Genome evolution II

repeated DNA promotes

genomic rearrangements

tandem repeat polymorphisms can arise by

unequal crossing over

direct repeats

in the same direction, the same sequence on the same DNA strand

genome evolution and direct repeats

the two can pair and recombine and lead to either intra or interchromosomal recombination

intrachromosomal recombination and direct repeats

leads to deletion

hypothetical circular fragment is lost—it does not possess a centromere

interchromosomal recombination and direct repeats

unequal crossing over with this causes deletion and duplication

inverted repeats

in the opposite direction, the same sequence is on the opposite DNA strand

intrachromosomal recombination and inverted repeats

leads to inversion of the intervening DNA sequence

functional consequences of such rearrangements are context dependent, from silent to lethal, as may be expected

over time, long- and short-range chromosomal rearrangements result in

reshuffling of genes and other elements

comparative genomics helps to recognize and study these processes

synteny

a set of homologous genes located on the same chromosome in different species (not necessarily in the same order)

microsynteny

maintenance of immediate adjacency with regards to these homologous genes

collinearity

a set of homologous genes located on the same chromosome and in the same order

outcome following a double-stranded DNA break will depend on

what repair mechanism fixes the wound

some are less likely to result in structural changes, others likely result in deletion, other likely result in rearrangements

DNA repair mechanism and genomic rearrangement outcome- homologous recombination

least likely to result in structural changes

DNA repair mechanism and genomic rearrangement outcome- single-strand annealing

likely to result in deletion

DNA repair mechanism and genomic rearrangement outcome- nonhomologous end joining

likely to result in long-range rearrangements such as translocations and inversions

paradigm of gene organization in proks

the operon

this determines that order of genes in genomes is strongly influenced by the functional nature of the genes, therefore not random

does gene order matter in eukaryotes?

in many cases, certain genes tend to appear in clusters as if they were kept together by selective forces

e.g. HOX genes in animals—organized in clusters, genes have maintained their order for over 500 million years

gene order and eukaryotes

genes from closely related species are arranged in the same order, but over time they will differentiate from each other because of many events of chromosomal rearrangements (large and small) occurring independently

over long evolutionary distances (e.g. mammals-insects, algae-plants), many genes become complete shuffled

Hi-C method

a proximity ligation approach

cross-link DNA with HindIII, cut with RE, fill ends and mark with biotin, ligate with Nhel, purify and shear DNA, pull down biotin, sequence using paired-ends

proximity ligation

sorts out what sequences (reads, contigs) are in close proximity in the original state (e.g. same chromosome)

proximity ligation limitations

requires additional rounds of Illumina sequencing, groups contigs into bins of proximity, not exact order

what can we study in detail with Hi-C or proximity ligation?

long range interactions within and among chromosomes

spatial organization of chromosomes affects

gene expression

what influences gene activity?

compactness of chromatin

what facilitates gene transcription?

movement of chromatin toward transcription machinery

what affects gene expression?

association of gene loci with nuclear pore complexes, nuclear periphery, or specific nuclear bodies

topologically associating domains

functional units that organize chromosomes into 3D structures of interacting chromatin

dozens to hundreds of kilobases in size and tend to contain genes with similar epigenetic states

speculation that genes which are required for similar processes may fall within these same domains, allowing them to share regulatory programs and efficiently switch between chromatin compartments

evidence that TADs do control coregulation

significant correlation of expression levels for genes within this domain, suggesting that they do function as genomic domains with shared regulatory features

evidence that TADs do not control coregulation

no association between genes sharing the same CTCF TADs and increased co-expression or functional similarity, other than that explained by linear genome proximity

what explains most of the observed co-regulation within TADs?

linear proximity