Chromosome Wilhelm Gottfried Waldeyer (1836 – 1921) Basics of chromosome structure Eukaryotic chromosomes • Usually linear • Variable in number • DNA interacts with proteins to form chromatin • Centromeres ensure segregation • Telomeres cap ends • Must be compacted to fit in nucleus • highly coiled DNA • histones • non-histone chromosomal proteins (DNA & RNA polymerase, transcription factors, topoisomerases, histone modifying proteins) chromatin (DNA & proteins) Chromatin helps to fit the long DNA molecules into small cells or nuclei Escherichia coli 4.6  106 bp = 1.5 mm (a 1000-fold compression) 1.5 m Histones and nucleosomes 10 nm 10-nm fibre 30-nm fibre Chromosome packing (loop domains) nucleosome not a regular structure ? 10-nm fibre A model for the hierarchical domain organization of an interphase chromosome based on packaging of 10-nm fibers Hansen et al. 2018, Biochem Soc Trans - the 30-nm fiber that may exist only transiently (?) Chromosome organisation: Strings & Binders Switch (SBS) model Barbieri M et al. (2012) Complexity of chromatin folding is captured by the strings and binders switch model. PNAS 109:16173-16178. Interphase chromosomes – chromosome territories The distribution of chromosomes and genes is nonrandom with some chromosomes preferentially occupying internal positions and others occupying peripheral positions. Chromosome territories Chromosome territories T Nagano et al. Nature (2013) doi:10.1038/nature12593 Chromosome territories Structural modelling of X chromosomes X Y Pecinka et al. (2004) Chromosoma Chromosome territories - Arabidopsis Chromosome Conformation Capture (3C) and 3C-Derived Methods A Hi-C map of chromatin interaction frequencies high levels of intra-chromosomal interactions less frequent inter-chromosomal interactions Model of nuclear organization (at different resolutions) described for animal models a particular locus can be surrounded by an active (A compartment) or repressive environment (B compartment) Chromosome territories - separate, yet interacting nuclear domains; important long-range chromatin interactions Territories partitioned in (i) megabasepair-long domains with frequent internal contacts = topological associated domains (TADs), and (ii) the lamina-associated domains (LADs) interacting with the nuclear lamina, and with other functional compartments Specialized transcription factories = genes come together; proximity between different transcription units Splicing factors (splicing nascent transcripts into messenger RNA) accumulated in splicing speckles - often associated with active genes Repressed chromatin associates with heterochromatic regions Chromosome territories Topological associated domains (TADs) • TADs show high levels of chromatin interaction and coincide with the presence of tissue-specific genes and their associated enhancers (the interactions of which with their cognate promoters are facilitated by the presence of cohesin and CCCTC-binding factor (CTCF)) • the border regions between TADs are enriched for housekeeping genes, which are often clustered together; show high levels of CTCF and cohesin binding, although only CTCF seems to prevent interactions between TADs. CTCF is not in plants. TAD TAD TAD = LADs = mainly CTCF („insulator“) protein • no typical TADs in Arabidopsis • but over 1,000 TAD-boundary-like and insulator-like regions; these regions possess similar properties to those of animal TAD borders (Wang et al. 2015) • TADs in other plant species, but organisation variable; this can be due to the absence of CTCF protein (associated with borders of conserved TAD boundaries in mammals) • presence/absence of TADs related to genome size (?); larger genomes → lower gene density → TADs Dogan and Liu (2018) Nat Plants The nonrandom organization of genes and chromosomes contributes to the formation of translocations. Proximity of chromosome territories and chromosome translocations Relative interphase positions of chromosomes in NHBE cells. Panel A shows chromosomes 1 (red) and 13 (green), Panel B shows chromosomes 9 (green) and 17 (red) while Panel C shows chromosomes 16 (red) and 21 (green). Panel D outlines a ‘map’ of the relative positioning of chromosome territories in NHBE cells. Foster et al. (2013): Relative proximity of chromosome territories influences chromosome exchange partners in radiation-induced chromosome rearrangements in primary human bronchial epithelial cells Chromosome organization at interphase (in plants) Rabl configuration Radial loop model more organisation models ? Cowan C R et al. Plant Physiol. 2001;125:532-538 Rabl configuration nucleolus Radial loop model: Arabidopsis NADs : genomic regions with heterochromatic signatures and include transposable elements (TEs), sub-telomeric regions, and mostly inactive protein coding genes. However, NADs also include active rRNA genes and the entire short arm of chromosome 4. Hypothesis: telomeres, NORs and NADs anchor chromatin loops to nucleolus TELs clustered around nucleolus nu Pontvianne et al. (2016) Cell Reports radial loop model NADs: nucleolus-associated domains Chromatin and chromosomes Heterochromatin and euchromatin DAPI-stained chromosomes of Fritillaria spp. (B/W, inverted) Chromosomes and nuclei stained by fluorescent dyes 4',6-Diamidino-2-phenylindole (DAPI) Caenorhabditis elegans AT-specific fluorescent dye Chromatin structure: eu- and heterochromatin heterochromatic bands • Traditional view: chromatin compaction limits or enhances access to transcription factors • Accessible chromatin is referred to as euchromatin and is active (Emil Heitz, 1928) (transcription facilitated) • Inaccessible chromatin is called heterochromatin and is generally inactive (thought that regulatory proteins, e.g. transcription factors, cannot access DNA templates) • Today - restriction of DNA accessibility is a local property of chromatin and not necessarily a consequence of microscopically visible compaction Histones 10 nm 10-nm fibre 30-nm fibre Histone modifications (marks) Histone modifications (marks) Histone modifications (marks) ▪ acetylation ▪ methylation ▪ phosphorylation Histone acetylation (ac) – relaxed chromatin structure, open chromatin conformation allows transcription factor binding and significantly increases gene expression Histone methylation (m) – activation or repression of gene expression (often depending on the number of methyl groups – for example, H3K4m1, H3K4m2, H3K4m3; H3K9me3 is a permanent signal for heterochromatin formation in gene-poor chromosomal regions with tandem repeat structures, such as satellite repeats, telomeres or pericentromeres) Histone phosphorylation (ph) – most commonly during cellular responses to DNA damage (phosphorylated histone H2A separates large chromatin domains around the site of DNA breakage) lysine (K) residues, arginine (R) residues serine (S) and threonine (T) residues lysine (K) residues [1, 2 or 3 methyl groups] in euchromatin in plants Methylation of X chromosome in mammals (Barr body) Methylation of X chromosome in mammals (Barr body) DNA methylation in plants Methylation at cytosines on the carbon no. 5 (within the pyrimidine ring) – m5C Arabidopsis (157 Mb) – c. 6% of the cytosine residues methylated Maize (2 300 Mb) – c. 25% Zhang et al. (2018) Dynamics and function of DNA methylation in plants. Nat Rev Mol Cell Biol 19: 489-506. Heterochromatin Di- and trimethylated histone H3 lysine 9 (H3K9me2 and H3K9me3) interspersed regions in euchromatin (i-Het) heterochromatic protein 1 Ambrožová et al. (2011) Diverse retrotransposon families and an AT-rich satellite DNA revealed in giant genomes of Fritillaria lilies, Ann Bot 107: 255-268. Heterochromatin in plant species Heterochromatin in plant species Arabidopsisbarley chromocenters heterochromatin density of inaccessible region protein-coding genes TEs along chromosomes Shu et al. (2012), Nature Comm heterochromatin Genomic features in inaccessible and hyper-accessible regions heterochromatin: 5-cytosine methylation, dimethylation of H3 (H3K9me2) euchromatin: trimethylation of H3 (H3K9me3) Heterochromatic pericentromere in plant species (Arabidopsis) in heterochromatin in animals Heterochromatic pericentromere in plant species (Arabidopsis) Scheme of plant chromosome (after Haslop-Harrison) centromere Arabidopsis chromosomes centromere Arabidopsis Genome Initiative, Nature 408, 2000 The frequency of features was given pseudo-colour assignments, from red (high density) to deep blue (low density). Gene density (`Genes') ranged from 38 per 100 kb to 1 gene per 100 kb; Transposable element densities (`TEs') ranged from 33 per 100 kb to 1 per 100 kb. ChTeAtEuSyCh ChTeAn BrHuAn (a) (b) (c) (d) DoMiAt HeSyAt MaInAt BuOrAt DoMiAn HeSyAn MaInAn BuOrAn (e) (f) (g) (h) (i) (j) (k) (l) Chromosome structure small genomes (c. 150 – 600 Mb) large(er) genomes (> c. 1400 Mb) (a) (b) (c) ChTeAt MaInAt BuOrAt (d) HeSyAt HeS y1 Chromosome structure – different interphase organization small genomes (c. 150 – 600 Mb) large(er) genomes (> c. 1400 Mb) Mitotic and meiotic chromosomes meiotic (pachytene) chromosomes of Antirrhinum mitotic chromosomes of Pinus 1 chromosome = 2 chromatids 1 bivalent = 2 chromosomes = 4 chromatids Cell cycle, chromosomes and chromatids interphase Mitosis Figure 3.16 Genomes 3 (© Garland Science 2007) Meiosis Chromosomes and chromatids during mitosis and meiosis 1 chromatid2 chromatids 2 chromatids 1 chromatid 1 chromatid 4 x 1 chromatid Mitosis Meiosis 2 chromatids Chromosome morphology Centromere structure, function & evolution Centromere function • chromosomes can be monocentric or holocentric (Luzula, Eleocharis, some insects) • dicentric chromosomes usuallly unstable (anaphase bridges >> breakage), one centromere has to be inactivated epigenetically (cf. dicentric Robertsonian fusions) • acentric chromosome fragments are unstable at mitosis/meiosis and lost • sister chromatid cohesion throughout cell cycle until sister chromatid segregation at mitosis/meiosis II (centromeres enriched with cohesin) • sites of kinetochore formation ensuring correct chromosome position on mitotic/meiotic spindle: chromosome congression (kinetochore: spindle microtubules attached) Centromere function: mitotic chromatid segregation Accurate chromosome segregation requires that kinetochores from each sister chromatid bind microtubules that emanate from opposing spindle poles (amphitelic attachment). This is achieved by a process called chromosome bi-orientation. Incorrect attachments can lead to improper chromosome segregation and aneuploidy. Chromosomal bi-orientation on a bipolar mitotic spindle Centromeres and microtubules (monocentric chromosomes) Wanner et al. (2015) Chromosoma Kinetochore inner kinetochore - associated with the centromere DNA; specialized form of chromatin persistent throughout the cell cycle outer kinetochore - interacting with microtubules; functional only during cell division. Even the simplest kinetochores consist of more than 45 different proteins! Many conserved between eukaryotic species, including a specialized histone H3 variant (called CENP-A or CenH3) which helps the kinetochore associate with DNA. Kinetochore Zhang and Dawe (2011) Mechanisms of plant spindle formation Microtubules (tubulin) CENH3 (an inner kinetochore protein) Chromosomes Microtubules interact with kinetochores even in the earliest stages of prometaphase (immediately following nuclear envelope breakdown). Mitosis in barley (immunofluorescence) CENP-A or CenH3 determines centromere location/activity Chittori et al. (2018) Science kinetochore proteins (methylation of H3 on lysine 9) (di-methylation of H3 on lysine 4) protein otr : outer repeat imr : innermost repeat cnt : central sequence Drosophila H. sapiens fission yeast S. pombe The overall chromatin structure of the centromere is conserved among different species Structure of plant centromeres CENH3 (CENP-A)-associated and H3associated nucleosomes The CENH3-binding domain contains active genes (red bars), but with a lower density than the flanking domains. centromere of rice chromosome 3 Rice centromeres contain a satellite repeat CentO and centromere-specific retrotransposon CRR. In monocentric chromosomes, the centromere is characterized by a single CenH3-containing region within a morphologically distinct primary constriction. This region usually spans up to a few Mbp composed mainly of centromere-specific satellite DNA. • long primary constrictions that contain 3–5 explicit CenH3-containing regions • the size of the chromosome segment delimited by two outermost domains varies between 69 Mbp and 107 Mbp (several factors larger than any known centromere length) • 13 distinct families of satellite DNA and one family of centromeric retrotransposons (unevenly distributed among pea chromosomes) Neumann et al. (2012) PLoS Genet Pea: monocentric chromosomes with multiple centromere domains Holokinetic Chromosomes Do Not Possess a Localized Centromere Chromosomes with more than one centromere: consequences and solution Neocentromeres •a de novo centromere formation occurring after chromosome breakage or endogenous centromere inactivation •kinetic motility of terminal or subterminal heterochromatin, which is pulled to the cell poles during meiosis in plants (heterochromatic knobs) Two meanings in literature: Formation and behavior of de novo centromeres PNAS 2013 The small chromosome has no detectable canonical centromeric sequences, but contains a site with protein features of functional centromeres such as CENH3, the centromere specific H3 histone variant, and CENP-C, a foundational kinetochore protein, suggesting the de novo formation of a centromere on the chromatin fragment. A Model of Centromere Evolution Gong Z et al. Plant Cell (2012) The satellite repeat may be derived from other centromeres, such as rice Cen8, or a new repeat, such as potato Cen9. Centromeres may survive for several million years without satellite repeat invasion (slow evolution through DNA mutations and accumulation of transposable elements). A de novo DNA amplification of a satellite repeat, possibly based on an eccDNA-mediated mechanism, and insertion of the repeat (yellow) in the CENH3 domain can turn an evolutionarily new centromere into a repeat-based centromere. new satellite repeat emerges in the neocentromere centromeric satellite repeats neocentromere emergence original centromere inactivation satellite array in the inactivated centromere degrades or eliminated during evolution new satellite repeats array expands A model of neocentromere-mediated centromere evolution in plants Centromere repositioning in curbit species • centromere repositioning (CR) extensively documented in mammalian species (e.g. 5 CRs in the donkey after its divergence from zebra) • scarce reports on CR in other eukaryots including plants Cucumis sativus 2n = 14 Cucumis melo 2n = 24 • centromeres of cucumber and melon chromosomes are associated with distinct pericentromeric heterochromatin • centromere activation or inactivation were associated with a gain or loss of a large amount of pericentromeric heterochromatin Centromere repositioning in curbit species Han et al. 2009, PNAS 106 Cross-species fosmid FISH in cucumber and melon (Cucurbitaceae) Fosmids (40 kb) are based on the bacterial F-plasmid. The cloning vector is limited, as a host (usually E. coli) can only contain one fosmid molecule. Low copy number offers higher stability than comparable high copy number cosmids. 75 Arabis alpina – centromere repositioning 5 reciprocal translocations 4 pericentric inversions 3 centromere repositions 1 centromere loss 1 new centromere emergence (?) D E 2 I J 4 O P Q R 6AK1 A B C 5 K L M N 7 S T U 8 V W X 3 F G H 2 D E AA1 Ab B Aa 4 T Jb C 5 M Na K L Nb 7 Ua Ub 8 Xb W Qb R Xa Qa 3 H Fa G Fb 6 I S O V Ja Pa Pb Willing et al., Nature Plants 2015 1.00 0.99 1.00 0.94 1.00 1.00 1.00 1.00 1.00 0.77 1.00 1.00 1.00 0.01 Arabis alpinaEurope Arabis purpurea Arabis alpinaAfrica Arabis montbretiana Arabis nordmanniana Arabis auriculata Arabis nova Aubrieta canescens Arabis verna Draba hispanica Draba aizoides Arabis hirsuta Arabis collina Sinoarabis setosifolia Arabis alpina clade Aubrieta clade Draba and Tomostima clade main Arabis clade Scapiarabis clade Arabis auriculata clade Arabis nord- mannianaclade Pseudoturritis turrita Arabis aucheri Arabis aucheri clade 12 5 3 >400 2 16 >65 12 Draba (Drabella) muralis Ar1 2 3 4 5 6 7 8 Pt1 2 3 4 5 6 7 8 A. alpina A. cypria A. montbretiana A. auriculata Au. parviflora A. blepharophylla D. muralis D. hispida D. nemorosa ~13.5 14.0 14.1 Centromere repositioning in Arabideae Mandakova et al. (2019), Plant Cell (in review) F16A14 F7A19 F10B6 T16N11 F3O9 F17F16 F20D23 F1L3 T10F20 F25I16 T29M8 F14P1 F5A9 T1K7 T24P13 F6F9 F5M15 T22I11 F8K7 F16L1 T22J18 F26F24 T23E23 F3I6 F15D2 T1P2 F17L21 F28L5 F3M18 Paleocentromere ENC conservedchromosomecollinearity CENTROMEREREPOSITIONING P. turrita (paleocen.) A. cypria (ENC) Ch1 P. turrita (paleocentromere) A. cypria (ENC) Centromere repositioning in Arabideae Centromere repositioning in Arabideae Pt T22C5 F28L5 T24D18 F3O9 Ar_univ4 T22C5 F28L5 ENC1 5.43 Mb (F7H2/T24D18) 6.45 Mb (F25I16/F14D16) 0 Mb 11.68 Mb Dm Aa, Ac, Am Dh, Dn Aup 9.62 Mb (T22C5/F28L5) 5.5 Mb (T24D18/F3O9) 6.07 Mb (F1L3/T10F20) PsTu P. turrita (paleocentromere) A. cypria ENC3 Pt T25N22 6.86 Mb (T31J18/MZE19) Ab 10.77 Mb (T25N22/T10F5) 4.23 Mb (MGH6/MRP15) 7.28 Mb (F3H11/MSA6) 0 Mb 14.06 Mb Aup Dn, Dm 5.18 Mb (F4B12/MQD17) Am Aa, Ac 6.33 Mb (MYF24/K24M9) MYF24 K24M9 Ar_univ4 T25N22 T10F5 PsTu T10F5 A. cypriaP. turrita (paleocentromere) Mandakova et al. (2019), Plant Cell (in review) Telomeres The Nobel Prize in Physiology or Medicine 2009 was awarded jointly to Elizabeth H. Blackburn, Carol W. Greider and Jack W. Szostak "for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase". Carol W. Greider Jack W. SzostakElizabeth H. Blackburn Telomeres Telomeres Nicotiana tabacum  T. Mandáková Keywords on telomeres • solving chromosome shortening (loss of DNA sequences) • protects against DNA repair (repair of double-strands) • evolutionary conserved telomeric repeats • telomere-binding proteins (shelterin complex) • synthesis by the telomerase enzyme • ribonucleoprotein, enzyme • adds telomeric repeats (e.g. TTAGGG in all vertebrates) to the 3‘ end of DNA strands at the ends of eukaryotic chromosomes • preventing constant loss of DNA sequences from chromosome ends • composed of own RNA and reverse transcriptase (TERT) Telomeres are made by telomerase Telomeres of plants human TTAGGG Tetrahymena TTGGGG Arabidopsis TTTAGGG Sequences of telomere repeats mutation altering the RNA template subunit of telomerase, c. 80 million years ago Telomeres – when something goes wrong telomere dysfunction → ring chromosomes Wikipedia: Human genetic disorders can be caused by spontaneous ring chromosome formation; although ring chromosomes are very rare, they have been found in nearly all human chromosomes. Disorders arising from the formation of a ring chromosome include ring chromosome 20 syndrome where a ring formed by one copy of chromosome 20 is associated with epilepsy; ring chromosome 14 and ring chromosome 13 syndrome are associated with mental retardation and dysmorphic facial features; ring chromosome 15 is associated with mental retardation, dwarfism and microcephaly. Ring formation of an X-chromosome causes Turner syndrome. Symptoms seen in patients carrying ring chromosomes are more likely to be caused by the deletion of genes in the telomeric regions of affected chromosomes, rather than by the formation of a ring structure itself. In the absence of a protein protecting telomeres, chromosomes fuse abnormally data from the T. De Lange lab Telomeres – when something goes wrong Murnane JP (2012) Telomere dysfunction and chromosome instability 1. telomere dysfunction 2. sister chromatid fusion (2 centromeres) 3. bridge during anaphase 4. breakage (breakage occurs at locations other than the site of fusion, resulting in large inverted repeats on the end of the chromosome in one daughter cell and a terminal deletion on the end of the chromosome in the other daughter cell) 5. fusion, bridge, breakage,… … the B/F/B cycles will continue until the chromosome acquires a new telomere, most often by translocation Telomeres – when something goes wrong Breakage-fusion-bridge cycle The telomeres (gray squares), centromeres (circles), subtelomeric sequences (horizontal arrows) rDNA loci on chromosomes - routinely detected by FISH - diagnostic value, position and the number usually species-specific - 45S rDNA usually in different position on chromosome(s) than 5S rDNA - 45S formed at nucleolar organizing regions (NORs) associated with nucleolus rDNA = ribosomal DNA = genes coding ribosomal RNAs Physical mapping of 45S rDNA (red) and 5S rDNA (green) to metaphase chromosomes of Larix leptolepis. Chromosomes counterstained with DAPI (blue) (Zhang et al. 2010) Satellites (different from satellite repeats), satellite chromosomes: chromosomes with nucleolar organizing region (NOR) = secondary constriction. Short chromosome part beyond the NOR is called a satellite (trabant). SAT chromosome: Sine Acid thymonucleinico (without thymonucliec acid or DNA). Because of relative deficiency of DNA in the nucleolar organizing region, NORs show less intense staining. Satellite (SAT) chromosomes, secondary constrictions CEN NOR NOR NOR Nucleolus - ribosomal DNA (rDNA = rRNA genes) is transcribed and ribosomes are assembled within the nucleolus - ribosomes are exported to the cytoplasm. They remain free or associate with the endoplasmic reticulum (rough endoplasmic retictulum). - one or several nucleoli in a nucleus - after a cell division, a nucleolus is formed around nucleolar organizing region (NOR) on some chromosomes (chromosomes are brought together by nucleolar organizing regions) - cell division: nucleolus disappears 18S, 5.8S, and 28S - genes coding 18S, 5.8S, and 28S RNA molecules NTS - nontranscribed spacer ETS - external transcribed spacer ITS - internal transcribed spacers 1 and 2 transcription of rDNA→ 45S pre-rRNA→ processing→ 18S RNA, 5.8S and 28S RNA molecules 45S and 5S ribosomal DNA (rDNA) Structure of the 45S rDNA tandem repeat Ribosomes – proteins and RNA molecules. In eukaryotes, small (40S) and large (60S) subunit. The 18S rRNA in the small subunit, large subunit contains 3 rRNA types (5S, 5.8S, and 28S rRNA). In eukaryotes, the 5S rRNA gene is separated from the 45S rRNA genes. But together in Artemisia, gymnosperms, and some other plants. Pecinka et al. (2004) Chromosoma Chromosome territories in Arabidopsis: NOR-bearing chromosomes associated more frequently than all other chromosomes NADs : genomic regions with heterochromatic signatures and include transposable elements (TEs), sub-telomeric regions, and mostly inactive protein coding genes. However, NADs also include active rRNA genes and the entire short arm of chromosome 4. Hypothesis: telomeres, NORs and NADs anchor chromatin loops to nucleolus TELs clustered around nucleolus nu Pontvianne et al. (2016) Cell Reports radial loop model NADs: nucleolus-associated domains Heterochromatin and heterochromatic knobs Het knobs are located on chromosomes: a) terminally b) insterstitially c) at pericentromeres meiotic (pachytene) chromosomes of Antirrhinum Het knobs in Brassicaceae species Myagrum perfoliatum Thellungiella halophila Mandáková & Lysak (2008), Plant Cell Het knobs in rice CEN het knobs rice chromosome 4 Jiao et al. 2005, Plant Cell 17 Heterochromatic segment 1 found in Brachycome dichromosomatica (Asteraceae) Houben et al. 2000, Chromosoma 109 The terminal knob contains the Bds1 tandem repeat. 174-bp satellite repeat Large Heterochromatin Knobs (Segments) in Ballantinia antipoda Het knobs ? origin ? composition ? function (if any) Het knob hk4S in Arabidopsis The hk4S originated by an inversion event that relocated pericentromeric sequence to an interstitial position. Fransz et al. 2000, Cell 100 Het knobs were discovered by McClintock in maize McClintock B (1929) Chromosome morphology in Zea mays. Science 69 Barbara McClintock (1902-1992) America’s most distinguished cytogeneticist, was initially denied acceptance to Cornell University’s Dept. of Plant Breeding because she was a woman. Eventually allowed to study plant genetics, McClintock received her Ph.D. from Cornell in 1927, and later formulated one of the most important genetic theories of the 20th century. • knobless and knobb-bearing accessions • the number, size and position of knobs are variable and they are found in 23 locations on the ten maize chromosomes Het knobs in maize CENs abnormal chromosome 10 Ab10 Rhoades 1952 (discovered by Albert Longley; 1937, 1938) the 180-bp and TR-1 (350-bp) tandem repeats are the major components of knob heterochromatin (Peacock et al. 1981, Ananiev et al. 1998) + different retrotransposons Het knobs in maize Wang et al. 2006, Plant Cell 18 mFISHed pachytene chromosomes of the Kansas Yellow Saline (KYS) inbred line 180-bp repeat (green) TR-1 element (pink) CEN 10 Kanizay et al. (2013) Heredity TR-1 repeat knob 180 repeat Structural variants of maize chromosome 10 (Ab10) Meiotic drive (transmission distortion) described by Marcus Morton Rhoades Rhoades MM (1942) Preferential segregation in maize. Genetics 27: 395–407. Birchler et al. 2003, Genetics 164 Meiotic drive the 1:1 segregation (normal chromosome 10) preferential transmission of the Ab 10 chromosome The ability of one homolog to enhance its probability of transmission at the expense of its partner (e.g. in Aa heterozygote, A-bearing gametes are produced more frequently than a-bearing gametes). Meiotic drive in maize Birchler et al. 2003, Genetics 164 Preferential transmission of the knob-bearing chromosomes during female meiosis. But only if the Ab 10 chromosome is present. heterozygote for Ab 10 crossing-over located between the knob and centromere cross-over products that carry the knob on only one of its two chromatids (heteromorphic dyad) pseudokinetochore activity of the knob direct the knob-bearing chromatides to two of the four products of meiosis II Megasporogenesis and meiotic drive in maize Birchler et al. 2003, Genetics 164 Female meiosis (megasporogenesis) is asymmetric: -out of 4 haploid products only one will become the egg; other three degenerate - the outermost (basal) megaspore differentiates into the megagametophyte via a few mitoses to produce the egg, polar nuclei, and associated cells Knob-bearing chromatids are pulled towards the outermost megaspores during meiosis II ahead of the centromeres. Consequently, instead of a 50% expected ratio of transmission in a heterozygote, knob transmission in female meiosis varies from 59 to 82%. Meiotic drive in maize