BMS 532.11 Chromosomal Structural Abnormalities and Rearrangements PDF

Questions: Errors in Segregation Meiotic nondisjunction during the first half of meiosis differs from meiotic nondisjunction during the second half of meiosis in what way? (LO2 and LO3) Maternal isodisomic UPD as a consequence of fertilization is most likely associated with what cause of UPD? (LO8)...

Questions: Errors in Segregation Meiotic nondisjunction during the first half of meiosis differs from meiotic nondisjunction during the second half of meiosis in what way? (LO2 and LO3) Maternal isodisomic UPD as a consequence of fertilization is most likely associated with what cause of UPD? (LO8) Mitotic segregation errors are more closely associated with errors in what? (LO2 and LO3) Chromosomal Structural Abnormalities and Rearrangements BMS 532 MOLECUL AR BIOLOGY AND GENETICS BLOCK 2 LECTURE 4 emphasis of this lecture is on chromosomal rearrangements, their generation, their consequences on chromosome behavior during meiosis, and their implications on viability and heredity. T H I S PA C K E T H A S B E E N B R O K E N D O W N I N T O SUBSECTIONS. T H E O B J E C T I V E S H AV E A L S O B E E N D I V I D E D A N D W I L L B E PRESENTED WITH EACH SUBSECTION. Overall Objectives This packet may take more than 1 session to cover and will emphasize the overall development of the following objectives: Summarize the types of abnormalities and rearrangements observed for chromosomes Compare and contrast chromosomal rearrangements, their causes, their activity in meiosis, and their phenotypic consequences ◦ Diagram and explain the following structural rearrangement types: deletions, duplications, inversions, and translocations ◦ Explain the consequences for gene expression for each of the following types of structural rearrangements: deletions, duplications, inversions, and translocations Understand, summarize, and assess how rearrangements are created, behave during meiosis, and affect viability Outline I. Introduction II. Deletions and Duplications III. Inversions IV. Translocations Introduction REARRANGEMENTS AND CHROMOSOMAL ARCHITECTURE  Objectives 1. Define the following terms: acentric, dicentric, neocentromere, pseudodicentric, chromosome breakage, straddling limbo, regions of homology, interchromosomal, intrachromosomal, nonallelic recombination, haploinsufficiency, and pseudodominance 2. Explain how rearrangements are possible, what features contribute to rearrangements, and how the size of a rearrangement/amount of genetic content correlates with the viability and phenotype 3. List the types of rearrangement that can occur and explain how they both occur and contribute to final chromosome architecture 4. Compare and contrast balanced and unbalanced rearrangements in terms of phenotypic consequences 5. Compare and contrast de novo and familial rearrangements in terms of inheritance and phenotypic consequences LO1 Altered Centromeres Dicentric ◦ Presence of two centromeres ◦ Major issue in chromosome segregation ◦ If opposite poles attach: Chromosome Breakage or Straddling Limbo leading to exclusion from both cells ◦ Closely placed centromeres can act as a single centromere and negate the effects ◦ There can also be one active and one inactive centromere = pseudodicentric Acentric ◦ Chromosomes without centromeres are rapidly lost and therefore not really observed in constitutional karyotypes Neocentromeres ◦ Centromeres that are generated via changes to nucleosome association ◦ Sometimes function as actual centromeres and can generate kinetochores LO1, LO2 Introduction to Rearrangements There are theoretically an almost infinite number of ways 23 pairs of chromosomes can rearrange In actuality, there are areas more prone to breakage and rearrangement due to underlying chromosome architecture Some rearrangements are benign/considered not clinically significant ◦ Some are considered expected population variation Structural rearrangements can occur when exchanges between nonallelic chromosome regions take place (A.K.A. different loci on homologous or nonhomologous chromosomes are exchanged) ◦ Approximately 75% are paternally derived though they can also inhibit sperm function 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, Chromosome Architecture LO2 Contributes to Rearrangement Size and type of rearrangement correlate with: ◦ Location ◦ Size ◦ Orientation ◦ Number of crossing over events between the low copy repeats Other Chromosome Architecture that contributes to rearrangement includes: ◦ Sequences capable of forming a particular secondary DNA structure (hairpin or cruciform-shaped secondary structures) ◦ Areas susceptible to double-strand breaks ◦ i.e. A-T rich palindromic sequences, Topo II cleavage sites, DNase I sensitive sites, Scaffold rearrangement regions, Expanded Tri-nucleotide repeat regions LO1, LO2 Types of Recombination 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 LO3 Types of Recombination Observed Unexpected/Abnormal Recombination: Nonallelic recombination events Exchanges occur between different loci ◦ Homologous Chromosomes ◦ Altered alignment so that loci/alleles are not exchanged evenly ◦ Sister Chromatids ◦ Within one single chromatid or across chromatids unevenly ◦ Nonhomologous chromosomes ◦ Inappropriate recombination LO3 Types of Rearrangement Events 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 LO5 De Novo vs. Familial Balanced Familial structural rearrangements can go generations without detection ◦ Typically associated with high incidence of infertility and multiple spontaneous pregnancy losses ◦ May also have some family members with abnormal phenotypes Familial rearrangements are often unique/family- specific (very rare exceptions) Risk for abnormal phenotype is higher for an individual with even apparently balanced de novo rearrangements than for an individual who has inherited a similar rearrangement from a parent LO1, Consequences of LO3 Some Rearrangements Loss ◦ in gene activity or transcription ◦ in function or protein-level activity Gains ◦ in gene activity or transcription ◦ in function or protein-level activity Pseudodominance ◦ Appearance of the recessive trait/phenotype in a pedigree due to loss of the dominant allele ◦ Showing the recessive version because the dominant is missing requires the recessive allele to be present Haploinsufficiency ◦ Loss of one copy with the remaining copy not enough to maintain full function LO3 General Categories of Structural Rearrangements 1) Deletions and Duplications MOST COMMON CL ASS OF CLINICAL CHROMOSOMAL REARRANGEMENTS Objectives 6. Define the following terms: terminal deletion, interstitial deletion, and tandem repeats 7. MODIFIED AIM 2 (Specific to Deletions/Duplications): Explain the unique features of dels and dups, how dels/dups can be generated AND how size of the del or dup correlates with the presence of a phenotype and/or the severity of the phenotype 8. Explain how deletions and duplications can be paired rearrangements and how they can both be found in the same individual 9. Explain the meiotic consequences of deletions and duplications 10. Identify the genes involved in the following deletion syndromes and link to syndrome to expected phenotypic outcomes: Williams Syndrome, Prader-Willi, and Angelman 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 Classic Deletions Terminal ◦ No discernable material beyond the site of breakage ◦ Likely still retain telomere (can be via acquisition from other chromosomes = telomere capture) or acquired new telomere all together (via telomerase) even though appears to be at end of chromosome Interstitial ◦ Proximal breakpoint and a more distal breakpoint after the missing material followed by continuation of the normal chromosome banding pattern  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 LO7, LO8 Paired Deletions and Duplications Postzygotic mitoses can generate del/dup paired mosaics If the rearrangement occurs in the initial division, all cells will be dels or dups that are complementary If the rearrangement occurs later in the divisions, there is potential for normal cell lines to be present Cell lines of lesser viability may be lost (potential for dynamic mosaicism and growth restriction) Duplications have the potential to have the opposite phenotype of their deletion counterparts LO9 Meiotic Consequences Subsequent meiosis in individuals with deletions and duplications Loops form to maximize alignment LO10 Syndromes associated with Deletions Microdeletion = Williams Syndrome Prader Willi and Angelman Syndromes LO10 Williams Syndrome ~1.5 Mb deletion within the proximal Strengths = spoken language, long arm of chromosome 7 ◦ Impacts ~30 known and predicted music, and rote memorization genes) ◦ ELN = elastin gene; implicated in Difficulties with visual-spatial cardiovascular anomalies and others ◦ LIMK1 = LIM-kinase 1; novel kinase in acuity (i.e. puzzles) brain; implicated in cognitive features ◦ Low-copy repeat sequences likely A.K.A. the condition that contribute to chromosome “makes you love everyone” breakage = unequal crossing- over/recombination = deletion ◦ Extreme interest in others (recurring Williams syndrome deletions) ◦ Heterozygosity for an inversion that Distinct facial features: broad spans the LCR region also contributes forehead, short nose, full ◦ Estimated higher risk (5X) for individuals who are heterozygous for this inversion to have cheeks, and wide mouth offspring with Williams syndrome (compared to those who are not heterozygous) Cardiovascular defects are also Absolute risk for Williams is still low observed (narrowing of aorta) = 1 in 7,500 to 10,000 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 Check-in Questions Deletion of just UBE3A from the paternal chromosome would generate which of the following? A. Prader-Willi Syndrome B. Angelman Syndrome C. 11q11 deletion syndrome D. Williams Syndrome E. No syndrome/phenotype is expected Uniparental disomy of chromosome 15 is expected to cause Prader-Willi when which parental chromosome is retained? A. Maternal B. Paternal C. Neither 2) Inversions Objectives 11. Define the following: pericentric inversions, paracentric inversions, asynapsis, homosynapsis, and heterosynapsis 12. Compare and contrast pericentric and paracentric inversions 13. Diagram and explain the meiotic pairing and consequences for pericentric inversions 14. Diagram and explain the meiotic pairing and consequences for paracentric inversions 15. Summarize the processes through which dicentric and acentric chromosomes are generated 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 LO11, LO12 Inversions Typically, no genes are gained or lost, just rearranged For the most part, balanced inversions are phenotypically normal Phenotype still possible ◦ Positional effects in viable offspring appear to be limited (i.e. X chromosome) but are possible (change in promoter, change in regulatory elements, transitioned into heterochromatin, etc…) ◦ Breakpoints within a gene = pathogenic ◦ Breakpoints within regulatory elements for key genes could also result in altered phenotypic outcomes (functional haploinsufficiency) There is evidence of preferential breakpoints in these rearrangements Can be “normal variants” rather than abnormal chromosomes ◦ Inversions in chromosomes 1, 9 , 16, and Y with breakpoints in heterochromatin LO12, LO13 Pericentric Inversions and Risk: Understanding Meiosis There may be affects of location of breakpoints on the type of synapsis Complications for acrocentric chromosomes ◦ Relocation of NOR to long arm Recombination results in formation of recombinant chromosomes ◦ Relationship between size of inversion and likelihood of recombination (evidence from evaluation of spermatogenesis) with some specific exceptions observed ◦ Larger inversions = more likely to recombine/inappropriately synapse LO11, LO12, Pericentric LO13 Inversions and Meiosis Altered configuration for the bivalent ◦ Reversed Loop Model with homosynapsis ◦ Complementary recombinant chromosomes ◦ Partial trisomy for one distal AND partial monosomy for the other OR vice versa ◦ Typically only one (least monosomic) is viable ◦ Shorter segments may only exhibit partial pairing (no loop) ◦ Balloon out (asynapsis of inversion) or lie adjacent but unmatched (heterosynapsis) ◦ No crossing-over within inverted segment under these conditions ◦ Only the inversion undergoes synapsis ◦ Recombination within the segment is possible LO12, Pericen LO13 tric Inversio ns LO12, LO14 Paracentric Inversions and Risk: Understanding Meiosis Practically all paracentric inversions are identified incidentally and not due to the birth of an abnormal child Alignment in meiosis can involve a reverse loop ◦ This version will have the centromeres outside the loop LO12, LO14 Paracentric Inversions and Risk: Understanding Meiosis Crossing-over within in the loop ◦ In theory, an ODD number of crossing over events = one dicentric (unstable) and one acentric chromosome ◦ Almost always lethal due to the errors in meiosis that result ◦ Monocentric recombinants have been observed in the offspring of paracentric inversion carriers ◦ Additional meiosis mechanisms are involved in this LO12, LO14, LO15 Paracentric Inversion in Meiosis Dicentric Acentric Chromosome fragment LO12, LO14, LO15 Paracentric Inversions  LO12, LO15 Crossingover in Inversion Loops Huang and Rieseberg. 2020. Front Plant Sci. Chromosomal Inversions in Plants https://www.frontiersin.org/articles/10.3389/fpls.2020.00296/full Check-in Questions Crossing-over outside the inversion loop for which of the following could involve the centromere? A. Pericentric inversions B. Paracentric inversions C. Translocations D. Insertions Crossing-over inside the inversion loop for which of the following could involve the centromere? A. Pericentric inversions B. Paracentric inversions C. Translocations D. Insertions Basic info needed to answer these questions: Which type of inversion is expected to have the centromeres within the inversion loop? 3) Translocations ALTHOUGH UNEVEN AND COMPLEX TRANSLOCATIONS CAN OCCUR, THIS SECTION WILL FOCUS ON RECIPROCAL AND ROBERTSONIAN ONLY Objectives 16. Define the following terms: reciprocal translocations, balanced carrier, heterozygous translocation, homozygous translocation, derivative chromosome, whole arm translocation, Robertsonian translocation, and quadrivalent 17. Compare and contrast reciprocal and Robertsonian translocations and explain the differences in phenotypes expected/phenotypic considerations when they are completely autosomal versus when sex chromosomes are involved 18. Compare and contrast alternate, adjacent-1, and adjacent-2 segregation patterns 19. Determine the consequences for each segregation pattern on offspring and identify which are capable of producing viable offspring from a given chromosomal rearrangement 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, Sex Chromosome LO17 Translocations Sex chromosomes can exhibit translocations with autosomes, the other sex chromosome, or even with a homolog One MUST consider silencing/imprinting when considering translocations involving the X ◦ Can mitigate or exacerbate the phenotypic outcomes Frequent outcomes for translocations involving X and Y are INFERTILITY and embryonic lethality All de novo X-autosome translocations studied thus far have been paternal in origin LO16, LO17 Reciprocal Translocations Translocation heterozygotes are at risk of having children with chromosomal imbalances/aneuploidy ◦ Carriers may have a high miscarriage rate Derivative Chromosome = Rearranged chromosome and is identified based on the centromere Can be de novo or observed in a family going back generations Whole-arm translocation = breakpoints within or near/at centromere 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 LO16, LO17 Robertsonian Translocations Nonhomologous Robertsonian Translocations ◦ Form between two nonhomologous chromosomes ◦ ~95% of Robertsonian Translocations are nonhomologous ◦ Most common = (13;14) 75% and (14;21) 10% ◦ Occur during oogenesis predominantly ◦ Most are actually dicentric ◦ Nonrandom suppression of one centromere OR both potentially function together as one centromere ◦ Location of breakpoint determines the type of translocation formed Under very rare conditions, a whole arm exchange may occur between homologous chromosomes = Homologous Robertsonian Translocations ◦ These may actually be misclassified “other” rearrangements (i.e. isochromosomes) LO16, LO17 Robertsonian Translocations Mechanisms ◦ Unions following breaks in both short arms ◦ Most common ◦ Causes a dicentric chromosome to form ◦ Centric fusion (fusion at centromere) ◦ Rare ◦ Union following breakage in 1 short arm and 1 long arm ◦ Rare Inheritance risk correlates with losses or gains in genetic material as well as imprinting risks 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 Meiotic Outcomes Multiple options each with different outcomes 2:2 segregation ◦ Alternate ◦ Adjacent ◦ Most frequent for children of translocation heterozygotes ◦ Adjacent 1 = Nonhomologous centromeres to same daughter/homologous separate ◦ Adjacent 2 = Homologous centromeres to the same daughter (rather uncommon) 3:1 segregation ◦ Demonstrates devastations of monosomies as interchange monosomies are only ever seen at preimplantation genetic diagnosis 4:0 segregation ◦ May only be of little consideration in preimplantation genetic diagnosis Some of the data may imply a mechanism that ensures like centromeres segregate 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 LO18, LO19 Reciprocal Translocation Alternate Segregation: half the gametes receive both parts of the reciprocal translocation and the other half receive both normal chromosomes; all gametes are euploid ◦ normal genetic content, but half are translocation carriers  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 Reciprocal Translocation Adjacent-1 segregation: homologous centromeres separate at anaphase I; gametes contain duplications and deletions  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  LO18, LO19 Reciprocal Translocation Adjacent-2 segregation: homologous centromeres stay together at anaphase I; gametes have a segment duplication and deletion Translocation Quadrivalent in Meiosis Tertiary trisomy: 2 normal and 1 translocatio Tertiary monosomy 3:1 combinations can Interchange trisomy: have varying More RARE outcomes but frequently involve trisomies and monosomies Interchange monosomy It is also known as 3:1 LO18, nondisjunction LO19  LO18, LO19 Translocation Quadrivalent in Meiosis There are actually 4, 3:1 options Interchange trisomy option Interchange monosomy option 2 Tertiary trisomy option 2 Tertiary monosomy option 2 LO18, Translocation LO19 Quadrivalent in Meiosis: 4, 0 segregation 4:0 = all chromosomes to one cell LO18, LO19 Gametogenesis and Meiotic Outcomes Spermatogenesis ◦ Alternate (44%) and adjacent 1 (31%) are predominant forms ◦ Adjacent 2 (13%), 3:1 (11%), and 4:0 (rarely) Oogenesis ◦ Data is more problematic and variable ◦ Likely exhibits age-related effects complicating the analysis of meiotic outcomes Acrocentric chromosomes exhibit different patterns due to marked asymmetry of the quadrivalent ◦ Fewer alternate segregants and more 3:1 have been observed LO18, LO19 Viability Correlates with genes involved and severity of information lost/gained Severe forms undergo spontaneous pregnancy loss perhaps even prior to implantation (common?) Usually the sole survivable imbalance is a partial trisomy Viable offspring outcomes ◦ 71% derived from adjacent-1 ◦ 4% derived from adjacent-2 ◦ 22% tertiary trisomy/monosomy ◦ 2.5% interchange trisomy Check-in Questions Centromeric fusion of acrocentric chromosomes can referred to as a(n) __________. A. Robertsonian translocation B. Centromeric recombinant C. Reciprocal translocation D. Isochromosome formation This segregation pattern following formation of the quadrivalent has two homologous centromeres end up together in the same daughter cell without an increase in number of chromosomes. A. What is alternative segregation? B. What is adjacent-1 segregation? C. What is adjacent-2 segregation? D. What is 3-1 segregation? E. What is 4-0 segregation?