S09GenExam1KEY - GENETICS EXAM ONE SPRING 2009 NAME: The...

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Unformatted text preview: GENETICS EXAM ONE SPRING 2009 NAME: The pedigree shows a disorder caused by mutation in a biallelically expressed gene (not imprinted). You don't know anything about the status of people marrying into the family. Given no information on the frequency of this mutation in the population. Which of the following are possible mode of inheritance? F1. Autosomal Recessive T2. Autosomal Dominant F3. X-linked Recessive T4. X-linked Dominant For which of the following types of inheritance would the risk of Individual II-3 and II-4 having another child with the disease be greatest? (if you already determined that some type of inheritance was impossible, don't select that) F5. Autosomal Recessive T6. Autosomal Dominant F7. X-linked Recessive T8. X-linked Dominant A9. Individual III-3 and III-4 are sisters who both have the disorder. III-3 has yet to marry and have children. III-4 is married and has two unaffected children. If III-3 were to marry a genotypically normal man (as III-4 did), and III-3 and III-4 were to both get pregnant, who has a greater risk of having an affected child? (based only on pedigree information) a. III-3 b. III-4 c. neither, they have the same risk You then run a DNA analysis to determine the precise inheritance pattern. D10. Based on this data the inheritance is: a. Autosomal Recessive b. Autosomal Dominant c. X-linked Recessive d. X-linked Dominant GENETICS EXAM ONE SPRING 2009 NAME: Further studies were done to look at the mature mRNA and protein from this family. The type(s) of mutation suggested by these tests are (select all that apply): F11. splicing mutation - introns left in, no stop codon in the intron T12. splicing mutation - introns left in, stop codon in the intron F13. insertion into the promoter region F14. deletion of the 5'UTR F15. a mutation in the termination sequence for transcription F16. nonsense mutation F17. elimination of the stop codon F18. large deletion in the transcription unit T19. large insertion in the transcription unit You do some further study and discover the DNA sequence of the transcribed portion of this gene, which is as follows: An RNA is in the middle of being produced from this piece of DNA. The bases so far are 5ʼ UUACUUC B20. Based on this information, transcription proceeds a. from left to right b . from right to left A21. The template strand is a. the top strand b. the bottom strand B22. This DNA sequence represents just the DNA base pairs that will be transcribed into the primary pre-mRNA, the promoter sequence is not depicted. In which direction is the promoter sequence located? a. off the page to the left b. off the page to the right GENETICS EXAM ONE SPRING 2009 NAME: If the protein produced from this DNA is Met-Leu-Ser-Arg-Ser-Val-Met-Val-Ala-Leu-Asp C23. How many nucleotides long is the final mature mRNA? (genetic code chart at end of exam!) a. 65 b. 60 c. 57 d. 44 e. 36 Valproic Acid (Depakote), an anti-seizure medication also used for migraine control and treatment of bipolar disorder has recently been discovered increase the degradation of a specific histone deacetylase. Based on this what would you expect to find in cells treated with this compared to untreated control cells? A24. Gene expression would be a. increased b. decreased c. not changed B25. Chromatin would be a. more condensed b. less condensed c. not changed C26. Methylation would be a. increased b. decreased c. not changed C27. Methyltransferases would be a. more active b. less active c. not changed C28. Binding of Methyl Binding proteins would be a. increased b. decreased c. not changed I-1 I-2 I-3 I-4 II-1 II-2 III-1 III-2 III-3 III-4 III-5 III-6 III-7 III-8 III-9 IV-1 IV-2 IV-3 IV-4 IV-5 IV-6 IV-7 IV-8 IV-9 The family above has a mutation in an imprinted gene. You may assume the following people are genotypically normal (III-1, III-4, III-6 and III-8). Neither II-1 or II-2 shows symptoms of the disorder but both had a mother with the disorder. This gene is T29. Maternally imprinted F31. Maternally expressed F30. Paternally imprinted T32. Paternally expressed A33. Individual III-2 inherited the mutation from his a. mother (II-2) only b. father (II-1) only c. definitely both B34. Individual III-5 inherited the mutation from his a. mother (II-1) only b. father (II-2) only c. definitely both d. maybe both d. maybe both GENETICS EXAM ONE SPRING 2009 NAME: True or False: T35. Individual I-3 could be a double mutant F36. If II-1 and II-2 had another child, there would be a 75% chance the child be affected. T37. Couple III-6 and III-7 will never have a child that has the disorder F38. IV-6, IV-7, IV-8 and IV-9 all have the same probability of having the mutation F39. The probability that III-8 has at least one mutation is 75% F40. Individual III-6 and III-8 are definitely genotypically normal F41. This imprinted gene could be located on the X-chromosome The possible genotypes of Individual I-2 could be: T42. He has no mutated alleles T43. He has one mutated allele that he got from his mom F44. He has one mutated allele that he got from his dad F45. He has two mutated alleles (got one from each parent) Which pairing would give the greatest risk of having a child with the disorder? (if more than one couple would have equivalent highest risk select any that apply). F46. IV-1 and IV-7 T47. IV-8 and IV-2 F48. IV-6 and IV-5 T49. IV-3 and IV-2 I-1 I-2 II-1 II-2 II-3 II-4 II-5 II-6 II-7 III-1 III-2 III-3 III-4 III-5 III-6 III-7 IV-1 The above family has a disorder due to some kind of issue with expression from Chromosome 15q11-q13, the location of genes for Angelman/Prader-Willi Syndrome. You may assume people marrying into the family are genotypically normal (II-1, II-4, II-7 and III-7) A50. Based on the inheritance pattern alone, affected people have: a. Angelman's b. Prader-Willi c. Females have Angelman's, males Prader-Willi d. Males have Angelman's, females Prader-Willi e. its impossible to determine imprinted expression of Atp10c, we performed RT-PCR analysis using primers spanning an Atp10c intron 20 GENETICS EXAM ONE SPRING 2009 (Fig. 2C). Only the spliced RNA was expressed in any NAME: tissues, suggesting the antisense transcript was not extending to this locus. Then, we analyzed methylation status caused by island of uniparental disomy NotI B51. If it was discovered that this disorder is in the CpG maternal Atp10c intron 1. The(which is site (Fig. 3) the family), affected people shown) have: unlikely given the frequency of affected people in and the SmaI site (data not would in this CpG island were unmethylated in any tissues, whether a. Angelman's Atp10c was imprinted or not. While it is possible for other b. Prader-Willi CpG dinucleotides in Atp10c to display allele-specific c. Females have Angelman's, males Prader-Willi . 1 Expression analysis of the mouse Atp10c gene in multiple Prader-Willi d. Males have Angelman's, females ues. RT-PCR with the specific primers for Atp10c showed a high el of expression in e. itstissues, suggesting determine brain impossible to that it has significant reciprocal crosses (JF1 x B6) 15 is JF1). A Schematic of Is this area of Chromosomeand (B6axdeletion of q11-13.the it transcribed sequence polymorphisms in possible that this family has the traditional deletion of Ch 15q11-q13? the ATP10c 3’ UTR and the primers used for amplification of ATP10c. An asterisk denotes a. yes b. no oligonucleotide spI. Allelic expression bias with preferential maternal the polymorphic site. Arrowheads representin brain tissues.primers. B Imprinted expression of Atp10c The pression was shown in hippocampus and olfactory imprinted expression was assessed by PCR-RFLP analysis. PCR In addition to the expression, but not products there are with MspI, producing the undigested 288lb with a small amount of paternaltraditional deletion mutation,were digestedseveral other abnormalities that can results in Angelman's/Prader-Willi. Given this pedigree, B6 allele and the digested 217-bp and 71-bp other brain tissues (Fig. 2B). Parent-of-origin-specific bp fragment (a) for thewhich of the following mechanism(s) are p observed pression was not ossible? in any other tissues exam- fragments (b) for the JF1 allele. Densitometric values are given T53. Mutation in the suggested that below each lane. Maternal allele-specific transcription is seen for d (data not shown). These results transcription of the gene itself Atp10c in hippocampus and olfactory bulb, in contrast to biallelic use Atp10c was imprinted in a region-specific controls expression in the other during meiosis T54. Mutation in proteins that distri- switching imprinting samples. C Intron-spanning RT-PCR analysis of Atp10c. Genomic DNA and cDNAs were amplified tion in the same manner as Ube3a. An antisense transcript extending to the Atp10c locus using the primers spanning the intron 20 (F3 and R2). Only the General Question: True or False: spliced transcripts were amplified, indicating that the antisense s not yet been identified, but it is tempting todisomy causes disease by repressing expression of maternally T55. Paternal Uniparental speculate transcript does not lie in the 3’ UTR region Atp10c (RT+ t it may also xpressed genes. e be associated with the imprinted reverse transcriptase-positive lane, RT)reverse transcriptase-negapression of Atp10c. To study the mechanism of the tive) ctions in CNS. Glyceraldehyde-3-phosphate dehydrogenase pdh) was used as a control most common mutation in B52. The Fig. 2A–C Imprinted expression of Atp10c in the F1 mice of You are investigating a gene that has been implicated in autism, and you suspect that this gene may be imprinted. First you carry out some experiments to look at expression of paternal and maternal alleles in different areas of the brain. NOTE: numbers under the gels = amount of expression of each allele (a maternal, b paternal) D56. This gene is a. monoallelically expressed in all tissues b. biallelically expressed in all tissues c. biallelically expressed in some tissues, maternally imprinted otherwise d. biallelically expressed in some tissues, paternally imprinted otherwise GENETICS EXAM ONE SPRING 2009 NAME: C57. If I were to mutate the maternal allele in this mouse, what would be true? a. no tissues would be effected b. all tissues would be effected equally c. all tissues would be effected but hippocampus would be most effected d. all tissues would be effected but olfactory bulb would be most effected e. all tissue would be effected but cerebellum, cerebrum and brainstem would be most effected You do further analysis to look at the methylation status of this gene, using the methylation sensitive enzyme Not I, and the enzyme ApaI which is not methylation sensitive. Lanes marked A are samples cut with only ApaI, lanes marked with N are cut with Apa I and Not I. 197 What while methylation status of not FISH, is the RT-PCR analysis could this detect allelic expression bias (Herzing et al. 2002;the data) al. 1994). gene? (select any that apply to Nakao et Here we demonstrated that mouse Atp10c was imprinted F58. both alleles are methylated in59. both allelesmanner, with a predominant expresT a tissue-specific are unmethylated sion from the maternal allele in hippocampus and olF60. one allele is methylated, also is factory bulb, where mouse Ube3a one shows imprinted unmethylated expression. This overlap suggests that the imprinted expression of these two genes is coordinately regulated in the CNS. Recently, a paternally expressed Ube3a antisense transcript was demonstrated, which is under control of an imprinting center (IC) (Rougeulle et al. 1998; Chamberlain and Brannan 2001; Runte et al. 2001). Although the role of this antisense transcript is unknown, it may regulate the imprinted expression of Ube3a. However, the antisense transcript extending to the Atp10c locus has not been identified. The DMR also has not been identified in Atp10c, as well as Ube3a. Although the mechanism of the imprinted expression of Atp10c is unknown, it is possible that Atp10c may play an important role in CNS development, and the absence of maternally expressed Atp10c may be causative of the phenotypes of AS and autism. Fig. 3A, B DNA methylation analysis of the CpG island of Atp10c intron 1. A Restriction map of the genomic fragment in the CpG island of Atp10c. The probe generated by PCR amplification is indicated by the black box. B Southern blot analysis of the Atp10c CpG island. Genomic DNA was digested with ApaI (A) or ApaI plus NotI (N). The 4.7-kb ApaI fragment was completely digested by the methylation-sensitive endonuclease NotI in all tissues, indicating absence of methylation on both alleles (M marker) Acknowledgements We thank Dr. Haruaki Ninomiya, Division of Neurobiology, Department of Biomedical Sciences, School of Life Sciences, Faculty of Medicine, Tottori University, and Dr. Kaoru Inokuchi, Mitsubishi Kasei Institute of Life Sciences, for discussion and technical advice. This study was supported by grants from the Ministry of Education, Culture, Sports, Science, and Technology of Japan. References differential methylation, our result may be related to no DMR identified in Ube3a. Albrecht U, Sutcliffe JS, Cattanach BM, Beechey CV, Armstrong D, Eichele G, Beaudet AL (1997) Imprinted expression of the murine Angelman syndrome gene, Ube3a, in hippocampal and Purkinje neurons. Nat Genet 17:75–78 Chamberlain SJ, Brannan CI (2001) The Prader-Willi syndrome imprinting center activates the paternally expressed murine Ube3a antisense transcript but represses paternal Ube3a. Genomics 73:316–322 Cook EH Jr, Lindgren V, Leventhal BL, Courchesne R, Lincoln A, Shulman C, Lord C, Courchesne E (1997) Autism or atypical autism in maternally but not paternally derived proximal 15q duplication. Am J Hum Genet 60:928–934 Dhar M, Hauser L, Johnson D (2000) A novel ATPase on mouse chromosome 7 is a candidate gene for increased body fat. Physiol Genomics 4:93–100 DiDonato M, Sarkar B (1997) Copper transport and its alterations in Menkes and Wilson diseases. Biochimica Biophysica Acta 1360:3–16 Halleck MS, Pradhan D, Blackman C, Berkes C, Williamson P, Schlegel RA (1998) Multiple members of a third subfamily of P-type ATPases identified by genomic sequences and ESTs. Genome Res 8:354–361 Discussion In the present study, expression analysis of Atp10c also showed higher levels in the CNS including cerebral cortex, cerebellum, hippocampus, olfactory bulb and brain stem. A previous study showed the localization of Atp10c in mouse CNS to subiculum, cerebellar granule cells, hippocampus, olfactory bulb mitral cells, hypothalamus by in situ hybridization (Halleck et al. 1999), and expression overlapped with regions where Ube3a was imprinted (Albrecht et al. 1997). These findings suggest that Atp10c had significant functions in the CNS. UBE3A is the only gene where mutations have been found in AS patients, strongly supporting its causative ...
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