Lecture #1 (Genome organization) Flashcards
Mitocondria genome
Simple genome - 37 genes –> 2 rRNAs ; 22tRNA ; 13 proteins
Mitocondria replicate independetley of nulcues (replicate genome sepertley)
NOT a lot of mitocondrial diversity - only have 7 anvestral origins to mitocondria
Mitocondrial Protein synthesis
Mitocondria make their own ribosomes (have 2 rRNAs)
Mitcondira make their own tRNA (have 22 tRNA)
Orgin of the mitocondria
Mitondria = endosymbiotic parasite
- Mitoncdria used to be a prokarytote that invaded another prokayote and became fixed in the cell and allowed the cell to do aerobic respiration
How do we know:
1. Ribosomes don’t like like Eukaryotic (look like prokaryoic)
2. Mitcodnria are like an autonmous organism in the cell (make their own protein synthesis machinery - make ribosomes ; makes things for oxidative phophorylation)
- NOW mitocndira need the nucleus - most things that support the mitocondria are encided by nuclear genes (Nuclear genes are translated in the cytoplasm and transported to the mitocondria)
3. Mitocondria have more compact genome
Mitocondria organization
Mitcondrial genome = very compact (each gene is close to another gene)
- Have tRNAs between the genes
Evoloved to be as tightly organized as possivle (common paradigm in Prokayotes but not Eukaryotes)
- In Prokaryotic - genetic material is tightly associated with each gene (more compact genome)
Phylogeny of tree of life
Tree of life is divided into 3 Phyla:
1. Bacteria
2. Archea
3. Eucarya
based on rRNA
Discovery of the phylogenetic tree of life
Carl Rosa anylyzed rRNA to make 3 Phyla system
Looked at rRNA and noticed the ribosomes were essentially the same BUT with SMALL differences
- Carl compared ribsomes between different bacteria –> saw they looked alike ; Looked at diference mammal species –> saw ribosomes look alike) ; had a weird class that didn’ look like animals or bacteria –> now know they are Archea
END - led to hypothesis that there are 3 ancestral lineages to life –> Bacteria + Archea + Eukrya (3 kingdom system)
Implications of the 3 phyla system
3 Phyla system implies that ribosomes is the most defining feature of life
Ribosomes are the only conserved macromolecular machinery across ALL life of earth
- Ribosomes look similar between different organisms
What is the main function of cells
Cells do one thing –> Supports the replication of ribosomes
MOST energy of the cell goes into making ribosomes
THEREFORE it is not suprising that the common ancestor across all life is the ribosome
Prokayotic genome
Often small BUT can vary in size
Gene number correlates with the types of envirnments organisms can survive in (correlates with envinrmental diveristy)
- Fewer genes = organsim can survive in liminited number of envirnmnetal niches
- Gene size correlates with envirnmental niche
Compact genome + smaller genetic composition
- Genes are closer together (Compared to Humans that have huge spaces of DNA between genes)
Prokaryotic = circular genomes Vs. Eukaroic = linear genomes
Size of Prokayotic Genome
Shows bacteria + acrhea genome sizes
- Bacteria + Archea = both prokaryotes
Size differs widley
- Some organisms with few genes (169) vs. some organisms with many genes (10,000)
Gene number correlates with size of genome (Bigger genome = higher gene number)
Gene number correlates with the types of envirnments organisms can survive in
- Because you organisms need to be able to survive whereever they land (they are not moving)
Gene number does NOT correlated with complexity
Gene number and complexity
Gene number does NOT correlate with complexity
- Gene number does not create complexity
Exaemple - Bacteria = 10,000 genes VS. humans = 20,000 genes BUT humans can do more complex things
Answer - 1 –> organisms that reside in unique stable niches have smaller genomes
Other answer:
2 - bacteria replicate very fast (Ex. E.coli = 20 mintues) – small genome could help BUT there are many bacteria with larger genomes that can replicate fast
3 - Temperture should not corelate with gene contnt
- Bacteria that could grow at different temperatures have more complex genomes (Ex. corn has more genes that humans because they need to be abel to grow at many different tempertures ; need bigger genomes to be able to survive at ALL temperatures)
E.Coli Geneme
Small (5,000 KB)
Circular Genome –> Allows it to supercoil
No Introns (true of many prokaryotes)
11% intergenic region
- Compared to humans (Have big intergenic regions)
Little repetative DNA
Has one replication orgin
IMAGE - shows genomic arrangment of DNA in E.coli –> Shows how compact teh genome is (green is coding ; grey is noncoding intergenic regions) - see veyr little grey
Supercoil
Supercoil = physical properties of helices
Ex. Because E.coli have helix in circular genome = can super coil on self –> important for DNA replication (need enzymes that displace supercoiling)
Intron
Intron - non-coding seqeunces that needs to be spliced out
- Unique to Eukaryotic organisms
Found that mammalian genes are split – have expanses of DNA seperated DNA that needes to come together to make a gene (DNA that seperates the DNA that needs to come together = intron)
Intergenic region
Space between genes
E.coli Cell division
E.oli = only have one replication orgin because of speed of replication that is needed
Every 20 minutes E.coli replicates DNA –> has 1 orgin –> orgine fires – Move the replication bubble around the circular DNA BUT before that intial replication is finished the replication origin of the new strand can fire –> once replication is done can do cell division
- Start the next round of divisiion before the last one finishes
Operons
Operon - genes of similar function arranged together in space
- Prokaryotic genes = often arranged in Operons
Example - Lac operon –> 3 genes needed to metabolize lactose (Surgar used by E.coli)
- The genes are arrangd in space in the genome –> ALLOWS the genes to be regulated in a conserted fashion
- Bacetria can make polycystronic mRNA (mRNA that codes for multiple proteins) vs Eukaryots have monocystron mRNA (1 mRNA = 1 protein)
- If E.coli has lactoes = turn on expression of the Lac operon (Lactose stimulates prooter of the genes = makes all three proteins = can metabolize lactose)
Genes need to be in the same location in order to have polycystronic mRNA (allows for common regulatory pathway)
Example 2 - Trp operon (4 genes)
What is needed for evolution
Evolution needs enetic divsierty = needs mutation
Eukayotes have sexual reproduction = can get divsierty BUT prokaryotes (bacteria) reproduce aesexually meaning they have limited oppertunity to get genetic divseirty
To get genetic diveristy Prokaroytes do Horizontal Gene transfer
Horizontal Gene Transfer
DNA material can be transfered independetley of cell division from one cell to another
Occurs in 3 ways:
1. Bacteria transformation
2. Bacterial Phage
3. Conjugations
ALL 3 = allows for rapid spread and evolution of bacteria
***Learned a lot about HGT from evolution of antibiotic resistance (HGT allows AB resistance spreads fast)
Bacteria transformation
DNA floating around the bacterial envirnment can be taken up by the host bacteria
- DNA could be
THIS can have advatangtes for bacteria BUT most of the time the aquisition of foreign DNA is bad
- In a colony of E.coli have many cells –> means there are many dead cells that have lysed and spilled out DNA
DNA could be coming from E.coli or from different bacteria –> IF DNA stciks to E.coli cell then it could be taken up and could be detrimental to the bacteria BUT it could also give the bacteria a selective advatage
Batcteria defense against DNA
Because somestime forgein DNA gives disadvatage bacteria have host defense mechansim if the DNA they took up is bad –> Restriction endonucleases are that defense
Restriction endonucleases = host defense mechanism that guards against foreign DNA
- Hosts make own nucleic acids in a special way so host knows own DNA vs. others
- Restriction endonucleases are restricted in sequence specificty (cut DNA at specific sequenues)
To make sure bacteria don’t igest own DNA (only wnat to digest foreign DNA) = make sure they dont evolove the sequence for the restcition endonuclease or methylate DNA so it can’t be cleaved
Bacteria scale vs. human scale
Bacteria operate at a different scale than humans
IF Horizontak Gene transfer is only good 1 in a trillion times THEN you would get that good transfer in 1 E.coli on the plate –> that cell would dominate the agar plate
- Woudn’t happen in humans
- Evolution of bacteria occurs at a higher scale in bacteria than Eukaryotic organisms
Bacteria Phage
Overall - Virus that infects bacteria (Virus injects DNA into bacteria)
- Phage can carry DNA from previous host or introdce own DNA –> creates exchnage of information
- Bacteriaphage = driver of evolution
Bacteria have a defense mechanism against phage (Mechanism = CRISPR) –> CRIPSR hives memory to defend against invasion
- NOW = use CRIPSR to maipulate mamalian DNA
Bacetrial Conjugation
Bacteria form structure with another bacteria and exchnage information
Usually exchnage a plasmid
Is Horizontal gene Transfer only in bacteria
Horizontal gene transfer is NOT only in bacteria
Ex. Monsanto company makes genetic modified crops that will survive in the prescence of a chemical they made (chemical kills everything else)
- Have a gene that allows the crop to survive in the presence of the chemical
Farmers plant crops and spray chemical –> the crops survive and eveyrthing else dies BUT eventually the weeds came back
- Weeds aquired the mansantos engineered gene = Horizontal gene transfer occured in plants
Horizontal Gene tranfser in mammals
HGT may occur in mammales
Don’t REALLY have evidence BUT do have evidnece in H.pylori (causes ulcers) – found that some genes in H/pylori are human in origin
- Human genes went to H.pylori
Genomes of Eukaryotic orgenneles
Genomes of Eukryotic organeels are decended from bacteria (mitocndiral + chrlorplast genomes)
- Chloroplast + mitocondra = look like bacteria (orginate from bacteria)
Notable features:
1 ~10 genomes per mitocondria
2. ~8000 genomes per cell
3. Different genetic code
4. 37 genes
5. Proteins are all part of the electron transport chain
Prokaryotic genome Overview
Prokayotes are comprised of bacteria and Archea
Genome size is proportional to the number of genes
Genes are frequencetey arranged as operons
Have a capcity for rapid evolution through horizontal gene transfer
Genomes of eukryotic organnelles are descended from free-living bacteria
Gene density varies (Ex. yeast are more dense)
Eukaryotic Nuclear Genome
Always liner –> allows it to be bigger
Chromosome number varies between difefrent Eukryotic
- There is no corelation between chromosome number and complexity OR between gene number and complexity
DNA is packaged
Genes are discontinous
gene density varies greatly
Eukrayotic genome packaging
DNA is packaged - exists with nucleosomes
Nucleosomes = protein complexes that wind DNA around it
Eukaryotic Nuclear Genome (discontinious genes)
Eukarotic genome has discontinous genes –> inteupted by introns
- Have non-coding DNA within a gene AND the genes are far away from each other
Most of mammalian genome is non-coding (90% doesn’t code for a protein)
Sequencing human genome
1990 - starting sequecning the human genome (all done by hand)
Early 1990s - Sequenced yeast (test case for the human genome)
- 1996 - yeast genome was finsihed sequenced (6,000 genes ; 16 chromsomes)
Humans = 23 chromosomes (2 pairs of each –> 46 total) –> People thought that human would have a HUGE amount of genetic information (thought people would have >120,000 genes)
2003 - genome was complete and it was SHOCKING that humans only have 20,000 genes
Why are humans more complex desite the number of genes
Humans are more complex despite gene numver - WHY ; how does gene number correlate with complexity –> DON’T KNOW
Complexity of human genome
Human genome = very complex
Conatains:
1. Genes
2. Repetative sequences (LINES + SINES + LTRs + Transprosons + microsatilites)
- Many things are reminents of retrociruses
Driver of speciation
Chromosome number and chromosome arrangment = major driver of mammalial speciation
Humans and chimps = similar BUT vary in chromosomes
- If 99.9% identical then could make viable offspring (Ex. Neanderthols and sapeins repdoucing BUT this all breaks downonce chromosmoes change
DNA can be the same BUT if the chromosomes look different = can’t form viable offspring = have speciation
- DNA in humans and chimps is almost idetofcal BUT chome have a chromsome split into twi = can’t reproduce together
Gene density
Gene density varies across species
Image: - Shows Human genome Vs. Yeast
- Green = coding exns ; Grey = introns ; Pink = LINE ; Orange = SINE
- Can see that there is a lot of pink between inhidividual genes (have lots of LINE elements)
Vs. Yeast have compact genes (genes are next to each other)
- Genes are 500 BP apart
- Easier to sequence yeast genome becasue there are less things between the genes (Compared to sequencing humans that has ALu and LINE elements between the genes)
Gene density table
Humans - 6 genes per megabase (mist DNA in humans is repeates (Mostly SINEs + LINES0
Fly - 80 genes per megabase
Yeast - 549 genes per megabase
Repetative DNA (Tandem repeats)
A lot of human genome = tandom repeats
Includes:
1. Salitile DNA repeates - centromeric DNA
2. Minisatelie DNA - Telemeric DNA
3. Microsatlite - Used for genetic fingerprinting
ALL arise due to recombination or slipage during replication
Often occur in cluster array
Image - See seperare region on two chrosmomes that likley arose from replication mistake
Repetative DNA (Interspersed repeat elements)
Overall - selfish DNA elements interspersed throughout the genome
- Arise due to transposition (artifcats of viruses)
- propegate and spread throughout the genome
Includes SINEs + LINEs
- SINEs + LINEs = artifcats of viruses
- Have different types of SINEs and LINEs (table - shows types and fraction in genome)
- MOST SINEs = Alu family
What do Repetative DNA (Interspersed repeat elements) look like
Look like virsues - has multiple proteins (vrisues can make polycystronic trasncripts)
- Virsues = can make polycystronic trasncripts –> virsues need to have compact genoomes to spread throughout popultion - reduce genome by putting open reaidng frames next to each other = virses have evoloved to have mutiple open reading frame exchnaged by frameshift event
See artificacts of viruses in elements = shows they are viruses that littered the genome
- Make up most of the genome ; most of genome is virus
Answer - 3 - Assumed the number of genes would correspond to the number of different proteins produced
Assumed that because humans are complex (motile + have immune system) that we must make a TON of proteins to do everything
Do humans make more proteins
Humans = do not have more protein coding genes BUT might still make more proteins
Humans = 23,000 genes BUT can make up to 100,000 proteins BECAUSE we have split genes that are interupted by introns
Can have alternative splicing:
Interuption = creates a need for splicing –> exons do not have to be spliced togetehr in one way (can put they together in different ways)
- Image - can have 2,3.4 or 1,2,5,6, = get two different proteins from 1 mRNA
- 20,000 genes can make 100,000 proetins
- creates alternativley spliced isoforms
- 95% of intron containing protein coding genes undergo alternative splicing
Gene organization (developmental onset)
Eukryotes = don’t have operons but can organize DNA occruding to function
Example - Hemaglobin has two types (alpha and beta types)
- The two types are organized in the genome in a similar fashion so have embryonic and adult form
- Chnage expressiion of hemoglobin depneding on age (baby is different than adults) BUT the genes are loctaed in the same area
Proximity to the LCR proposed to guide the orger of globon gene expression during development
Gene organization (Spatial expression patterns)
Genes can be organized accoding to spatial expression pattens
- Genes can be arranged occurding to bpdy patterning
- Order of genes on the chromosoms is the same as teh expresison of the genes in the developing embryo
Have body patterning in ALL multi ceullar organisms
- Genes involoved in bdy patterning locatiion = found on teh same chromsomes AND in a predictable pattern (true through lineages)
Example - Drosophilla genes are similar to humans and mice (arranged in the same fashion)
- Ancient way to arrange DNA
Chromosome territories
Regions of the nucelus are preferentially occupied by a particular chromosome
- May affect regulation and might faciliatte their ability to match up in mitosis and meiosis
Image - each chromosome is stained –> can see they go to different locations in the nucleus
TADs
Regions of the chromosome that bind to eachother (regions that are far away that bind to eachother?)
- Allows for higher order regulation
Found based on 3D structure of chromosomes
To find them:
Proteins bind to DNA in chromosomes –> cross link DNA –> cut DNA with rstcition enzymes –> NOW have two peices of DNA that are stuck because you criss linked them –> fill end and mark with biotin –> ligate –> purify and shear DNA ; pull now biotin –> sequence the two peices of DNA (see that they should not have been near each other)
- Saw there is patterns to where chromosomes line up with themselves (called TADs)
- Chromsome confirmation capture provides a contact map
TADs vs. Operon
TADs = functional domains that have genes that are expressed similarly
Rather than ranging genes linearly (like in operon) INSTEAD they are arranged in space by tethering them together
Domains are close together because of chromatin (protein around DNA)
- Protein brings peice of DNA close together –>THEN have transcription in envirnment of several genes of similar function
Sanger sequencing
90s - used Sanger sequencing –> usses ddNTPs to get fragments of distcit length that you resolve on a gel
Uses:
1. ddNTP - stops DNA replication
2. Primer
3. DNA polymerase
Have 4 test tubes - each with a different ddNTP
End get different strands of different sizes where you knwo the last nucleotode
- Run segments ona gel = get ladder that is 1 nucleide different = can read sequuence
IMAGE - shows 5’ and 3 end AND dNTP which replaces 3’ OH with H ; see that have different fragments where know the last nucleotide
Genome Assembly
Random breakage by sonification THEN need to realign to reference genome
90s - sequencing by hand = someone needed to match everything to see what assmebled on what
NOW - shotgun sequencing –> have sequencing fragments of DNA (few dozed nucleotides at a time) –> computer assmbles genome
Metagenomics
Obtain DNA sequences from all genomes in a particular habitat
Copy Number variation
Sequencing reads used as a method of counting the numver of times a sequence appears
Exome Seuqnecing
umans have 48 Mb of coding DNA (1.5% of genome_
Use oligionucletides as baits to hydridize to DNA of interest
RNA sequencing
To do - Prepare cDNA library and subject to NGS
Sequence reads that corespond to segments of trasncripts in original RNA
Bisulfate sequencing
Bisulfae converts C–> U (U is read of thymine)
Evolution of CpG islands
Humans genome has 42% GC content
Expected = 0.21 X 0.21 = 4.41% CpG BUT <1% is observed
Illumina Sequencing (new notes)
Sample prep
1. Add Adpatpters tp the end of teh DNGA fragments
2. Add the Sequence binidng site + Inidcies + regions complemenrray to the oligios
Clutering - Isothermal amplification of the fragemnts
1. Region compleentary to the oligio binds
2. DNA plymerase extends and makes dsDNA
3. Unattached DNA strand gets washed away
4. Second end of DNA frament binds to 2nd oligo on slide (forms birdge)
5. DNA polymerase extends and makes dsDNA -> stands will seperate (both starnds are attached to the slide)
6. Repeat to keep amplifying
7. Reverse strand is washed away (only have the foward strand)
Sequencing -
1. Extned the sequencing primer ; Nucleoodes have floruecent tages –> flruencent when added to the growing DNA strand
- Base call is determined by teh wL and the sigla intesity
- # of cylcles determiens the read length
2. Read is washed away
3. Index 1 primer binds (lower on starnd) –> extend primer –> index 1 read is washed away
4. Other end of opligio binds and forms bridge–> Index 2 primer binds
5. DNA polymerase extends and makes dsDNA
6. Foward strand is wahsed away
7. Complete the reverse read
Anylysis - have foward and reverse reads that forms contnuogs that are assmbed onto a refernce genome
- Samples are pooled based on unique indicies
