Chapter 6

prokaryotic gene structure

Includes Bacterial and Archaean domainsGene structureun-interrupted - no introns w/in genesSmall or no intergenic regionsOrganized into operons (review), Coordinate control and the operator repressible system

how do micro and minisatellites form?

Replication slippage occurs when the daughter strand slips back one repeating unit in pairing with the template strand. Each slippage adds one repeating unit to the daughter strand, similar to unequal crossing over, just less of a degree (1 sequence instead of a whole gene), mispairing can occur too, can see slippage from parent to child, happens fairly commonly but not constant

concerted evolution (coincidental evolution)

The ability of two or more related genes to evolve together as though constituting a single locus.

mini and microsatellites

VNTR (variable number tandem repeat) regions describe very short repeated sequences 2 kinds- Minisatellite DNAs, Microsatellite DNAs: How do they form??Mispairing or slippage Utility of repeats Parentage studies Forensics Fingerprinting Who done it cases Tracing famous mob boss

Hb Kenya

A fusion gene produced by unequal crossing-over between the Aγ- and β-globin genes, contains N-terminal sequence of A gamma gene and C- terminal sequence of beta gene, 2 genes differ by about 20% in sequence

dna profiling

A procedure that analyzes DNA fragments to determine whether they come from a specific individual. assigns heredity, 50% of bands in any individual are inherited from particular parent

cryptic satellite

A satellite DNA sequence not identified as such by a separate peak on a density gradient; that is, it remains present in main band DNA.

Bam islands

A series of short repeated sequences found in the nontranscribed spacer of Xenopus rDNA genes

how do copies of tandem repeated rRNA stay the same

Best hypothesis is concerted evolution maintains unit the same -constrained by function of ribosome which we need a lot ofTwo mechanisms for concerted evolution 1: Enzymatic homogenation of copies driven by function- looks at hundreds of rRNA genes and checks for mutations/errorsEnzyme senses if varying then acts on to correct = gene conversion2: Continually regenerated from single copyHere repeats vary so are replaced by original = crossover fixation which could maintain identical repeats, Unequal recombination allows one particular repeating unit to occupy the entire cluster- repeating unit can lose 1 base and get crossed over unequally in a way that correct copy is still maintained-crossover fixation?

gene structure

Big differences between prokaryotic and eukaryotic systems

repeats

Can be coding or repeated non coding regionsSmall to large areas include satellite DNA

Duplicated genes provide a means for further evolution by recombination

Crossing-over and recombination involve pairing between complementary strands of the two parental duplex DNAs.Classical homologous recombination creates different combinations of alleles providing the raw material for natural selectionDuplicated sequences allow events to occur which changes the number of copies of genes not just the combination of alleles

Unequal crossing over resulting from gene duplication events

Divergent introns can reduce the chance aberrant pairing and therefore unequal crossing over Unequal crossing over can cause aberrations in genes or clusters For example blood related maladies loss of some of the β or α parts of gene, changes in intergenic regions are favored, if there's mutations in introns it reduces aberrant/diff pairing, Can have serious consequences on gene regions

Microsatellites

are repetitions of extremely short (typically <10 bp) repeating units Repeating units can be in twos, threes, four basesForm dinucleotide repeats (CA, GT, AT, GC)Trinucelotide repeats (ACT, etc...) Quatranucleotide repeats (ACGT, etc...)Each genome has different groupsCA most common type in mammals

Minisatellites

are repetitions of longer repeating units usually >10 - 100 bp, [often associated w heterochromatic regions of chromosomes, in particular w centromeres, show some of same evolutionary patterns as tandem gene clusters- all this applies to satellite dna in general]

operons

genes that coordinate the regulation of gene expression, multiple genes of 1 pathway close together, a lot of prokaryotic genomes work like lac operons, regulatory regions close by & not a lot of stuff interspersed in it, have promoter, genes of operon, repressor determines if mrna is transcribed depending on if it is present or not

gene clusters, tandem duplication, translocation

group of adjacent genes that are identical or related, Some members of gene families and gene clusters are pseudogenes which can't be transcribed or translated The initial event that allows for the formation of gene families is gene or exon duplicationTandem duplication is when the duplicates are next to each other- can range from 2 to hundreds of variable copies in tandem array Duplicates can separate to new chromosomes by translocation- transfers material from 1 chromosome to another

complex satellites

in multicellular euks, have longer repeat units than simple sequence dna, usually in heterochromatin

Satellite DNAs Often Lie in Heterochromatin

in situ hybridization-Hybridization performed by denaturing the DNA of cells squashed on a microscope slide so that reaction is possible with an added single-stranded RNA or DNA.The added preparation is radioactively labeled and its hybridization is followed by autoradiography.

ITS

internal spacer regions, have diffs b/c species specific (in image for ribosomal gene region in ppt)

eukaryotic gene structure

interrupted genes - exons large intergenic regions Not organized into operons Clusters, tandem repeats, gene families, large intergenic regions- gene deserts, noncoding regions, enhancers aren't as close to what they enhance (compared to prokaryotes), introns in between exons, mrna processing w poly-A tail and 5' G cap, 5' UTR (untranslated regions) before start codon and after stop codon

mammalian satellites consist of hierarchical repeats

key concept- mouse satellite dna has evolved by duplication and mutation of short repeating unit to give basic repeating unit of 234 bp in which original half, quarter and eighth repeats can be recognized. in mammals, the sequences comprizing each satellite show appreciable divergence between tandem repeats, series of variants of short unit can constitute longer repeating unit that is itself repeated in tandem w some variation, can be detected by reassociation analyses or by restriction enzyme digestion, read book for details section 6.7

arthropod satellites have very short identical repeats

key concept- repeating units of arthropod satellite dnas are only a few nucleotides long, most of the copies of the sequence are identical, easy to determine sequence, satellites have pronounced asymmetry in orientation of base pairs on 2 strands ex. 1 strand is more rich in T and G bases which increases buoyant density so that upon denaturation this heavy strand can be separated from complementary light strand

minisatellites are useful for dna profiling

key concept- researchers can use the variation between microsatellites or minisatellites in individual genomes to identify heredity unequivocally by showing that 50% of bands in individual are inherited from particular parent, diff bands based on # of repeats. This means there is variation between individual genomes at micro and minisatellitesDNA profiling - Analysis of the differences between individuals of restriction fragments that contain short repeated sequences, or by PCR.The lengths of the repeated regions are unique to every individual, so the presence of a particular subset in any two individuals shows their common inheritance (e.g., a parent-child relationship).

NTS

nontranscribed spacers, NTS can have species specific mutations, repeats are identical but NTS can have diff lengths, NTS don't have dna pol but other parts in fig. 6.7? do, can be same size but size varies between clusters

classical recombination

occurs between alleles that differ only by 1 SNP, basically identical but diff versions, 1) bivalent contains 4 chromatids, 2 from each parent 2) chiasma is caused by crossing over between 2 of the chromatids, 2 chromosomes remain parental, 3) recombinant chromosomes contain material from each parent and have new genetic combinations, recombinant chromosomes have same organization as parental chromosome, precisely same loci in same order but include diff combinations of alleles

nucleolar organizer

particular chromosomal regions associated w a nucleolus, each corresponds to cluster of tandemly repeated 18/28S rRNA genes on 1 chromosome, concentration of tandemly repeated rRNA genes together w their very intensive transcription is responsible for creating chracteristic morphology of nucleoli

highly repetitive DNA

renatures most rapidly in eukaryotic genome, consists of very short sequences repeated many times in tandem in large clusters, as a result of its short repeating unit, it is sometimes described as simple sequence dna, present in almost all multicellular eukaryotic genomes but its overall amt is extremely variable

gene family- def, how many do humans have and how are they related and formed

set of genes encoding related or identical proteins or RNAs, descended by duplication and variation from single ancestral gene Humans have ~20,000 genes and ~15,000 gene families so the average gene has 2 relativesThe members were derived by duplication of an ancestral gene followed by accumulation of changes in sequence between the copies.Most often the members are related but not identical.Usually related only by exons (introns have a lot more diversity/mutation than exons), initial event that allows formation of related exons or genes is a duplication- when a copy of some sequence is generated w/in the duplication

tandem repeats

tandem repetition of short sequence has distinct physical properties, repetitive sequence has base composition distinct from genome avg, allows it to form separate fraction by virtue of its distinct buoyant density (can be determined by centrifuging dna through density gradient of CsCl)- satellite dna does this (essentially synonymous w simple sequence dna, might or might not be transcribed but isn't translated), tandemly repeated sequences are especially liable to undergo misalignments during chromosome pairing, sizes of tandem clusters tend to be highly polymorphic

why do pseudogenes occur, what are pseudogenes

things aren't necessary anymore and change intergenic stuff, have sequences that are related to those of functional genes but can't be transcribed or translated into functional polypeptide, some have same general structure as functional genes w sequences corresponding to exons and introns in usual locations, might have been rendered inactive by mutations that prevent any or all of the stages of gene expression, changes can take form of abolishing the signals for initiating transcription, preventing splicing at exon-intron junctions or prematurely terminating transcription

Tandem repeated rRNA

(rRNA) is encoded by a large number of identical genes that are tandemly repeated to form one or more clusters -makes of ~80-90% of the cellular RNA Each ribosomal DNA (rDNA) cluster is organized so that transcription units give a joint precursor to the major rRNAs alternate with nontranscribed spacers (separate rRNAs).The genes in an rDNA cluster all have an identical sequence, many rna polymerases are simultaneously engaged in transcription on 1 repeating unit. rRNA are encoded in the nucleolus region of nucleus rRNA genes are organized into clusters or tandem repeats Tandem units are separated by non-transcribed spacers - NTS- b/c they are not transcribed they are not evolutionarily constrained, Independent genes of repeat unit are separated by internal spacer regions - ITS-Also not evolutionarily constrained rRNA genes are not translated Non-allelic Clusters are repeated 100s of times in genome, Tandem rRNAs are types of gene clusters, What we know about tandem repeats and variation- All copies of repeated units are the same within an organism and NTS between tandem repeats may vary in size but are internally repetitious between and sometimes w/in species

D. virilus satellite amt

40% of its genome is satellites- unusually large amt, satellite I is found in all Drosophila, II and III evolved by slightly changing sequence

hemoglobin H disease

Alpha-globin chain disease in which three of the four genes are deleted

Hb Lepore

An unusual globin protein that results from unequal crossing over between the β and δ genes. The genes become fused together to produce a single β-like chain that consists of the N- terminal sequence of δ joined to the C-terminal sequence of β, several types are known depending on where transition occurred

clusters

Are gene coding clustersRange from two exact copies to hundreds of repeating clusters or groupsMany form gene families like histone proteins or globin, Can range from two identical adjacent copiesTo many identical or near identical copies to hundreds of variable copies in 1 clusterCan be expressed or functional in different tissues or different developmental stagesSome duplications can take on new functionsOthers degrade to pseudogenesComplications from duplication events. tandem duplication- can range from 2-hundreds of variable copies in 1 cluster

Many kinds of satellite DNAs Vary across lineages

For e.g. in arthropods Short most copies/sequence the same Each satellite is homogeneous a single, short repeating unit, ex. D. virilis, In mammals...like the mouse- Evolved by duplication of central repeat ~ 234 bp in which the original half-, quarter-, and eighth-repeats can be recognized- the 234 bp repeats are almost identical, they are divided into 2 (creating 4) and those are almost identical, can divide those in 2 again and there are some mutations still, so you can see how it evolved from mutations in consensus? can see homologies when quarter repeats are aligned, alignment of eighth-repeats shows that each quarter-repeat consists of an α and a β half, existence of an overall consensus sequence is shown by writing the satellite sequence as a 9-bp repeat in figure 6.16

satellite dna- what is it, what makes it diff from other dna, functions, location, features

Highly repetitive DNA with very short sequences Renature very quickly - form the highly repetitive fraction of the genome, 10-50% of genomes Satellite = simple sequence DNA Discovered by CsCl banding (CsCl separates things by density when spun) Found DNA would form distinct bands by density differences due to diffs in base composition (C-G content) Part of heterochromatin Highly coiled DNA very common at centromeres Thus has function in kinetochore attachment and mitosis/meiosis Because is highly coiled and repeated it is difficult to sequence, types of satellites you find is specific to each genome

Genes for rRNA Form Tandem Repeats Including an Invariant Transcription Unit

The nontranscribed spacers consist of shorter repeating units whose number varies so that the lengths of individual spacers are different, spacers make transcription easier

Microsatellite Development

Traditional enriched library construction and screeningGenome or EST searching and loci screeningNGS methods - mine with sequencing run

thalassemias

caused by various deletions that eliminate α- or β-globin genes, diff types (summarized in fig. 6.5 & 6.6), severity of the disease depends on the individual deletion (how many genes were deleted), organism doesn't want this to happen b/c not advantageous but can occur

Hydrops fetalis

complete absence of alpha globin genes, fatal at or before birth

how often does unequal crossing over occur

depends on how many repeated units they have, right amt exists for organisms, if lots of repeated units then it will happen more frequently

Unequal Crossing-over or Nonreciprocal Recombination

describes recombination event occurring between 2 sites that are similar or identical but not precisely aligned. unequal crossing over results from an error in pairing and crossing-over in which nonequivalent sites are involved in a recombination event (one copy of a repeat in 1 chromosome misaligns for recombination w diff copy of repeat in homologous chromosome instead of w strictly homologous copy).It produces one recombinant with a deletion of material and one with a duplication. This creates clusters of related sequences - gene clusters and highly repeated DNA, can rearrange gene clusters- mutations in parental genes and get mixed sequences or chromosomes, Gene number can be changed as well as sequence if the crossing over was within a gene and the two genes were not completely identical, look at figure p. 146, mispairing between parental chromosomes, nonreciprocal recombinant chromosomes produced