Tandem Repeats and Satellite DNA in Bovideae - Colloquium on Animal Cytogenetics
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Tandemly repeated satellite DNA in the Artiodactyla Pat Heslop-Harrison Trude Schwarzacher Raquel Chaves niversity of Leicester, UK niversidade de Trás-os-Montes e Alto Douro, Portuga www.molcyt.com Twitter/slideshare Path [email protected]
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Tandemly repeated satellite DNA in the Artiodactyla - a lecture Tandemly repeated, satellite, DNA sequences are an abundant component of the genome of most species, including the Artiodactyla. Multiple DNA familes are present, each in long tandem arrays, with members of each family present on one or more chromosomes at characteristic positions. In particular, several familes are located at the centromeres of most chromosomes, including acrocentrics, metacentrics and the sex chromosomes. Individual arrays are made up of variants of particular sequence motifs, which may be longer than 1,500 bp. In this presentation, we will discuss aspects of the evolution of repetitive sequences within and between chromosomes, with comparative data between different species. With pig, we will show details of the localization of tandem repeats at meiosis, and how these sequences relate to sequence amplification and loss, as well as the epigenetic behaviour of the resulting heterochromatin. In the Bovinae, we will show how molecular cytogenetic methods are essential to build up a full picture of the behaviour and distribution of satellite DNA where current sequencing methods are unable to assemble the sequences blocks accurately. P. Heslop-Harrison1, T. Schwarzacher1 and R. Chaves2 ([email protected]) University of Leicester, Biology, Leicester LE1 7RH UK; 2Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
Transcript of Tandem Repeats and Satellite DNA in Bovideae - Colloquium on Animal Cytogenetics
Tandemly repeated satellite DNA in the Artiodactyla
Pat Heslop-HarrisonTrude SchwarzacherRaquel Chaves
University of Leicester, UKUniversidade de Trás-os-Montes e Alto Douro, Portugal
www.molcyt.comTwitter/slideshare [email protected]
Chromosomal changes are one of the most important features of evolution
Bovideae: 58 autosomal arms
Cow: 2n=60 (29 pairs of acrocentric autosomes + X, Y)
Sheep: 2n=54 (25 acrocentric + 2 submetacentric pairs + X, Y)
Bos taurus taurus vs Bos taurus indicus:2n=60, XY
But: B. taurus submetacentric Y B. indicus acrocentric Y
Robertsonian Fusion of 1 and 29 to give 2n=58 or 59: Gustavson 1964
Heterozygous rob(1;29) example in Portuguese cattle Barrosa Chaves et al. Chromosome Research
Repetitive DNA sequences – LINE/SINE transposons and satellite DNA – are
the most abundant genome component
- Often ‘masked’ (ignored) during sequence assembly- Satellites ‘collapse’ from hundreds
of tandem repeats to a few- Often functional regarding centromeric
behaviour and methylation/ heterochromatinization
Robertsonian Fusion
(+ )
Chaves et al. Chromosome Research
Complex satellite DNA reshuffing in the polymorphic t(1;29) Robertsonian translocation and evolutionarily derivedchromosomes in cattle Chaves, Adega, Heslop-Harrison et al. 2003
Barrosa¬
Barrosa¬
Order Artiodactyla (Even-toed ungulates)
3 groups: 1. Suiformes (pigs, peccaries,
hippopotamuses), 2. Tylopoda (camels, llamas)
3. Ruminantia (cattle, goats, sheep, deer, antelopes, giraffes)
9 families (13 tribes) including Bovidinae
Family Bovidae c. 137 species Last species (new genus) discovered in
1992
Domestic pig Sus scrofa domestica
Centromeric satellites
METACENTRIC CLONES:
GC rich centromeric heterochromatin
• Clone pAL7.5 (“Al”): present in all metacentric chromosomes (SSC1 – SSC12 and X ); 294bp
• Clone pAv1.5 (“Av”): present only in SSC1; 313bp
ACROCENTRIC CLONES: AT rich centromeric
heterochromatin• Clone pMb3.5 (“3.5”):
present in all acrocentrics (SSC13-SSC18); 309bp
Karyotype: Jantsch et al., 1990
Domestic pig Sus scrofa domestica
Centromeric satellitesMETACENTRIC CLONES:
GC rich centromeric heterochromatin
diverse
ACROCENTRIC CLONES: AT rich centromeric heterochromatin
homogeneousBouquet at meiotic pachytene promotes clustering of acrocentric centromeres and homogeneisationSchwarzacher et al., 1984
XY
SSC1
The synaptonemal complex at meiotic pachytene
SCP1: central element proteinFISH probe for centromere of chromosome 1 SSC1
Defria and Schwarzacher 2014
Diagram: 2004Page and Hawley
Acrocentric chromosomes
cluster and are associated
via their repetitive DNA sequences not the SC itself
SSC1
Ac
Ac
Ac
Ac
Ac
Ac
SCP1: central element proteinFISH probe for centromeres of all Ac and SSC1
Alnajar and Schwarzacher 2010
DNA methylation
Immunostaining with anti-SCP1 (red) and anti-methyl-5-cytosine (green) on SC spreads.The methylation signal is amplified towards ends of the chromosomes (yellow tips) and more methylation occurs in the chromatin loops.
The Ac chromocentre stains strongly with DAPI and is not methylated
5MeC Mc1
5MeC Ac2Sheperd and Schwarzacher 2013 (unpub.)
conventionally spread pachytene nuclei
Sheep satellite I OaSatI
Sheep satellite I OaSatI
Hughes and Heslop-Harrison 2014
BtSatI homology in sheep
73.6%
Dotplot of bovine satellite I against a region of goat chromosome 5
Dotplot of ovine satellite I repetitive unit against a region of goat chromosome 10
BtSatI BtSatIVGaspar, Hughes, Chaves and Schwarzacher 2014
FISH on cattle (Brakman) chromosomes
Satellite I and II collocalize, Satellite IV has separate arrays
BtSatII BtSatI BtSatII BtSatIVGaspar and Schwarzacher 2014
pBtKB5
BtSatI-2BtSatI-4
SINE A2/tA is part of Satellite IV and hybridizes to euchromatin and centromeric
heterochromatin
SINE A2/tA is part of Satellite IV and hybridizes to euchromatin and centromeric
heterochromatin
But it is outcompeted when hybridized together with SatIV probe and appears on euchromatin only
Conventional and synaptonemal complex spread of male sheep
BtSatII
Cluster of some acrocentric centromeres
BtSatIISchwarzacher, Chaves, Heslop-Harrison & students 2014
Cattle Sat I organisation
Clone pBtKB5 is part of BtSatI and indicates subrepeats and higher order structures
Hughes and Heslop-Harrison 2014; Chaves et al 2004 Chromosome Research
94.3%.
BtSatI homology between cattle and sheep
Laetita Gaspar
Pairwise identity 54.7%
Satellite I Satellite IISatellite III Satellite IV SINE A2/tA
A element
Cattle Sheep Cattle Sheep Cattle Sheep Cattle Sheep
Shared by
ruminants.
Density Gradient
(g/cm3)
1.715 1.714 1.723 1.723 1.706 X 1.709 X
Length (bp)
1402 820 700 700 X X 3808 X
Pairwise identity
(%)
54.7 % 61.3% X X
BtSatI homology in goat
Hughes and Heslop-Harrison 2014
60.3%
1.715 satellite IDivergence between cattle and sheep/goatLess cross hybridization in FISH experimentsBut strong homogeneisation within each species acrocentric association during meiosis
.
.
Tandemly repeated satellite DNA in the Artiodactyla
Pat Heslop-Harrison [email protected] Trude Schwarzacher & Raquel Chaves
Molecular cytogenetic approaches build a full picture of the behaviour of chromosomes (translocations/fusions) and satellite DNA organization and evolution
Current sequencing methods are unable to assemble the sequences blocks or cope with chromosomal rearrangements
