gene imprinting(edited)
TRANSCRIPT
VBMS 7720 Developmental Molecular BiologyPresented by: Chris Ramhold Ph.D. Student
2/25/15
GENE IMPRINTING
• What is imprinting?– Expand your vocabulary
• Inheritance– Mendelian/Non-Mendelian– Pattern of Imprinting
• Importance• Mechanisms
– Big Picture• Disease
– Detection of imprinted genes• Disclaimer *Your results may vary*
OVERVIEW
• Epigenetics- “On genes,” modifications to DNA that retain sequence fidelity yet alter gene expression
• Imprinting- Gamete-specific differential modification– Unique to placental mammals, marsupials and flowering
plants– Typically marked with DNA methylation– Often occur in clusters– Gene is silenced
• Epigenetic memory- The set of epigenetic modifications inherited in descendant cells
WHAT IS IMPRINTING?
• 2 broad categories of inheritance– Mendelian– Non-mendelian
• Law of Segregation- Each parent contributes a single gamete containing single alleles from either maternal or parental chromosomes
MENDELIAN GENETICS…. INHERITANCE
IMPRINTING INHERITANCE PATTERN (GAMETES)
http://hihg.med.miami.edu/code/http/modules/education/Design/Print.asp?CourseNum=2&LessonNum=2
• Imprinting established in gametes
IMPRINTING INHERITANCE PATTERN (POST FERTILIZATION)
http://hihg.med.miami.edu/code/http/modules/education/Design/Print.asp?CourseNum=2&LessonNum=2
• Imprinting maintained during embryogenesis
• Genome-wide epigenetic reprogramming
• Paternal X inactivation
IMPRINTING INHERITANCE PATTERN (DIFFERENTIATION)
http://hihg.med.miami.edu/code/http/modules/education/Design/Print.asp?CourseNum=2&LessonNum=2
• Imprinting maintained in adult somatic tissues
IMPRINTING INHERITANCE PATTERN ( BACK TO GAMETES)
http://hihg.med.miami.edu/code/http/modules/education/Design/Print.asp?CourseNum=2&LessonNum=2
• Imprinting erased and modified based on sex
• Imprinted genes– Are crucial for normal development– Bypass epigenetic reprogramming– Are vulnerable to epigenetic copying machinery
• Roles in– Growth– Behavior– Stem cells– Disease
IMPORTANCE
• Paternal expression– Placental development– Enhance growth– Large offspring (benefit for father)
• Maternal expression– Suppress growth– Limit expression of paternal genes– Small offspring (benefit for mother)• Resource use
IMPORTANCE
Moon, Y. S., Smas, C. M., Lee, K., Villena, J. A., Kim, K.-H., Yun, E. J., & Sul, H. S. (2002). Mice lacking paternally expressed Pref-1/Dlk1 display growth retardation and accelerated adiposity. Molecular and Cellular Biology, 22, 5585–5592. doi:10.1128/MCB.22.15.5585-5592.2002
MECHANISM- HOW DOES IT WORK?
Zakhari, S. (2013). Alcohol metabolism and epigenetics changes. Alcohol Research : Current Reviews, 35, 6–16.
• DNA Methylation– CpG- Cytosine-
phosphate-guanine
– DNMT- DNA methyltransferase
– 5’Methyl-cytosine can easily be deaminated to form thymine
• CpG Islands- Regions with high concentrations of Cpg motifs– Promoter region– ~70% of human promoter regions
contain CpG islands• Imprinting Control Regions (ICR) &
Differentially Methylated Regions (DMR)– Cis-acting– Control gene clusters ~3.0 Mb away– Deletion of ICR leads to loss of
imprinting
DNA METHYLATION
http://biol10005.tumblr.com/post/31972466118/epigenetics
DNA METHYLATION
Li, E. (2002). Chromatin modification and epigenetic reprogramming in mammalian development. Nature Reviews. Genetics, 3, 662–673. doi:10.1038/nrg887
• Dnmt3 family facilitates imprinting in gametes
• Dnmt1 maintains methylation states post-embryogenesis
• 98% of genome 1 CpG/100bp- Me
• <2% of genome 1 CpG/10bp- Un-Me
• Chromatin condensation• Gene imprinting on rare
occasions will modify histones through acetylation/methylation
DNA METHYLATION- QUICK STEP BACK
Duygu, B., Poels, E. M., & da Costa Martins, P. A. (2013). Genetics and epigenetics of arrhythmia and heart failure. Frontiers in Genetics, 4, 219. doi:10.3389/fgene.2013.00219
• Acetylation generally leads to increased expression
• Methylation generally leads to decreased expression
• Ideas on why imprinting occurs in clusters?
HISTONE MODIFICATION
Duygu, B., Poels, E. M., & da Costa Martins, P. A. (2013). Genetics and epigenetics of arrhythmia and heart failure. Frontiers in Genetics, 4, 219. doi:10.3389/fgene.2013.00219
• Imprinted genes contain regions of ncRNAs
• Air paternally expressed
• Repress flanking protein-coding genes in cis
LNC-RNA
Fatica, A., & Bozzoni, I. (2014). Long non-coding RNAs: new players in cell differentiation and development. Nature Reviews. Genetics, 15, 7–21. doi:10.1038/nrg3606
• CTCF- 11-zinc finger protein
• Binds Imprinting Control Element
• Prevents methylation of ICE and H19
• Ins2- Insulin 2• H19- lnc-RNA,
negative regulator of growth and proliferation
INSULATOR MODEL
• “Random” X-chromosome inactivation– Cell-to-cell basis– Actually regulated by several cis-Elements (Choice elements)
• Xist- X-Inactive Specific Transcript- encodes lnc-RNA• Tsix- Antisense to Xist- negative regulator of Xist
X CHROMOSOME INACTIVATION CO-EVOLUTION?
Reik, W. & Lewis, A. Co-evolution of X-chromosome inactivation and imprinting in mammals. Nature Rev. Genet. 6, 403–410 (2005).
• Xist
X CHROMOSOME INACTIVATION CO-EVOLUTION?
• Xist lncRNA acts cis- coating chromosome• Histone modification silences coated chromosome• Very similar to imprinting
Reik, W. & Lewis, A. Co-evolution of X-chromosome inactivation and imprinting in mammals. Nature Rev. Genet. 6, 403–410 (2005).
X CHROMOSOME INACTIVATION CO-EVOLUTION?
• DNA methylation steps identical to imprinting
Reik, W. & Lewis, A. Co-evolution of X-chromosome inactivation and imprinting in mammals. Nature Rev. Genet. 6, 403–410 (2005).
• Xist
X CHROMOSOME INACTIVATION CO-EVOLUTION?
• Methylation is maintained in placenta• Lost in embryonic tissue
Reik, W. & Lewis, A. Co-evolution of X-chromosome inactivation and imprinting in mammals. Nature Rev. Genet. 6, 403–410 (2005).
• Paternal genome undergoes rapid de-methylation
• Maternal genome de-methylates more slowly
• Imprinted genes escape methylome reprogramming
UNDERSTANDING THE TIMELINE OF METHYLATION
Vertino, P. (2011), "DNA methylation in cancer", in Issa, J. (ed.), DNA Methylation: Physiology, pathology and disease, The Biomedical & Life Sciences Collection, Henry Stewart Talks Ltd, London
THE METHYLOME AND YOU (BIG PICTURE)
Vertino, P. (2011), "DNA methylation in cancer", in Issa, J. (ed.), DNA Methylation: Physiology, pathology and disease, The Biomedical & Life Sciences Collection, Henry Stewart Talks Ltd, London
• Angelman Syndrome (AS)– 1/20k births– Severe mental retardation– Lack of speech– Ataxic gait– Unnaturally happy disposition• Random bouts of laughter
– Hand flapping
DISEASE
• Prader-Willi Syndrome (PWS)– 1/25k births– Mild mental retardation– Chronic hunger- obesity– Stunted height– Most common syndromal cause of
human obesity
DISEASE
• Loss of function• Chromosome 15
– Loss of expression in 15q11-13
• AS- Maternal• PWS- Paternal
DISEASE
• Beckwith-Wiedemann Syndrome– Microcephaly- small head– Macroglossia- enlarged tongue– Visceromegaly- enlarged organs– Macrosomia- large body size– Umbilical hernia
• Loss of imprinting on chromosome region 11p15.5
DISEASE
http://health.shorehealth.org/imagepages/17076.htm
• Cancer– Wilms’ tumor• Embryonic kidney cancer
– Loss of imprinting control on H19– Hypermethylation of imprinting control
region– Overexpression of IGF2
DISEASE
Martens-Uzunova ES, Bottcher R, Croce CM, Jenster G, Visakorpi T, Calin GA. Long noncoding RNA in prostate, bladder, and kidney cancer. Eur Urol. 2013;65:1140–51. doi: 10.1016/j.eururo.2013.12.003.
DISEASE
• Cancer– Bladder cancer
– Loss of imprinting on H19– Hypomethylation of imprinting control
region– Overexpression of IGF2
Martens-Uzunova ES, Bottcher R, Croce CM, Jenster G, Visakorpi T, Calin GA. Long noncoding RNA in prostate, bladder, and kidney cancer. Eur Urol. 2013;65:1140–51. doi: 10.1016/j.eururo.2013.12.003.
• Bisulfite sequencing– Cytosine converted to
uracil– Methylated cytosine
unaffected
DETECTION OF IMPRINTED GENES
• Sequencing after treatment should reveal no bands in lane C
• Bands in lane C represent methylated cytosines
DETECTION OF IMPRINTED GENES
Herman, J G et al. “Methylation-Specific PCR: A Novel PCR Assay for Methylation Status of CpG Islands.” Proc of Nat. Ac. of Sci. 93.18 (1996): 9821–9826.
• Hongerwinter 1944– Dutch period of starvation during WWII– Childen born were short, and
diagnosed with anemia, edema, diabetes, and depression
– The women who were born of this era were shown to have children that mimicked the same symptoms as their mothers.
– Hyopmethylation of IGF2 six decades later
– Implication in environmental imprinting
YOU ARE WHAT YOU DON’T EAT?
Veenendaal M, Painter R, de Rooij S, Bossuyt P, van der Post J, Gluckman P, et al. Transgenerational effects of prenatal exposure to the 1944-45 Dutch famine. BJOG (2013) 120(5):548–5410.1111/1471-0528.12136
• Duygu, B., Poels, E. M., & da Costa Martins, P. A. (2013). Genetics and epigenetics of arrhythmia and heart failure. Frontiers in Genetics, 4, 219. doi:10.3389/fgene.2013.00219
• Fatica, A., & Bozzoni, I. (2014). Long non-coding RNAs: new players in cell differentiation and development. Nature Reviews. Genetics, 15, 7–21. doi:10.1038/nrg3606
• Herman, J G et al. “Methylation-Specific PCR: A Novel PCR Assay for Methylation Status of CpG Islands.” Proceedings of the National Academy of Sciences of the United States of America 93.18 (1996): 9821–9826.
• http://health.shorehealth.org/imagepages/17076.htm• http://biol10005.tumblr.com/post/31972466118/epigenetics• Li, E. (2002). Chromatin modification and epigenetic reprogramming in mammalian development. Nature Reviews. Genetics, 3,
662–673. doi:10.1038/nrg887• Martens-Uzunova ES, Bottcher R, Croce CM, Jenster G, Visakorpi T, Calin GA. Long noncoding RNA in prostate, bladder, and kidney
cancer. Eur Urol. 2013;65:1140–51. doi: 10.1016/j.eururo.2013.12.003.• Moon, Y. S., Smas, C. M., Lee, K., Villena, J. A., Kim, K.-H., Yun, E. J., & Sul, H. S. (2002). Mice lacking paternally expressed
Pref-1/Dlk1 display growth retardation and accelerated adiposity. Molecular and Cellular Biology, 22, 5585–5592. doi:10.1128/MCB.22.15.5585-5592.2002
• Reik, W. & Lewis, A. Co-evolution of X-chromosome inactivation and imprinting in mammals. Nature Rev. Genet. 6, 403–410 (2005).• Veenendaal M, Painter R, de Rooij S, Bossuyt P, van der Post J, Gluckman P, et al. Transgenerational effects of prenatal exposure to
the 1944-45 Dutch famine. BJOG (2013) 120(5):548–5410.1111/1471-0528.12136• Vertino, P. (2011), "DNA methylation in cancer", in Issa, J. (ed.), DNA Methylation: Physiology, pathology and disease, The
Biomedical & Life Sciences Collection, Henry Stewart Talks Ltd, London• Zakhari, S. (2013). Alcohol metabolism and epigenetics changes. Alcohol Research : Current Reviews, 35, 6–16.
REFERENCES