Functional Genomics and Gene Expression

What is genomics?

the study of genomes

What is structural genomics?

sequenced-based approach to look at the structure and components of genomes and to analyze the similarities between genomes

What is functional genomics?

experimental-based approach to understand gene function on a genome-wide scale

What does transcriptomics focus on?

RNA

What does proteomics focus on?

proteins

What does metabolomics focus on?

metabolites

What information can provide valuable insight into gene functions?

tissue-specific or temporal expression patterns, subcellular localization, physical interactions with other gene products or cellular components, genetic interactions with other gene products

What is the goal of functional genomics?

understand the relationship between an organism’s genome and its phenotype

What techniques does functional genomics use?

high-throughput techniques

What is transcription?

DNA to RNA

What is translation?

RNA to protein

What direction is RNA made?

5’ to 3’

What direction is the protein made?

N to C

What end of the mRNA encodes N?

5’

What genes are likely expressed in all cell types?

house keeping genes, certain proteins are involved in the basic metabolic processes common to all cell types

Why do different cell types arise?

because of differential gene expression

What are the expression patterns for tissue-specific?

basis for different cell types in an organism

What are developmental gene expression patterns?

temporal and spatial expression patterns

What are environmental gene expression patterns?

induction in response to external stimuli

What are most eukaryotic genes interrupted by?

non-coding DNA that is spliced out

What is coupled in prokaryotes?

transcription ad translation

What are the 3 domains of life?

Bacteria, archaea, eucarya

Are eukaryotes mono or polycistronic?

monocistronic

Are prokaryotes mono or polycistronic?

polycistronic

What does polycistronic mean?

more than one protein per mRNA

What does monocistronic mean?

one protein per mRNA

What does metazoan mean?

multi-cellular

What are the names of his kids?

Rachel and Carl

What are the two divisions of gene control?

changes in gene content or position, changes in gene activity

What is the general rule of the control of gene expression?

the DNA of different cell types does not vary in either amount or type

What is the general method of gene regulation?

changes in gene activity

What are the types of changes in gene content or position?

gene loss, gene amplification, gene rearrangment

What are the four main levels of control?

transcriptional, post-transcriptional, translational, post-translational

What are the parts of a mature mRNA?

5’ cap, 5’ UTR, coding region, 3’ UTR, 3’ poly A tail

What do the 5’ and 3’ cap/poly A tail do?

stabilizes mRNA, helps with ribosomal regulation

What is transcriptional control?

determines if, how much, and when an mRNA is made, controlled by proteins that interact with specific gene sequences

What is post-transcriptional control?

determines how an mRNA is available for translation into a protein, changes in the rate of synthesis of a particular protein occur without a corresponding change in the transcription rate of the corresponding gene

What are examples of post-transcriptional control?

gene expression regulated by controlling pre-mRNA splicing, mRNA stability, and mRNA location

What does post-transcriptional control rely on?

specific RNA-protein interactions

What is translational control?

determines how a protein is made

What is post-translational control?

determines how a protein is functional, extensive chemical alterations

What are examples of post-translational control?

amino acid modifications and proteolytic cleavages

What is the half-life of mRNA?

few minutes to more than a day

What can the half-life of an mRNA be affected by?

nutrient levels, hormones, viruses, changes in temperature

What does changing the rate of mRNA degradation usually change?

the rate of protein synthesis

What is RNA processing?

collection of events required to convert primary gene transcripts into biologically or functionally active RNA

What are the covalent events of RNA processing?

modify bases, cleave, trim, add, splice, edit

What are the non-covalent events of RNA processing?

RNA folding/unfolding, protein binding, transport in cells

What is step 1 of mRNA synthesis?

synthesis by RNA polymerase II in nucleus

What is step 2 of mRNA synthesis?

5’ capping

What is step 3 of mRNA synthesis?

internal base and sugar modification

What is step 4 of mRNA synthesis?

hnRNP assembly

What is step 5 of mRNA synthesis?

3’ end formation/polyadenylation

What is step 6 of mRNA synthesis?

splicing

What is step 7 of mRNA synthesis?

editing

What is step 8 of mRNA synthesis?

export

What is step 9 of mRNA synthesis?

mRNP protein binding

What is step 10 of mRNA synthesis?

translation or degragation

What is RNA editing?

alteration of nucleotides

What can RNA processing result in?

synthesis of more than one protein from a single gene

What is the split gene concept?

many eukaryotic genes have their coding sequences interrupted by stretches of non-coding sequences

What is alternative splicing?

multiple introns may be spliced differently in different circumstances

What is DsCAM?

dramatic example of multiple proteins from one gene using alternative splicing, 38,000 different proteins from one gene

What is the importance of post-transcriptional control?

key role in controlling gene expression both quantitatively and qualitatively

What are the normal mRNA decay pathways?

enzymes (exo and endoribonucleases), sequences that determine half-life

What is step 1 of the major pathway of mRNA degradation?

shorting of poly A tail by a 3’ to 5’ exoribonuclease

What is step 2 of the major pathway of mRNA degradation?

decappingW

What is step 3 of the major pathway for mRNA degradation?

degradation by 5’ to 3’ exoribonuclease

What can RNA editing do?

create two or more proteins from a single genes, remove frameshifts, create stop or start codons, or alter codons

What type of RNA editing has been seen in mammals?

only single nucleotide changesW

What type of mRNA is commonly edited in trypanosomes?

mitochondrial mRNA, insertion/deletion of U residues

What was the first example of a mammalian RNA undergoing editing?

apolipoprotein

What happens to apoB transcripts in the small intestine?

a C is converted to a U, causing a premature stop codon

What is a C to U conversion brought about by?

a simple deamination reactions

What editing happens for glutamate-gated cation channel receptors?

deamination of A generating I, I is recognized as G

What does the Glu to Arg change in glutamate-gated cation channel receptors cause?

altered calcium permeability of the channel which alters brain function

What is the site-selective deamination in mammalian genes brought about by?

RNA-dependent deaminases

What is the deaminase responsible for apoB editing?

APOBEC`

What are the deaminases that deaminate A to I called?

ADARs

What provide genetic info for trypanosome editing reactions?

small trans-acting guide RNAs