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PracticeExam1 - 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? 1. Autosomal Recessive 2. Autosomal Dominant 3. X-linked Recessive 4. 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) 5. Autosomal Recessive 6. Autosomal Dominant 7. X-linked Recessive 8. X-linked Dominant 9. 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. 10. 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): 11. splicing mutation - introns left in, no stop codon in the intron 12. splicing mutation - introns left in, stop codon in the intron 13. insertion into the promoter region 14. deletion of the 5'UTR 15. a mutation in the termination sequence for transcription 16. nonsense mutation 17. elimination of the stop codon 18. large deletion in the transcription unit 19. 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 20. Based on this information, transcription proceeds a. from left to right b . from right to left 21. The template strand is a. the top strand b. the bottom strand 22. 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 23. 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? 24. Gene expression would be a. increased b. decreased c. not changed 25. Chromatin would be a. more condensed b. less condensed c. not changed 26. Methylation would be a. increased b. decreased c. not changed 27. Methyltransferases would be a. more active b. less active c. not changed 28. 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 29. Maternally imprinted 31. Maternally expressed 30. Paternally imprinted 32. Paternally expressed 33. Individual III-2 inherited the mutation from his a. mother (II-2) only b. father (II-1) only c. definitely both 34. 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: 35. Individual I-3 could be a double mutant 36. If II-1 and II-2 had another child, there would be a 75% chance the child be affected. 37. Couple III-6 and III-7 will never have a child that has the disorder 38. IV-6, IV-7, IV-8 and IV-9 all have the same probability of having the mutation 39. The probability that III-8 has at least one mutation is 75% 40. Individual III-6 and III-8 are definitely genotypically normal 41. This imprinted gene could be located on the X-chromosome The possible genotypes of Individual I-2 could be: 42. He has no mutated alleles 43. He has one mutated allele that he got from his mom 44. He has one mutated allele that he got from his dad 45. 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). 46. IV-1 and IV-7 47. IV-8 and IV-2 48. IV-6 and IV-5 49. 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) 50. 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 GENETICS EXAM ONE SPRING 2009 NAME: 51. If it was discovered that this disorder is caused by maternal uniparental disomy (which is unlikely given the frequency of affected people in the family), affected people would have: imprinted expression of Atp10c, we performed RT-PCR a. Angelman's analysis using primers spanning an Atp10c intron 20 b. Prader-Willi (Fig. 2C). Only c. Females have Angelman's, males Prader-Willi the spliced RNA was expressed in any tissues, suggesting the antisense transcript was not exd. Males have Angelman's, females Prader-Willi tending to this locus. Then, we analyzed methylation e. its impossible to determine status in the CpG island of Atp10c intron 1. The NotI site (Fig. 3) and the SmaI site (data not shown) in this 52. The most common mutation in this islandof Chromosome 15 in a deletion ofwhether Is it CpG area were unmethylated is any tissues, q11-13. possible that this family has the traditional deletion of Chnot. While it is (assuming other inherited Atp10c was imprinted or 15q11-q13? possible for this is not sporadic) CpG dinucleotides in Atp10c to display allele-specific a. yesmouse Atp10c no in multiple b. gene pression analysis of the T-PCR with the specific primers for Atp10c showed a high xpression in brain tissues, suggesting thattraditional deletion mutation, there are several other abnormalities that can In addition to the it has significant in CNS. Glyceraldehyde-3-phosphate dehydrogenase Fig. 2A–C Imprinted expression of Atp10c in the F1 mice of results in Angelman's/Prader-Willi. Given this pedigree, which of the following mechanism(s) are was used as a control reciprocal crosses (JF1 x B6) and (B6 x JF1). A Schematic of the possible? transcribed sequence polymorphisms in the ATP10c 3’ UTR and 53. Mutation in the transcription of the gene itself amplification of ATP10c. An asterisk denotes the primers used for oligonucleotide 54. Mutation in proteins that controlspolymorphic imprinting during meiosis llelic expression bias with preferential maternal the switching site. Arrowheads representin brain tissues.primers. B Imprinted expression of Atp10c The ion was shown in hippocampus and olfactory imprinted expression was assessed by PCR-RFLP analysis. PCR th a small amount of paternal expression, butFalse: products were digested with MspI, producing the undigested 288General Question: True or not brain tissues (Fig. Paternal Uniparental disomy causes disease the B6 allele and the digested 217-bp maternally 55. 2B). Parent-of-origin-specific bp fragment (a) for by repressing expression of and 71-bp ion was not observed in any other tissues exam- fragments (b) for the JF1 allele. Densitometric values are given expressed genes. below each lane. Maternal allele-specific transcription is seen for ata not shown). These results suggested that Atp10c in hippocampus and olfactory bulb, in contrast to biallelic Atp10c was imprinted in a region-specific distri- expression in the other samples. C Intron-spanning RT-PCR analysis of Atp10c. Genomic DNA and cDNAs were amplified in the same manner as Ube3a. You are investigating a gene that has been implicated in autism, and you suspect that this gene ntisense transcript extending to the Atp10c locus using the primers spanning the intron 20 (F3 and R2). Only the may be imprinted. First you carry spliced transcripts were amplified, indicating that the of out some experiments to look at expression antisense yet been identified, but it is tempting to speculate transcript does not lie in the 3’ UTR region of Atp10c paternal and (RT+ may also be maternal alleles in different areasreverse transcriptase-positive lane, RT)reverse transcriptase-negaassociated with the imprinted of the brain. ion of Atp10c. To study the mechanism of the tive) 56. 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: 57. If I were to mutate (loss of function) 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. What is the methylation status of this gene? (select any that apply to the data) 58. both alleles are methylated 59. both alleles are unmethylated 60. one allele is methylated, one is unmethylated 197 FISH, while RT-PCR analysis could not detect allelic expression bias (Herzing et al. 2002; Nakao et al. 1994). Here we demonstrated that mouse Atp10c was imprinted in a tissue-specific manner, with a predominant expression from the maternal allele in hippocampus and olfactory bulb, where mouse Ube3a also shows imprinted 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 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, hip- ...
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