between individuals and species.
Big Ideas
Differences between genotype in noncoding DNA explain how bodies develop different cell types.
Differences between genotype in noncoding DNA explain how different phenotypic forms develop between organisms.
Information in the Genome
Two Types of Information
Instructions for making gene products (proteins):
Codons for amino acid sequences
In coding regions of genes
Easily found by computer software
Instructions for when, how much, and in what cells to transcribe genes:
In non-coding regions of DNA
Harder to distinguish; requires experimental work
Usually nearby the coding region but can be far away (hundreds of thousands of base pairs).
Comparison of Coding vs. Non-Coding DNA
E. Coli: 90% of the genome codes for proteins.
Humans: Less than 5% of the genome codes for proteins.
The remaining greater than 95% contains regulatory information.
We've discovered only a small fraction of regulatory sequences.
A large fraction of non-coding DNA may have no specific function ("junk DNA"), remnants of past genomic elements like viruses and transposable elements.
Gene Transcription and Regulation
Transcription Levels and Regulation
Genes/alleles are DNA sequences in chromosomes. They are transcribed to mRNA, which are translated to proteins.
The amount of mRNA transcribed from an allele varies. Different levels of mRNA are produced for different genes, leading to varied protein production.
It depends on the gene, cell type, time, and environmental factors.
Some genes are transcribed at high levels (high protein production), others at low levels.
Some genes are repressed (no mRNA or protein production).
Transcription level varies with:
Cell type
Time (development, lifetime)
Environmental factors (internal and external)
Control of Transcription Level
Key factor: non-coding DNA near (or far from) the coding region.
Genes have coding and non-coding regions.
Coding region: transcribed (transcription start and stop sites).
Non-coding region: regulatory sequences.
Importance of Transcriptional Regulation
Allows different cells in the same organism to perform different functions.
Gene Regulatory Switches and Cell Types
Cell Diversity
All cells in an organism have the same DNA sequence (descended from a single zygote via mitosis).
Gene regulatory switches enable cells to transcribe different genes, resulting in different mRNAs, proteins, and cell phenotypes (cell types).
How Gene Regulatory Switches Work
Genes contain coding (amino acid sequences) and non-coding sequences.
Non-coding DNA contains gene regulatory switches
Gene expression: transcription and protein production.
Non-coding regions determine:
How much transcription takes place
What cells the gene is transcribed in
When the gene is transcribed
Basics of Transcription
RNA Polymerase
RNA polymerase acts at promoters (sequences adjacent to the coding region).
Activation of RNA polymerase requires transcriptional activating proteins.
Each cell type has its own set of transcriptional activating proteins.
These proteins bind to gene regulatory switches (specific DNA sequences in non-coding DNA).
Binding causes DNA to bend, allowing the gene regulatory proteins to interact with RNA polymerase and activate transcription.
Gene Regulatory Switch
Short sequence of DNA in the non-coding part of a gene.
Specific transcriptional regulatory proteins (transcription factors) recognize and bind to specific switch sequences.
Mutating a base pair in the switch can prevent protein binding.
Binding affects transcription (increases/activates or decreases/represses).
Muscle Cell vs. Nerve Cell Example
In a muscle cell nucleus, muscle-specific transcriptional activating proteins are present.
Gene regulatory switches are DNA sequences in non-coding DNA, the same in every cell.
If there's a nerve-specific regulatory switch sequence nearby, it won't be used in the muscle cell because the nerve-specific protein isn't present.
In a nerve cell nucleus, nerve-specific transcriptional activating proteins are present, so the nerve-specific switch will be used to activate transcription.
Gene Regulation Specificity
Different gene regulatory switches determine transcription levels in:
Different cell types/body parts
Different developmental stages
Different environmental conditions
Responding to different signals (e.g., hormones)
A gene may have different switches for different contexts.
Mutation in one switch might only affect transcription at one stage.
Different genes have different regulatory switches.
Negative Regulation and Expression Levels
Some gene regulatory switches act as negative regulators, binding repressors to prevent transcription.
Transcriptional regulation isn't just on/off but occurs over a range of expression levels. Most genes expression level is somewhere between repressed, intermediate, and high transcription based on the gene.
Gene regulatory switches often have multiple binding sites for transcriptional regulatory proteins (activators and repressors), acting like a dimmer switch.
Dimmer Switch Example
Repressor bound (DNA Transcription off): dimmer switch off.
One binding site bound: low-level transcription; dimmer switch low.
Two binding sites bound: intermediate-level transcription; dimmer switch intermediate.
All three sites bound: high-level transcription; dimmer switch highest position.
Location and Components of Gene Regulatory Switches
Gene regulatory switches don't need to be near the promoter; they can be far away, on the other side of the gene, or in introns.
Gene regulatory switches are part of the non-coding DNA.
Gene regulatory switches are specific sequences of noncoding DNA in the genome
Gene regulatory switches are not proteins, and proteins are not part of the gene regulatory switch itself.
Proteins bind to gene regulatory switches, which influences transcription of the nearby gene either by increasing it or decreasing it as we have described.
Gene regulatory switch = light switch; transcriptional regulatory protein = person's hand operating switch.
Summary of Gene Regulatory Switches
DNA sequences in the non-coding DNA of genes.
The same in all cells (all switches are present).
Each switch type has a different sequence and binds to a specific transcriptional regulatory protein.
Transcriptional regulatory proteins can activate (activators) or repress (repressors) transcription.
First Big Idea Recap
Cells of an organism with identical DNA sequences can have different characteristics because transcriptional regulatory switches enable cells to transcribe different genes.
This leads to different mRNAs, proteins, and cell phenotypes (cell types).
There are approximately 200 different cell types in humans, with many subtypes.
Important Points
Proteins that bind to gene regulatory switches are encoded by other genes in the genome.
Humans have approximately 1,500 to 2,000 different transcriptional regulatory proteins.
Transcriptional regulatory proteins can regulate expression of the gene that encodes them
Each gene is regulated by several transcriptional regulatory proteins.
Each gene has different non-coding DNA sequences and different transcriptional regulatory switches.
Genes expressed in the same cell types/patterns may be similar but always have some differences in sequence and configuration.
Each gene sequence evolves separately with random mutations.
Revisiting the Chicken and Egg Problem
How do cells come to have different proteins if all cells have the same DNA?
Before the zygote, in the egg cell, there are different proteins in different areas and concentrations.
After fertilization, the zygote has different proteins/concentrations in different areas.
These are key transcriptional regulatory proteins for early development.
As the zygote undergoes cell division, daughter cells have different proteins/concentrations.
This leads to different regulatory proteins and different genes expressed in different parts of the developing body.
Differences in protein between cells are due to the placement of proteins and mRNAs in egg cells before zygote formation.
Transcriptional Regulation during Development
How can transcriptional regulatory switches explain different phenotypes at different developmental stages (e.g., caterpillar to butterfly)?
Comparing Cell Types and Developmental Stages
Liver and kidney cells in a person vs. caterpillar and adult butterfly cells.
Same DNA sequence in all cells, including coding and non-coding DNA (gene regulatory switches).
Different genes are transcribed, and transcription amounts vary.
Different mRNAs and proteins are expressed.
These differences in gene products cause different structures and functions.
Case Studies Revisiting
Huntington's Disease and Keratin Genes
Allele differences in coding parts of the gene (amino acid sequences) cause structural/functional protein differences.
No difference in the amount of protein expressed.
No difference in the cell types in which the protein is expressed.
Huntington's: expressed in the same brain cells.
Keratin: expressed in the same skin cells.
There are no meaningful DNA sequence differences in the non-coding parts of the gene between the allele types of Huntington and the allele types of keratin.
Importance of Non-Coding DNA
Non-coding DNA is important for Huntington and keratin genes.
Gene regulatory switches are necessary for expression in certain cell types.
Huntington: transcription in certain brain cells.
Keratin: transcription in certain skin cells.
Switches are critical; without them, neither allele would be expressed.
Gene regulatory switches of the noncoding DNA are essential parts of all genes.
Asymmetric Cell Division
If all cells have the same DNA, how do they get different transcriptional regulatory proteins?
Mitosis produces genetically identical cells.
Many cell divisions are asymmetric, with unequal division of proteins and mRNAs.
Some cells get more mRNA/protein than others.
These mRNAs/proteins cause cells to express different genes or have different expression levels, eventually resulting in different protein sets and cell types.
Summary of Big Ideas
Non-coding DNA allows genes to be expressed at different levels in different cell types, creating cell/tissue diversity.
Differences between alleles in non-coding DNA sequences play a major role in causing the diversity of phenotypes among individual organisms.
Genotype to Phenotype: Noncoding DNA
Learning Objectives
Describe the two types of information in the genome.
Explain how gene regulatory switches and transcriptional regulatory proteins function to cause structural and functional differences between cell types in the same organism and different phenotypes between individuals.
Explain how transcriptional regulation can cause the same individual to have different phenotypes at different stages of development.
Introduction
Genetics explains biodiversity. It helps us understand why different organisms and individuals within a species exhibit distinct traits.
Genetic differences occur in:
Protein-coding DNA sequences: Variations in these sequences can directly alter the structure and function of proteins.
Non-coding DNA sequences: These regions regulate when, where, and how genes are expressed.
Differences between alleles in non-coding sequences explain phenotype differences between individuals and species. These differences affect gene expression, leading to variations in traits.
Big Ideas
Differences between genotype in noncoding DNA explain how bodies develop different cell types. Gene regulatory elements in noncoding DNA control cell differentiation and specialization.
Differences between genotype in noncoding DNA explain how different phenotypic forms develop between organisms. Variations in regulatory sequences drive evolutionary changes in morphology and physiology.
Information in the Genome
Two Types of Information
Instructions for making gene products (proteins):
Codons for amino acid sequences: Three-nucleotide sequences that specify which amino acid should be added to the growing polypeptide chain.
In coding regions of genes: Exons that are transcribed and translated into proteins.
Easily found by computer software: Bioinformatics tools can identify open reading frames (ORFs) that are likely to encode proteins.
Instructions for when, how much, and in what cells to transcribe genes:
In non-coding regions of DNA: Regulatory sequences such as promoters, enhancers, and silencers.
Harder to distinguish; requires experimental work: Identifying these regions often involves techniques like ChIP-seq and reporter assays.
Usually nearby the coding region but can be far away (hundreds of thousands of base pairs).: Enhancers can act over long distances by looping back to interact with the promoter.
Comparison of Coding vs. Non-Coding DNA
E. Coli: 90% of the genome codes for proteins. This reflects the streamlined nature of prokaryotic genomes, where most DNA directly contributes to protein production.
Humans: Less than 5% of the genome codes for proteins. This small fraction underscores the complexity of gene regulation in eukaryotes.
The remaining greater than 95% contains regulatory information. These sequences control gene expression, development, and responses to environmental stimuli.
We've discovered only a small fraction of regulatory sequences. The functions of many non-coding regions remain unknown, representing a frontier in genomics research.
A large fraction of non-coding DNA may have no specific function ("junk DNA"), remnants of past genomic elements like viruses and transposable elements. These elements can contribute to genome evolution and plasticity.
Gene Transcription and Regulation
Transcription Levels and Regulation
Genes/alleles are DNA sequences in chromosomes. They are transcribed to mRNA, which are translated to proteins. This is the central dogma of molecular biology.
The amount of mRNA transcribed from an allele varies. Different levels of mRNA are produced for different genes, leading to varied protein production. This is a key mechanism for controlling gene expression.
It depends on the gene, cell type, time, and environmental factors. Gene expression is highly context-dependent.
Some genes are transcribed at high levels (high protein production), others at low levels. This differential expression is essential for cell specialization and function.
Some genes are repressed (no mRNA or protein production). Repression ensures that certain genes are only expressed under specific conditions.
Transcription level varies with:
Cell type: Different cell types express distinct sets of genes, allowing them to perform specialized functions.
Time (development, lifetime): Gene expression patterns change dramatically during development and aging.
Environmental factors (internal and external): Genes respond to signals from the environment, allowing organisms to adapt to changing conditions.
Control of Transcription Level
Key factor: non-coding DNA near (or far from) the coding region. Regulatory sequences in non-coding DNA control the rate and timing of transcription.
Genes have coding and non-coding regions.
Coding region: transcribed (transcription start and stop sites). This region contains the instructions for building a protein.
Non-coding region: regulatory sequences. These sequences determine when and where the gene is transcribed.
Importance of Transcriptional Regulation
Allows different cells in the same organism to perform different functions. Transcriptional regulation is essential for cell differentiation and tissue organization.
Gene Regulatory Switches and Cell Types
Cell Diversity
All cells in an organism have the same DNA sequence (descended from a single zygote via mitosis). Despite having identical genomes, cells can have very different characteristics.
Gene regulatory switches enable cells to transcribe different genes, resulting in different mRNAs, proteins, and cell phenotypes (cell types). These switches control which genes are turned on or off in each cell.
How Gene Regulatory Switches Work
Genes contain coding (amino acid sequences) and non-coding sequences. Both types of sequences are crucial for gene function.
Non-coding DNA contains gene regulatory switches. These switches are the key to cell-specific gene expression.
Gene expression: transcription and protein production. This is the process by which genes exert their effects.
Non-coding regions determine:
How much transcription takes place: Regulatory sequences can enhance or repress transcription.
What cells the gene is transcribed in: Cell-specific transcription factors bind to these sequences.
When the gene is transcribed: Temporal control of gene expression is essential for development.
Basics of Transcription
RNA Polymerase
RNA polymerase acts at promoters (sequences adjacent to the coding region). Promoters are the sites where transcription begins.
Activation of RNA polymerase requires transcriptional activating proteins. These proteins help recruit RNA polymerase to the promoter.
Each cell type has its own set of transcriptional activating proteins. This is how cell-specific gene expression is achieved.
These proteins bind to gene regulatory switches (specific DNA sequences in non-coding DNA). Binding of these proteins regulates transcription.
Binding causes DNA to bend, allowing the gene regulatory proteins to interact with RNA polymerase and activate transcription. This interaction is essential for initiating transcription.
Gene Regulatory Switch
Short sequence of DNA in the non-coding part of a gene. These sequences are typically 6-10 base pairs long.
Specific transcriptional regulatory proteins (transcription factors) recognize and bind to specific switch sequences. Each transcription factor recognizes a unique DNA sequence.
Mutating a base pair in the switch can prevent protein binding. This can alter gene expression.
Binding affects transcription (increases/activates or decreases/represses). Transcription factors can act as activators or repressors.
Muscle Cell vs. Nerve Cell Example
In a muscle cell nucleus, muscle-specific transcriptional activating proteins are present. These proteins activate the expression of muscle-specific genes.
Gene regulatory switches are DNA sequences in non-coding DNA, the same in every cell. The switches themselves are identical, but the proteins that bind to them differ.
If there's a nerve-specific regulatory switch sequence nearby, it won't be used in the muscle cell because the nerve-specific protein isn't present. This ensures that nerve-specific genes are not expressed in muscle cells.
In a nerve cell nucleus, nerve-specific transcriptional activating proteins are present, so the nerve-specific switch will be used to activate transcription. This allows nerve cells to express their unique set of genes.
Gene Regulation Specificity
Different gene regulatory switches determine transcription levels in:
Different cell types/body parts: This is how cells differentiate and specialize.
Different developmental stages: Gene expression patterns change during development.
Different environmental conditions: Genes respond to signals from the environment.
Responding to different signals (e.g., hormones): Hormones can trigger changes in gene expression.
A gene may have different switches for different contexts. This allows for fine-tuned control of gene expression.
Mutation in one switch might only affect transcription at one stage. This can lead to developmental abnormalities.
Different genes have different regulatory switches. This is why different genes are expressed in different patterns.
Negative Regulation and Expression Levels
Some gene regulatory switches act as negative regulators, binding repressors to prevent transcription. Repressors block RNA polymerase from binding to the promoter.
Transcriptional regulation isn't just on/off but occurs over a range of expression levels. Most genes expression level is somewhere between repressed, intermediate, and high transcription based on the gene. This allows for fine-tuned control of gene expression.
Gene regulatory switches often have multiple binding sites for transcriptional regulatory proteins (activators and repressors), acting like a dimmer switch. The combination of activators and repressors determines the level of transcription.
Dimmer Switch Example
Repressor bound (DNA Transcription off): dimmer switch off. When a repressor is bound, transcription is blocked.
One binding site bound: low-level transcription; dimmer switch low. A small amount of transcription occurs.
Two binding sites bound: intermediate-level transcription; dimmer switch intermediate. More transcription occurs.
All three sites bound: high-level transcription; dimmer switch highest position. The maximum amount of transcription occurs.
Location and Components of Gene Regulatory Switches
Gene regulatory switches don't need to be near the promoter; they can be far away, on the other side of the gene, or in introns. Enhancers, for instance, can be located far from the genes they regulate.
Gene regulatory switches are part of the non-coding DNA. These sequences are not translated into protein.
Gene regulatory switches are specific sequences of noncoding DNA in the genome
Gene regulatory switches are not proteins, and proteins are not part of the gene regulatory switch itself. Proteins bind to gene regulatory switches, which influences transcription of the nearby gene either by increasing it or decreasing it as we have described.
Gene regulatory switch = light switch; transcriptional regulatory protein = person's hand operating switch.
Summary of Gene Regulatory Switches
DNA sequences in the non-coding DNA of genes. These sequences are not translated into protein.
The same in all cells (all switches are present). Every cell contains the same set of regulatory switches.
Each switch type has a different sequence and binds to a specific transcriptional regulatory protein. This allows for specific regulation of gene expression.
Transcriptional regulatory proteins can activate (activators) or repress (repressors) transcription. Activators increase transcription, while repressors decrease it.
First Big Idea Recap
Cells of an organism with identical DNA sequences can have different characteristics because transcriptional regulatory switches enable cells to transcribe different genes. This leads to cell differentiation and specialization.
This leads to different mRNAs, proteins, and cell phenotypes (cell types). Different cell types express distinct sets of genes.
There are approximately 200 different cell types in humans, with many subtypes. This diversity allows for complex tissue organization and function.
Important Points
Proteins that bind to gene regulatory switches are encoded by other genes in the genome.
Humans have approximately 1,500 to 2,000 different transcriptional regulatory proteins. These proteins control the expression of thousands of genes.
Transcriptional regulatory proteins can regulate expression of the gene that encodes them: This creates feedback loops that fine-tune gene expression.
Each gene is regulated by several transcriptional regulatory proteins. Combinatorial control allows for complex regulatory patterns.
Each gene has different non-coding DNA sequences and different transcriptional regulatory switches.
Genes expressed in the same cell types/patterns may be similar but always have some differences in sequence and configuration. This allows for subtle differences in gene expression.
Each gene sequence evolves separately with random mutations. This leads to diversity in gene regulation.
Revisiting the Chicken and Egg Problem
How do cells come to have different proteins if all cells have the same DNA? This question addresses the initial establishment of cell diversity.
Before the zygote, in the egg cell, there are different proteins in different areas and concentrations. These proteins are deposited in the egg during oogenesis.
After fertilization, the zygote has different proteins/concentrations in different areas. This asymmetry is crucial for early development.
These are key transcriptional regulatory proteins for early development. These proteins initiate the process of cell differentiation.
As the zygote undergoes cell division, daughter cells have different proteins/concentrations. This leads to different developmental fates.
This leads to different regulatory proteins and different genes expressed in different parts of the developing body. This is how cell diversity is established during embryogenesis.
Differences in protein between cells are due to the placement of proteins and mRNAs in egg cells before zygote formation. This maternal contribution is essential for early development.
Transcriptional Regulation during Development
How can transcriptional regulatory switches explain different phenotypes at different developmental stages (e.g., caterpillar to butterfly)? This addresses how gene expression changes over time.
Comparing Cell Types and Developmental Stages
Liver and kidney cells in a person vs. caterpillar and adult butterfly cells. These comparisons highlight the differences between cell differentiation and developmental changes.
Same DNA sequence in all cells, including coding and non-coding DNA (gene regulatory switches). The genome remains constant, but gene expression patterns change.
Different genes are transcribed, and transcription amounts vary. This leads to different protein sets in different cells and at different times.
Different mRNAs and proteins are expressed. These differences drive the changes in cell structure and function.
These differences in gene products cause different structures and functions. This is how cells and organisms develop their unique characteristics.
Case Studies Revisiting
Huntington's Disease and Keratin Genes
Allele differences in coding parts of the gene (amino acid sequences) cause structural/functional protein differences. These differences directly affect protein function.
No difference in the amount of protein expressed. The amount of protein produced is the same for different alleles.
No difference in the cell types in which the protein is expressed.
Huntington's: expressed in the same brain cells. The protein is expressed in the same cells, but its function is altered.
Keratin: expressed in the same skin cells. The protein is expressed in the same cells, but its structure is altered.
There are no meaningful DNA sequence differences in the non-coding parts of the gene between the allele types of Huntington and the allele types of keratin. The regulatory sequences are similar, so expression patterns are unchanged.
Importance of Non-Coding DNA
Non-coding DNA is important for Huntington and keratin genes. Regulatory sequences control where and when these genes are expressed.
Gene regulatory switches are necessary for expression in certain cell types.
Huntington: transcription in certain brain cells. The gene must be expressed in these cells to function properly.
Keratin: transcription in certain skin cells. The gene must be expressed in these cells to function properly.
Switches are critical; without them, neither allele would be expressed. Without regulatory sequences, the genes would not be transcribed.
Gene regulatory switches of the noncoding DNA are essential parts of all genes.
Asymmetric Cell Division
If all cells have the same DNA, how do they get different transcriptional regulatory proteins? This addresses how cell diversity is initially established.
Mitosis produces genetically identical cells. However, the distribution of proteins and mRNAs can be unequal.
Many cell divisions are asymmetric, with unequal division of proteins and mRNAs. Some cells inherit more of these molecules than others.
Some cells get more mRNA/protein than others. This leads to differences in gene expression.
These mRNAs/proteins cause cells to express different genes or have different expression levels, eventually resulting in different protein sets and cell types. This is how cell diversity is generated.
Summary of Big Ideas
Non-coding DNA allows genes to be expressed at different levels in different cell types, creating cell/tissue diversity. Regulatory sequences control cell differentiation and specialization.
Differences between alleles in non-coding DNA sequences play a major role in causing the diversity of phenotypes among individual organisms. Variations in regulatory sequences drive