Control of Eukaryotic Genome
Chapter19. Control of Eukaryotic Genome a The BIG Questions How are genes turned on & off in eukaryotes?
How do cells with the same genes differentiate to perform completely different, specialized functions? Prokaryote vs. eukaryote genome
Prokaryotes small size of genome circular molecule of naked DNA DNA is available to RNA polymerase control of transcription by regulatory proteins operon system most of DNA codes for protein or RNA no introns: small amount of non-coding DNA regulatory sequences: promoters, operators prokaryotes use operons to regulate gene transcription, however eukaryotes do not. since transcription & translation are fairly simultaneous there is little opportunity to regulate gene expression after transcription, so control of genes in prokaryotes really has to be done by turning transcription on or off. Prokaryote vs. eukaryote genome
Eukaryotes large genome how does all that DNA fit into nucleus? DNA packaged in chromatin fibers regulates access to DNA by RNA polymerase cell specialization Genes turned on and off at different times most of DNA in humans does not code for protein 97% non-coding DNA Points of control The control of gene expression can happen at any point along the way: unpacking DNA transcription mRNA processing mRNA transport translation protein processing protein degradation a Why turn genes on & off? Specialization Development
each eukaryotic cell expresses only a small fraction of its genes Development different genes are needed at different points in the life cycle of an organism afterwards need to be turned off permanently Responding to organisms needs homeostasis Response to environment must turn genes on & off A prokaryote has most of its genes turned on most of the time. Whereas in a multicellular organism, each cell has most of its genes turned off. A brain cell expresses many different proteins than a muscle cell. a a DNA packing How does all that DNA fit into nucleus?
DNA coiling & folding double helix nucleosomes chromatin fiber chromosome nucleosomes beads on a string 1st level of DNA packing histone proteins have high proportion of positively charged amino acids (arginine & lysine) bind tightly to negatively charged DNA from DNA double helix tocondensed chromosome Nucleosomes Beads on a string 1st level of DNA packing
8 histone molecules Nucleosomes Beads on a string 1st level of DNA packing histone proteins many positively charged amino acids arginine & lysine bind tightly to negatively charged DNA DNA packing tightly packed = no transcription = genes turned off
darker DNA (H) = tightly packed lighter DNA (E) = loosely packed DNA methylation Methylation of DNA winds up chromosome tighter think of pill bug no transcription = genes turned off attachment of methyl groups (CH3) to cytosine C = cytosine can be permanent inactivation of genes ex. inactivated X chromosome a a Histone acetylation Acetylation of histones unwinds DNA
loosely packed= transcription = genes turned on attachment of acetyl groups (COCH3) to histones Changes shape in histone proteins Transcription can proceed when unwound 2 You are more than your DNA
EPIGENETICS You are more than your DNA University of Utah Transcription initiation
Control regions on DNA promoter nearby control sequence on DNA binding of RNA polymerase & transcription factors base rate of transcription enhancers distant controlsequences on DNA binding of activatorproteins enhanced rate (high level)of transcription a Model for Enhancer action
Enhancer DNA sequences distant control sequences Activator proteins bind to enhancer sequence & stimulates transcription Silencer proteins bind to enhancer sequence & block gene transcription Much of molecular biology research is trying to understand this: the regulation of transcription. Silencer proteins are, in essence, blocking the positive effect of activator proteins, preventing high level of transcription. a Gene movie https://www.youtube.com/watch?v=ysxtZJUeTCE Post-transcriptional control
Alternative RNA splicing different exons removed = different proteins a Regulation of mRNA degradation
Life span of mRNA determines pattern of protein synthesis mRNA can last from hours to weeks RNA processing movie a RNA interference Small RNAs (sRNA) short segments of RNA (21-28 bases)
bind to mRNA create sections of double-stranded mRNA death tag for mRNA triggers degradation of mRNA cause gene silencing siRNA a a functionally turns gene off
One of the Newer biology topics RNA interference Small RNAs mRNA double-stranded RNA sRNA + mRNA mRNA degraded functionally turns gene off a a RNA Degradation: HHMI Roy Barker
https://www.youtube.com/watch?v=d7nmojex01c (3 mins. Only) RNAi: (gene silencing) https://www.youtube.com/watch?v=cK-OGB1_ELE Control of translation
Block initiation stage regulatory proteins attach to5 end of mRNA prevent attachment of ribosomal subunits & initiator tRNA block translation of mRNA to protein Control of translation movie Protein processing & degradation
folding, splitting, adding sugar groups, targeting for transport Protein degradation ubiquitin tagging proteosome degradation The cell limits the lifetimes of normal proteins by selective degradation. Many proteins, such as the cyclins involved in regulating the cell cycle, must be relatively short-lived. Protein processing movie Ubiquitin 1980s | 2004 Death tag mark unwanted proteins with a label
76 amino acid polypeptide, ubiquitin labeled proteins are broken down quickly in "waste disposers" proteasomes Since the molecule was subsequently found in numerous different tissues and organisms but not in bacteria it was given the name ubiquitin (from Latin ubique, "everywhere") Aaron Ciechanover Israel Avram Hershko Israel Irwin Rose UC Riverside a Proteosome / Ubiquitin (UPS)
https://www.youtube.com/watch?v=hvNJ3yWZQbE(~ 6 min.) Structure of the Eukaryotic Genome
a a How many genes? Genes only ~ 3% of human genome
protein-coding sequences 1% of human genome non-protein coding genes 2% of human genome tRNA ribosomal RNAs siRNAs a a What about the rest of the DNA?
Non-coding DNA sequences regulatory sequences promoters, enhancers terminators Non-Coding DNA introns repetitive DNA centromeres telomeres tandem & interspersed repeats transposons & retrotransposons Alu in humans a a Genetic disorders of repeats
Fragile X syndrome most common form ofinherited mental retardation defect in X chromosome mutation causing many repeats of CGG triplet in promoter region 200+ copies normal = 6-40 CGG repeats FMR1 = Fragile X Mental Retardation gene FMRP = Fragile X Mental Retardation Protein a a Fragile X syndrome The more triplet repeats there are on the X chromosome, the more severely affected the individual will be mutation seems to increase severity with each generation mutation seems to increase severity with each generation A summary of existing research conducted by the Centers for Disease Control and Prevention in 2001 estimated that approximately one in 3,500 to 8,900 males is affected by the full mutation of the FMR1 gene, and that one in 1,000 males has the premutation form of the FMR1 gene. This study also estimated that one in 250 to 500 females in the general population has the premutation. Another study6 estimated that one in 4,000 females is affected by the full mutation. Huntingtons Disease Rare degenerative neurological disease
1st described in 1872 by Dr. Huntington most common in white Europeans 1st symptoms at age 30-50 death comes ~12 years Mutation on chromosome 4 (dominant) CAG repeats copies normal = CAG repeats CAG codes for glutamine amino acid When the HD gene was found, researchers discovered that HD belongs to a newly discovered family of diseases called "triplet repeat" diseases. A gene's DNA bears coding molecules which are translated into specific amino acids, the building blocks of proteins. In the HD gene, the coding molecules cytosine, adenine, and guanine (CAG) - the triplet - repeat in a stretch more than they do in the normal gene. Normally the CAG sequence repeats between 11 and 30 times. People with HD may have CAG repeated between 36 and 125 times. The onset of the disease generally is in the 30s and 40s (with a range of age 2 to 82), but more than 60 repeats of CAG often are associated with an onset of HD before age 20. With the majority of people who have fewer than 60 repeats, there is great variability. A person can have 40 CAG repeats in his or her DNA sequence and have onset at age 17 or 70. On average, however, a feature dubbed "genetic anticipation" occurs. Each time the unstable DNA is passed on to offspring, the affected person experiences an earlier onset. a a Huntingtons disease Abnormal (Huntington) protein produced
chain of charged glutamines in protein bonds tightly to brain protein, HAP-1 Woody Guthrie Interspersed repetitive DNA
Repetitive DNA is spread throughout genome repetitive DNA makes up ~ 25-40% of genome of mammals in humans, at least 5% of genome is made of a family ofsequences called, Alu elements 300 bases long Alu is an example of a "jumping gene" a transposon DNA sequence that "reproduces" by copying itself & inserting into new chromosome locations 5% of genome = millions of copies of this sequence! Alu doesnt seem to be active anymore. No useful function to organism. Used to study population genetics = relatedness of groups of people a a Rearrangements in the genome
Transposons piece of DNA that can move from one location to another in cells genome One gene of an insertion sequence codes for transposase, which catalyzes the transposons movement. The inverted repeats, about 20 to 40 nucleotide pairs long, are backward, upside-down versions of each other. In transposition, transposase molecules bind to the inverted repeats & catalyze the cutting & resealing of DNA required for insertion of the transposon at a target site. Transposons Insertion of transposon sequence in new position in genome
This can cause mutations when theyland within the coding sequence of a gene a Transposons 1947|1983 Barbara McClintock
discovered 1st transposons in Maize =(corn) in 1947 She found that transposons were responsible for a variety of types of gene mutations, usually insertions deletions and translocations a a Retrotransposons Transposons actually make up over 50% of the corn (maize) genome & 10% of the human genome. a a a a Any Questions?? a a