D2.2: Gene Expression

Gene Expression

process in which genotype gives rise to phenotype through production of proteins

-guides development by activating and silencing different genes in different cells

Regulation of Gene Expression (3)

transcription, translation, protein products

Transcription

DNA --> mRNA using RNA polymerase II

-regulates access to genes

-controls production of mRNA via transcription factors

Translation

mRNA --> AA sequence using ribosomes

Protein Products

regulate structure (skin) and/or function (enzymes) of organisms

Differentiation

all cells in an organism contain the complete genome

-gene expression is what determines differentiation

although genome is identical, transcriptome and proteome will vary significantly over time depending on development stage

genome

Genome

total genetic information, both coding and noncoding

Transcriptome

complete set of RNA produced in a cell

-includes all mRNA, rRNA, tRNA, and ncRNA (non-coding)

Proteome

Complete set of proteins produced or modified by a cell, tissue, or organism at a specific time

Epigenesis

concept that organisms develop from a simple undifferentiated state through a series of progressive changes

Epigenetic Modifications

change phenotype without changing genotype

-potentially reversible

*methylation, acetylation, phosphorylation*

Epigenesis Example

Sex determination in crocodiles is determined by environmental temperature during a thermosensitive period

-high temp represses Sox9 gene, which causes them to develop as females

Epigenetic Tags

chemical modifications made of DNA or histone proteins that control gene expression without changing DNA structure

-switches genes "on" or "off"

DNA Methylation

changes DNA activity without altering its sequence by attaching a methyl (-CH3) group

-occurs primarily on cytosines next to guanines, known as a CpG island

CpG Island

aligns two methyl groups diagonally on opposite DNA strands because C and G are complementary

-often located within the promoter and their methylation blocks RNA polymerase activity

-represses expression by switching "off" genes

CpG Island and Mutations

high CpG methylation increases frequency of mutations

-methylated cytosines can deanimate into thymines

-in cancer, hypermethylation silences essential genes (tumor suppressor genes)

Deanimate

removal of nitrogen-containing molecule

Histones in Nucleosomes

histones have positively charged, protruding tails that interact with negatively charged DNA

Histone Acetylation

adding acetyl groups neutralizes the positive positive charge of histones, making DNA less tightly coil and increasing transcription

Histone Methylation

adding methyl groups maintains the positive charge on histones, making DNA coil more, reducing transcription

Heterochromatin

DNA that is tightly coiled, unavailable for transcription

*dark in microscope image*

Euchromatin

DNA that is loosely coiled, available for transcription

Environmental Impact on Gene Expression

Certain external conditions encourage DNA methylation by regulating enzyme DNA methyltransferase (DNMT)

*ex air pollutants*

Air Pollutants

air pollutants like nitrogen oxides and polyaromatic hydrocarbons have been found to be responsible for DNA methylation

causes methylation in immunoregulatory genes, leading to increased inflammation and altered immunity

-further leads to cardiopulmonary complications, including high BP and respiratory conditions like asthma

*also changes expression of other genes which often leads to cancer*

Monozygotic Twins

methylation patterns of monozygotic twins can be studied to identify the role of environment in phenotypic development

-MZ twins with identical genomes result when a fertilized egg divides into two embryos

Methylation in MZ Twins

DNA methylation patterns diverge over time as environmental exposure varies (nutrition, physical activity, stress levels)

-can be compared to identify genes involved in the development of specific diseases present in only one twin

cancer, autism, lupus

Cancer

hypermethylation of tumor suppressor genes (BRCA1)

Autism Spectrum Disorder

abnormal methylation of genes involved in synaptic function; prompted by prenatal stress, maternal infections

Lupus

abnormal methylation in immune-related genes, prompted by UV exposure, medications

Epigenetic Inheritance

undifferentiated cells develop into multicellular organisms by regulating gene expression through epigenetic tags

sperm and eggs must be reprogrammed (by removing epigenetic tags) to return them to a "blank slate"

-ensures that early embryos have a clean epigenome and can produce every type of cell that the body needs

**pre-existing epigenetic tags are believed to be the reason why cloning of animals (from adult cells) often fails

Imprinted Genes

small proportion of genes are not reprogrammed during gamete production and remain epigenetically silenced

-therefore, often times, only one active copy of these genes exist in the offspring (from 1 parent)

-imprinted genes retain their epigenetic tags and allow phenotypic changes to be passed onto their offspring

Imprinted Genes Consequences

have a higher mutation rate

-methylated DNA is more easily deanimated (C-->T)

more vulnerable to selective pressures due to their small number (only 1 allele) leading to higher evolution rates

Ligers and Tigons

certain epigenetic tags within sperm or ovum are responsible for size differences seen in ligers and tigons

Ligers

male lion + female tiger

-noticeably larger than both lions and tigers

Tigons

male tiger + female lion

-about the same size as an average lion

Lions

live within social groups (prides) in which a single lioness may have cubs from multiple male lions

-therefore, male lion benefits from having largest offspring so that his cub outcompetes the others

-lion sperm contains imprinted genes that promote growth

however lioness benefits from having smaller offspring so that pregnancy is successful and all cubs are prioritized equally

-eggs contain imprinted genes that restrict growth

*combination of two cancel each other out and results in cubs that are average size*

Tigers

solitary animals and a tigress will only have cubs with a single male tiger

-both male and female tigers share the same reproductive goal and do not have imprinted genes

Liger vs Tigon Result

different imprinting strategies btwn male and female lions determine size of offspring when a lion and tiger mate

in ligers, lion sperm imprinted to promote growth produces larger offpsring

in tigons, lion egg imprinted to restrict growth produces normal-sized offspring

Promoter

DNA sequence that RNA Polymerase II binds to, to begin transcription

-regulated by transcription factors and regulatory proteins

Transcription Factors

Group of proteins that guide RNA Polymerase II to the promoter, making it easier to bind

-RNA Polymerase II usually cannot begin transcription without them

Regulatory Proteins

Bind to DNA upstream of promoter and affects transcription factors

Either activators or repressors

Activators

Proteins that encourage transcription factors and RNA Polymerase II to bind to DNA, increases transcription

Repressors

Proteins that prevent transcription factors and RNA Polymerase II from binding, decreases transcription

Control Elements

DNA sequences that regulatory proteins bind to (most genes have multiple to control gene expression)

Either Proximal elements or Distal elements

Proximal Elements

Located close to promoter, transcription factors typically bind here

Distal Elements

Located farther upstream from promoter, activators and repressors typically bind here

-have enhancer and silencer sites

Enhancer Sites

activators bind here to increase transcription

Silencer Sites

repressors bind here to decrease transcription

Factors that Impact Gene Expression

both internal and external factors trigger cellular signals that control transcription factors and gene expression

Ligand-Activated Transcription Factors

require the presence (or absence) of specific molecules to function

ex. humans produce varying amounts of melanin depending on light exposure

Hormones

chemical messengers that are manufactured by the endocrine glands, travel through the bloodstream, and affect other tissues

Steroid Hormones

lipophilic and freely cross membrane to influence gene expression

-they bind to receptors in either the cytoplasm or nucleus of target cell and form a receptor-hormone complex

-this complex moves into nucleus to bind to DNA and act as a transcription factor for gene expression

Protein Hormones

Lipophobic and cannot cross membrane

-they bind to transmembrane receptors on membranes that activate secondary messengers (like Ca2+)

-signal transduction initiates changes in gene expression

lac operon

metabolism of lactose is controlled by a group of genes known as the ___________

Inducers

in E. coli, lactose (nutrition as stimulus) is the inducer that regulates expression of lactase

Absence of Lactose

the lac repressor turns off transcription of the lac operon

binds to operator that blocks RNA polymerase

Presence of lactose

when lactose levels rise, it acts as an inducer

-binds to the repressor to deactivate it so that transcription can begin

once lactose is digested, repressor is reactivated, inhibiting transcription (negative feedback)

Degradation of mRNA

translation may be regulated by controlling the degradation of mRNA transcripts

-in humans, mRNA persists for minutes to days before being broken down (regulated by hormones)

length of time transcript remains influences the amount of protein made, therefore gene expression

-eventually, nuclease breaks down mRNA and recycles individual nucleotides, altering the transcriptome