GenomeandArchitectureofChromosomes

SharadTiwariDepartmentofPlantBreeding&Genetics

LectureFundamentalsofGenetics

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Overview

• Eachspecieshasauniquesetofgeneticinformation,itsgenome.

• ThegenomeiscomposedofoneormoreDNAmolecules,eachorganizedasachromosome.

• Theprokaryoticgenomesaremostlysinglecircularchromosomes.

• Eukaryoticgenomesconsistofoneortwosetsoflinearchromosomesconfinedtothenucleus.

• Viralgenomescanbelinearorcircular,singleordouble-strandedandconsistofeitherDNAorRNA.

Genomesizeandgenenumber

Amoeba dubia: 670 billion base pairs

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TheNatureofGenomes• Genomics:studyofstructure/functionofgenomes• Genomesize

– variable,byordersofmagnitude– #ofgenesroughlyproportionaltogenomesize?

• Howmanychromosomes?• Howmanygenes?

Which genes are on which chromosome?

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Question

If species A has more DNA per nucleus than species B, does A necessarily have more genes than B? Explain.

No, the average size of genes can vary from one organism to another because the number and length of introns can vary. In addition, the amount of repetitive DNA can vary from one organism to another.

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SmallGenomes• Plasmids

– symbioticDNAmolecules;notessentialforcellviability• Dependonhostforreplication

– mostlycircularinprokaryotes– frequentlyencodeantibioticresistanceorsomeotherfunctionbeneficialtothehost

• OrganellarDNA– chloroplast,mitochondrion– multiplecopiesperorganelleandmultipleorganellespercell

• ThetotalamountoforganellarDNAcanbequitehigh– encodegenesspecifictotheirfunction– derivedbyendosymbiosisfrombacterialancestors

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PlasmidDNA/mtDNA

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ViralGenomes

• Nonlivingparticle– Subvertshostcellularmachinerytoitsownreproduction

– nucleicacidgenome– Proteincoat

• DNAorRNAgenome– single-strandedordouble-stranded– linearorcircular

• CompactgenomeswithlittlespacerDNA

In prokaryotes, viruses are sometimes referred to as bacteriophages.

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Prokaryoticgenome• Usuallycirculardoublehelix

– asmoregenomesaresequencedtherearemoreexamplesoflineargenomes

– occupiesnucleoidregionofcell– attachedtoplasmamembrane

• Genesareclosetogetherwithlittleintergenicspacer• Operon

– tandemclusterofcoordinatelyregulatedgenes– transcribedassinglemRNA

• Intronsareextremelyrare• DNAisefficientlypackaged(i.e.1mmDNApackagedina1µMcell)

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Eukaryoticnucleargenomes• Eachspecieshascharacteristicchromosomenumber• Indiploids,chromosomescomeinhomologouspairs

(homologs)– structurallysimilar– samesequenceofgenes– maycontaindifferentalleles

• Ploidyreferstonumberofcompletesetsofchromosomes– haploid(1n):onecompletesetofgenes– diploid(2n)– polyploid(≥3n)

• GenesaresegmentsofnuclearchromosomesIn humans, somatic cells have 2n = 46 chromosomes.

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HomologousChromosomesgene A

gene C gene B gene A

gene B gene C

Each member of the pair of homologs is alike in size and gene content

Same genes are in the same relative position

What about alleles of a gene?

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Question

An organism has 5 chromosomes in its body cells. Can you tell if it is likely to be haploid or diploid?

It is likely to be haploid due to the odd number of chromosomes.

An organism has 6 chromosomes in its body cells. Can you tell if it is likely to be haploid or diploid?

It may be diploid due to the even number of chromosomes (3 pairs of chromosomes) but it could also be haploid. There is really no way to know from this information.

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EukaryoticChromosomes(1)• Cytogenetics:microscopicstudyofchromosomes

– Combinesgeneticsandcytology• Considerabledifferenceinsizeandnumberofgenesonan

individualchromosome• Variablecentromereposition

– telocentric:centromereatend– acrocentric:centromereclosetoend– metacentric:centromereinmiddle– parmisshortest,qarmislongest

• Telomere:endofchromosome• Nucleolarorganizer(rRNA)

– SiteofrRNAsynthesis;tandemarraysofrDNAgenes– Uniquetooneorafewchromosomes

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QuestionsChromosomes 21 and 22 of humans are almost the same size, 33.55 Mb (21) and 33.46 Mb (22). Each chromosome contains about 1% of the human genome. Chr 21 contains 225 genes and Chr 22 contains 545 genes. From these data estimate the number of genes in the human genome. What are some of the possible errors?

225 + 545/2 = 385 genes per 1% of genome on average

385 X 100 = 38,500 genesOn the human chromosome 22 there are 55,664 repetitive DNA elements totaling about 14 Mb. What proportion of chromosome 22 consists of repetitive DNA?

0.418 or ~42%

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Eukaryoticchromosomes(2)

• Heterochromatin– denselystainedregionsofhighlycompactDNA– mostlyrepetitivesequences

• Euchromatin:poorlystained,lesscompact,containstranscribedgenes

• Bandingpatterns(metaphasechromosomes)– differentialuptakeofdyes– Gbands,Giemsastain(A/Trich)– Rbands,reverseofGiemsa(G/Crich)

• Polytenechromosomes– replicated,unseparatedchromosomes– presentincertaintissuesofdipteraninsects

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HumanKaryotype

G banding pattern for human karyotype

Human female

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ArchitectureofaChromosome• Eachchromosome

consistsofasingleduplexDNAmolecule

• Ahumancellcontains2metersofDNA– Mustbehighlycompacted

– DNAinyourbodywouldstretchtomoonandbackmanytimes

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NuclearDNA• Highlyorganized,variousdegreesofcoiling• Nucleosome

– fundamentalunitofchromatin– DNAwoundaroundhistonecore(octamer)

• histonesarehighlyconservedproteins• H2A,H2B,H3,H4

– 10nmfiber– solenoid,30nmfiber

• Higherordercoiling– solenoidloopsattachtoscaffold– scaffoldattachmentscontaintopoisomeraseII– formlargerdiameterfibers

A haploid set of human chromosomes consists of about 1 meter of DNA.

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ChromosomePackaging

~2mDNAispackedinahumancell

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QuestionsWhat does the word homologous mean?Diploid organisms have two copies of each of their different chromosomes. The term homologous is used to refer to the two members of each pair. Homologous chromosomes carry the same genes in the same relative positions.

Chromosome

Chromomere

Chromocenter

Single DNA molecule containing many genes, often associated with protein

Small beadlike structure visible on chromosome during propase

Point at which polytene chromosomes appear to be attached together

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OrganizationofHumanGenome

human genome 3200 Mb

genes and gene-related sequences 1200 Mb

intergenic DNA 2000 Mb

genome-wide repeats 1400 Mb

other intergenic regions 600 Mb

genes 48 Mb

related sequences 1152 Mb

psuedogenes

gene fragments

introns UTRs

micro-satellites 90 Mb

unique 510 Mb