Block 2 Review; Chromosomes Quick Summary; PDF

Block 2 Review SUMMARY SLIDES IN ADVANCE OF REVIEW SESSION  Chromosomes Quick LO1 Introduction Chromosomes consist of linear sequences of genes ◦genetic information which specifies the physical expression of a phenotypic tr...

Block 2 Review SUMMARY SLIDES IN ADVANCE OF REVIEW SESSION  Chromosomes Quick LO1 Introduction Chromosomes consist of linear sequences of genes ◦genetic information which specifies the physical expression of a phenotypic trait  Meiosis: Prophase I Multiple Distinct Stages for Chromosome Condensation Leptoten e Zygotene Pachyten e Diplotene Diakinesi s LO1, LO2  Alignment and Segregation Each homologous pair is independent. Random segregation can produce >8.3 million unique combinations of human chromosomes. Premature separation of chromosomes is a major mechanism of aneuploidy Multiply this by the amount of variation that comes from recombination (unknown large LO1, LO3, LO4 number). 4 LO1, LO3, LO4 Recombination Recombination between linked genes located on the same chromosome involves homologous crossing-over ◦ allelic exchange between them Recombination changes the allelic arrangement on homologous chromosomes = recombinant  Cis, Trans, Parental, and Recombinants In double heterozyote: Cis configuration = mutant alleles of both genes are on the same chromosome = ab/AB Trans configuration = mutant alleles are on different homologues of the same chromosome = Ab/aB LO1, LO3, LO4 LO1, LO3, Making Connections to Past and LO4, LO5 Future Homologous recombination repair utilizes many of the mechanisms we associate with traditional homologous recombination ◦ Regions of homology enabling strand crossover and exchange is very similar to homology search and strand invasion Recombination when done correctly as intended should not produce error Inappropriate alignment can result in duplications and deletions similar to our strand slippage during replication ◦ Repetitive regions do not always align perfectly ◦ If crossing over occurs after inappropriate alignment, one copy will have too much info (duplications) and one will have too little (deletion) ◦ Chromosome deletions are among the most common genetic abnormality observed clinically Cytogenetics and Chromosomes Terminology Autosome vs Sex chromosome and normal human karyotypes Chromosome condensation Key features of the chromosome ◦ Telomere, centromere, kinetochore, heterochromatin, euchromatin Chromosome analysis basics (role of FISH and microarray and comparative analysis) LO1 Human Normal Karyograms Karyotyp es:  LO1, LO4, LO5, LO6 Centromeres Centromeres may be located in different regions of a chromosome: Metacentric = located in middle of chromosome Submetacentric = located closer to one end of chromosome Acrocentric = located near one end of chromosome Telocentric = located at the telomere  LO1, LO3, Centromere and Histone LO4, LO5 Variants To form key structures in chromatin and chromosomes, a combination of DNA sequences and proteins are needed Centromeres have a combination of repetitive DNA and key histone variants CENP-A = histone H3 variant ◦ Found exclusively at functional centromeres ◦ Helps form the structures necessary for formation of the kinetochore Inappropriate or unexpected incorporation of centromeric histones to regions of DNA not intended to serve as a centromere forms a centromere = Neocentromere LO4, LO5, LO6 Kinetochore: Another Perspective The kinetochore is a highly conserved structure Part of the structure holds the microtubule while other components are regulatory Kinases and phosphatases play a critical role in regulating the process particularly in regards to microtubule attachment ◦ Aurora B kinase ◦ CDK1 Connecting LO4, LO5, the Kinetochore with Prevention of Erroneous Cell LO6 Division As hinted at in Block 1, inappropriate attachment is monitored by a different mechanism than separation Erroneous attachments are eliminated by an poorly understood mechanism that likely relates to tension on the kinetochore and the activity of Aurora B kinase and chromosome oscillation ◦ This is an interesting area of research with much that remains to be understood  LO1, LO4, Telomeres and LO6 Telomerase Sufficiently long telomeres are able to protect the ends of chromosomes vis capping Loss of capping = reduced chromosome integrity ◦ Critically short telomere is associated with cellular senescence and DNA repair triggers at G1 Telomerase activity maintains telomere length in stem cells but should NOT be active in normal somatic cells hTERT hTR  LO1, LO4 Chromosome Structures: Nucleolar Organizer Regions (NORs) Located on the satellite stalks of acrocentric chromosomes (p arm) Location of nucleoli formation in interphase Site of ribosomal RNA genes and production of rRNA  LO1, LO3 Trisomies and Monosomies Whole chromosome aneuploidies can be classified by the amount of increased or decreased information ◦ Trisomy = 3 copies of the corresponding chromosome ◦ Monosomy = 1 copy of the corresponding chromosome Trisomies for all autosomes have been reported in products of conception from spontaneous pregnancy losses ◦ The observed frequencies of trisomies varies greatly ◦ Trisomy for chromosome 1 has been reported in spontaneous pregnancy losses though no fetal pole had developed in the reported cases ◦ Trisomy 16 ~30% of all spontaneous losses ◦ In livebirths, trisomies other than 13, 18, and 21 are RARE and typically only mosaic Monosomies are extremely rare in both spontaneous losses and live births implying lethality before sufficient tissue is present for analysis ◦ Sole Exception for Adult viability = Turner syndrome; sex chromosome monosomy  LO2 Mechanism of Meiosis I Nondisjunction BOTH TO ONE POLE PREMATURE SEPARATION Meiosis **Studies show that I this method is actually more common  Mechanisms of LO1, LO2, LO3, LO6 Mitotic Nondisjunction In mitosis, sister chromatid split to give each daughter cell as close to the same genetic content as possible and ensuring each cell has a copy of material from each source (paternal and maternal) Mitotic Nondisjunction is about failure to split or failure to capture properly and can have multiple outcomes l na al rn er S Phase l te na at al Pa rn M er te at Pa M l Expected na al rn er Outcomes te at Pa M  Timing and Consequences LO3, LO6 Continued  LO4, LO6 MOSAICISM There are multiple types of mosaicism Can exhibit segmental mosaicism ◦ CPM: confined placental ◦ Fetal mosaicism (with and without normal placenta) NOTE: mosaicism does NOT have to be orderly or even organized  LO7 Uniparental Disomy Reminder: Each autosome is intended to be inherited with 1 copy from the maternal parent and one copy from the paternal parent Uniparental disomy is when both copies are derived from a single parent (2 copies of the chromosome or region of chromosome from maternal source or paternal source exclusively) Most appear without any phenotypic consequence but can have significant implications in differentially methylated regions Can also result in homozygosity for autosomal recessive genes Distinctions ◦ Both chromosomes are identical = isodisomy ◦ Both chromosomes are different = heterodisomy  LO8 UPD Mechanisms: Whole Chromosomes 3 Monosomic rescue Step 1: Monosom 1 Fertilization ic Gametic Complementation Conceptu s Step 2: Postzygotic Mitosis Replicatio n 2 Trisomic Rescue ◦ Mechanism behind most UPD Trisomic Step 1: Conceptu 4 Mitotic Error and Rescue Fertilization s Disomic Conceptus Error Trisomic Embryo Step 2: Postzygotic Mitosis Subsequent Mitosis Summary of Aneuploidies: Errors in Chromosome Segregation Learning Objectives 9 and 10: Compare and contrast trisomy 21, 18, 13, 16, Turner and Klinefelter syndromes in terms of causes, phenotypic consequences, and viability Explain why there is variable viability across autosomal and sex chromosome aneuplodies Aneuploidy Karyotype and Unique Clinical Features Additional Considerations Chromosome Details Trisomy 21 47,XY,+21 or 47,XX, Variable/spectrum Most common trisomy in viable +21 most common; Multiple systems impacted offspring partial also clinically Atrioventricular septal defect (AVSD) Additional meiotic relevant (q-arm Most common single known cause of intellectual considerations (possible critical region = disability segregation with y chrom) 21q22.1-21q22.2) Edwards 47,XY,+18 or 47,XX, Viability is variable with significant losses in utero or Mosaicism is considered rare but Syndrome/ +18 within first few days of life mosaics tend to be the more Trisomy 18 95% do not survive past 1 year of life viable/favorable outcomes 90% exhibit congenital heart defects Patau 47,XY,+13 or 47,XX, Variable consequences Acknowledged recurrence risk Syndrome/ +13 80% will not survive past 1 month of life for future pregnancies Trisomy 13 Chromosome 47,XY,+16 or 47,XX, Cardiac malformations and pulmonary hypoplasia Full trisomy is most frequent 16 anomalies +16 common embryonic lethal (identified in Mixed evidence with in utero health a stronger 30% of tested early pregnancy indicator of potential losses) Only viable forms are mosaic, partial, UPD, or partial deletions Turner 45,X; missing all or Considered the most viable human monosomy There are multiple mechanisms Syndrome part of 2nd X Can go undetected with minimal impact on some to lead to loss of X chromosome chromosome individuals (fertility issues may be present) material that will present as Turner LO1, Chromosome Architecture LO2 Contributes to Rearrangement Many recurring and some sporadic rearrangements occur secondary to nonallelic recombination due to regions of homology CALLBACK to DNA repeats… ◦The majority of regions of homology involve low copy repeats ◦High copy repeats can also be involved in rearrangements ◦ Alu-mediated recombination (role for SINEs) ◦ alpha satellite recombination and centromeric fusions (i.e. short arms of acrocentric chromosomes)  LO1, Types of Recombination LO2 Observed REMINDER: Chromosomes exist in 3-D space! They can take on complicated structures and orientations Expected/Normal Recombination: Occurs at the same loci/alleles ◦Homologous chromosomes ◦ Interchromosomal = across homologs ◦Sister chromatids ◦ Intrachromosomal = within or between sister chromatids  LO4 Balanced vs. Unbalanced Balanced = no net loss or gain of genetic information ◦ Generally phenotypically normal with positional effects leading to any observable phenotype Unbalanced = additional and/or missing material ◦ Clinically affected (degree dependent on amount gained or lost) The more apparent the change (i.e. larger, swapping hetero and euchromatin, etc…), the more likely it is to be detected Molecular cytogenetic techniques are essential to this diagnostic process LO3 General Categories of Structural Rearrangements  LO7 Deletions A.K.A. partial aneuploidies, segmental aneusomies, or contiguous gene disorders ◦ Losses or gains of material have the potential to affect adjacent material Cytogenetic Rearrangement ◦ Small size can follow Mendellian inheritance ◦ Most are de novo ◦ Considerations for expressivity and penetrance ◦ Gonadal mosaicism in parent is possible as is dynamic mosaicism from postzygotic mitoses  LO6, LO7 Duplications Presence of an extra copy of a genomic segment = partial trisomy ◦ Pure duplication = no other imbalances ◦ Combination with other rearrangements being present is also possible Tandem duplication ◦ Contiguous doubling of a segment ◦ Direct = same orientation as original ◦ most common form of detectable tandem duplications in humans ◦ Inverted = opposite orientation as original Phenotypes of duplications = less severe than deletions Many of the figures are derived from: Genetics: A Conceptual Approach W.H. Freeman et al  LO10 Disease Examples: Prader-Willi vs. Angelman Normal Maternal Imprinting Prader-Willi Syndrome ◦ Shuts off SNRPN and NDN Loss of 15q11-13 from paternal ◦ UBE3A is active source Gene = UBE3A expressed; loss of Normal Paternal Imprinting SNRPN and NDN ◦ Shuts off UBE3A Hypotonia, obesity, hypogonadism ◦ SNRPN and NDN are active ANGELMEN SYNDROME Loss of the maternal copy of the chromosome means full Loss of 15q11-13 from maternal loss of UBE3A source Loss of the paternal copy of the Genes = SNRPN and NDN expressed; chromosome means full loss of loss of UBE3A both SNRPN and NDN https://www.nature.com/articles/gim0b013e31822bead0 Developmental and intellectual https://www.nature.com/articles/nn0307-275 deficiencies, epilepsy and tremors LO10 Prader-Willi vs. Angelman OFF OFF ON ON ON OFF OFF OFF ON ON ON OFF OFF OFF ON ON ON OFF OFF OFF ON ON ON OFF  LO11, LO12 Inversions Intrachromosomal rearrangements where two breakpoints exist and the material between the breakpoints reverses orientations * Pericentric ◦ Breakpoints on either side of centromere * ◦ Involves centromere and changes chromosome arm ratio Paracentric ◦ Breakpoints on same side of centromere * ◦ Only one arm of chromosome affected and centromere * position is unaffected Presence is indicated by alteration of typical banding pattern  LO12, Crossingover in Inversion LO15 Loops Huang and Rieseberg. 2020. Front Plant Sci. Chromosomal Inversions in Plants https://www.frontiersin.org/articles/10.3389/fpls.2020.00296/full  LO16, LO17 Reciprocal Translocations Two nonhomologous chromosomes exchange segments One of the most common structural rearrangements When balanced carriers = phenotypically normal with increased risk of offspring with unbalanced karyotypes Reciprocal translocation may affect one or both of the chromosome copies/pairs ◦ Heterozygous translocation = Only one pair of non-homologous chromosomes is affected ◦ Homozygous translocation = Both pairs are affected  LO16, LO17 Robertsonian Translocations Among the most common, balanced structural rearrangements Long arms of any two acrocentric chromosomes join to produce a single metacentric or submetacentric chromosome All 5 acrocentric chromosomes (13, 14,15, 21, 22) are capable of fusion events The close association of NORs within the nucleus may promote the formation of these translocations  LO18, LO19 Complications for Meiosis In meiosis, has the potential to form the QUADRIVALENT ◦ 4 chromosomes aligning and exchanging information ◦ The bigger the change (i.e. the more genetic material exchanged) the greater the probability of forming the quadrivalent Translocations result in the potential for complicated alignments and crossing over-events ◦ Further recombination can occur further reducing the likelihood of viability ◦ Autosome-Sex Chromosome translocations are particularly problematic ◦ Are not intended to align or exchange material ◦ Concerns with X inactivation potentially resulting in inactivation of autosomal segments and genes ◦ X-inactivation has been found to exhibit a preferential process designed to inactivate the least problematic X in these conditions ◦ However, if both X chromosomes have translocated material some autosomal material will be inactivated and some critical X material will not be LO18, LO19 The Quadrivalent and Meiosis LO18, LO19 Translocation Quadrivalent in Meiosis Normal 2:2 refers to each Balanc daughter cell ALTERNATE ed receiving 2 of the 4 chromosomes involved in the quadrivalent  Translocation Quadrivalent in Meiosis Unbalanced Adjacent is defined by centromeres next to each other around the Adjacent-1 quadrivalent Adjacent -1 has homologous Unbalanced centromeres separate  LO18, LO19 Translocation Quadrivalent in Meiosis Unbalanced Adjacent is defined by centromeres next to each other Adjacent-2 around the quadrivalent Adjacent-2 has Unbalanced homologous centromeres together LO1, LO2 Euchromatin Loosely coiled during interphase ◦Beads-on-a-string conformation Condensed during mitosis Often undergoing active transcription G-banding: Light Bands LO1, LO2 Heterochromatin Late Replicating; highly inaccessible by the replication machinery Remains condensed from prophase through the mitotic cycle Can be constitutive or facultative NOT transcriptionally active G-banding: dark bands  Methylation Process LO3 43 LO1, Heterochromatin vs LO2, LO3 Euchromatin LO5, Summarizing Methylation and LO6, LO7 X-inactivation LO1, LO6 Epigenetics and Imprinting Core phenotypic changes due to changes in gene expression WITHOUT changes in the core DNA sequence Differentially methylated domains of imprinted genes contain CpG-rich, imperfect tandem repeats resulting in a RELATED DNA STRUCTURE implicated in imprinting ◦ Specifically, the establishment and maintenance of parent of origin-specific methylation patterns PATERNALLY imprinted ◦ Paternal gene is OFF ◦ Maternal gene is ON MATERNALLY imprinted ◦ Maternal gene is OFF ◦ Paternal gene is ON LO1, LO6 Imprinting in Gametogenesis Original imprinting in the gamete is erased prior to spermatogenesis and oogenesis Selective silencing Different genes are silenced during oogenesis than spermatogenesis leading to specific maternal vs paternal imprinting patterns De-methylation and Re-methylation cycles to add and erase imprinting  Process of LO1, LO7 X- Inactivation Determine Number of Xs Choose extra X to inactivate Initiate Inactivation Expand/Spread the Inactivation Signal along appropriate regions of chromosome Maintain the inactivation LO1, LO2, LO3 G G gg Law of Segregation In the production of gametes ◦ Two copies of the same gene separate ◦ Each gamete only receives 1 copy ◦ HOMOLOGOUS CHROMOSOMES separate during meiosis G G gg LO1, LO2, LO3 Law of Independent Assortment Forms of different genes assort independently of one another during gamete formation ◦Forms of genes = alleles Dihybrid cross = cross evaluating 2 traits Limitations ◦ONLY applies to genes on SEPARATE chromosomes ◦Genes in close proximity on the same chromosome do NOT sort independently (linked genes) LO1, LO2, LO3 Hypotheses and Observation Phenotype is what we can physically observe T T Punnett Squares ◦ Allow for a quick and easy determination of the outcomes of crosses ◦ Defines what the likelihood of obtaining a particular outcome is Punnett squares are HYPOTHESES for the genotypes and expected corresponding phenotypes of a given cross ◦ WITHOUT EXPERIMENTATION (i.e. gene sequencing) THERE IS NO WAY TO DETERMINE DEFINITIVELY A t Tt Tt GENOTYPE If you think of Punnett squares as a hypothesis of what you think will happen, then you can reduce even the most complicated gene combinations to a basic math problem t Tt Tt T = tall t = short plant Confirming Inheritance: Backcross or Testcross Heterozygote vs homozygote TY Ty tY ty recessive In a dihybrid cross, heterozygotes TtY Tty ttY tty for two traits are crossed to ty homozygotes that are recessive for y y y y both traits TtY Tty ttY tty ◦ TtYy X ttyy ty This type of cross is particularly y y y y useful for demonstrating the law of TtY Tty ttY tty independent assortment ty y y y y Enables visualization of all potential phenotypes for the traits being TtY Tty ttY tty evaluated ty y y y y T = tall t = short Y = yellow y = green LO1, LO2, LO3 Autosomal Inheritance of Linked Genes This is the first Nonmendelian Inheritance pattern observed Linked genes are genes located on the same chromosome Linked genes will be inherited together more frequently than unlinked genes thus they will most likely NOT follow independent assortment Recombination enables these genes to be observed differently than in the parental generations (recombinant offspring) Genes can be linked in cis (dominant forms together) or in trans (dominant form is with recessive form of other gene) LO1 Terminology Sex Chromosomes = chromosomes that contain the genetic information necessary to confer biological sex and influence development of secondary sexual characteristics Homogametic = has gametes with the same sex chromosomes Heterogametic = has gametes with different sex chromosomes Hemizygous = containing only 1 copy of a chromosome that can be or is typically observed in a pair Haploinsufficiency = loss of 1 copy results in a situation where the remaining copy cannot compensate and make sufficient product; reduced function is expected due to the insufficient levels of product ◦ genes exclusive to the Y or X in humans are NOT haploinsufficient as proper gene dosage is 1 LO2 Sex Chromosomes and Sex Determination In sexual reproduction, differences between the 2 sexes are established by key genes often located on specific sex chromosomes Sex chromosomes can vary across different organisms Sex chromosomes do NOT have to involve 2 distinct chromosome types in the pair ◦ Humans: XX females vs XY males ◦ Grasshoppers: XX females vs XO males (males have fewer chromosomes than females) When the chromosome pairing involves one biological sex having fewer chromosomes, meiosis will result in gametes that have unequal chromosome numbers LO1, LO2, LO3, LO4 More on Sex Chromosomes and Sex Determination Heterogametic Sex = sex with 2 different chromosomes ZZ vs ZW ◦In many species, the heterogametic sex is the female ◦This system is found in birds, snakes, butterflies, some amphibians and some fish LO1, LO3, LO4 XY Heredity (Humans) In humans, males are heterogametic X and Y can pair during Meiosis because of structural similarity in the chromosomes (regions of homology) ◦ Pseudoautosomal regions Crossing-over occurs in these regions Because these are regions of similarity that do contain genes, these regions escape X- inactivation ensuring proper gene dosage for those genes LO6, LO7 More on Pseudoautosomal Regions Distal region of short arms of X and Y = highly similar DNA sequences (PAR1) ◦ Areas for crossing over in male meiosis that resembles autosomal crossing-over Region of homology at distal end of long arms that also experience alignment and crossing-over (PAR2) All genes within PAR1 are NOT inactivated in women ◦ Need 2 copies (dosage compensation) There is a high recombination frequency in PAR1 LO1, LO2, LO5 Sex Determination without Sex Chromosomes (Genic or Environmental) Environmental Sex Determination ◦ For turtles, warmer temperatures result in more females, colder temperatures yield more males ◦ For alligators, colder temperatures result in more females, warmer temperatures yield more males ◦ For bearded dragon lizards, environment influences the phenotype rather than the genotype. ◦ ZZ is male except when the embryo is incubated at high temperatures, then ZZ is phenotypically female even though genotypical male. https://www.sciencedirect.com/science/article/pii/B9780123749307100019 LO1, LO2, LO5 Sex Determination without Sex Chromosomes (Genic or Environmental) Environmental Sex Determination ◦Crocodiles ◦Sex determination is more complex ◦32-33°C nest temperature = male crocs ◦Any other temperature = females https://www.sciencedirect.com/science/article/pii/B9780123749307100019 LO6 Determining Inheritance Two individuals of a species have offspring. The maternal individual is heteroplastic while the paternal individual is homoplastic. Answer the following questions: ◦ If maternal mitochondrial inheritance is expected: ◦ What is the potential for the offspring? ◦ What is the potential for the next generation if the offspring are all female? All male? ◦ If paternal mitochondrial inheritance is expected: ◦ What is the potential for the offspring? ◦ What is the potential for the next generation if the offspring are all female? All male?