Single-neuron transcriptome and methylome sequencing for epigenomic analysis of aging

Methods in Molecular Biology

Volumn 1048, Issue , 2013, Pages 323-352

  Moroz, Leonid L ^a   Kohn, Andrea B ^a  

^a UNIVERSITY OF FLORIDA   (United States)

Author keywords

Aging; Aplysia; DNA methylation; Epigenetics; Epigenomics; Memory; Next generation sequencing; Single cell RNA seq; Transcriptome

Indexed keywords

DNA; METHYLOME; RNA; TRANSCRIPTOME; UNCLASSIFIED DRUG;

AGING; APLYSIA; ARTICLE; DNA METHYLATION; EPIGENETICS; GENOMICS; NERVE CELL; NONHUMAN; POLYPLOIDY; PRIORITY JOURNAL; RNA SEQUENCE;

APLYSIA;

AGING; ANIMALS; APLYSIA; BASE SEQUENCE; DNA METHYLATION; EPIGENOMICS; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; NEURONS; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84934441202     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-556-9_21     Document Type: Article

References (61)

1. Moroz LL, Kohn AB (2010) Do different neurons age differently? Direct genomewide analysis of aging in single identified cholinergic neurons. Front Aging Neurosci 2:1-18
2. Day JJ, Sweatt JD (2011) Epigenetic modifications in neurons are essential for formation and storage of behavioral memory. Neuropsychopharmacology 36:357-358
3. Day JJ, Sweatt JD (2010) DNA methylation and memory formation. Nat Neurosci 13:1319-1323
4. Penner MR, Roth TL, Barnes CA, Sweatt JD (2010) An epigenetic hypothesis of agingrelated cognitive dysfunction. Front Aging Neurosci 2:9
5. Miller CA, Gavin CF, White JA, Parrish RR, Honasoge A, YanceyCR, Rivera IM,RubioMD, Rumbaugh G, Sweatt JD (2010) Cortical DNA methylation maintains remote memory. Nat Neurosci 13:664-666
6. Sweatt JD (2010) Neuroscience. Epigenetics and cognitive aging. Science 328:701-702
7. Feng J, Zhou Y, Campbell SL, Le T, Li E, Sweatt JD, Silva AJ, Fan G (2010) Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. Nat Neurosci 13:423-430
8. Miller CA, Sweatt JD (2007) Covalent modification of DNA regulates memory formation. Neuron 53:857-869
9. Levenson JM, Roth TL, Lubin FD, Miller CA, Huang IC, Desai P, Malone LM, Sweatt JD (2006) Evidence that DNA (cytosine-5) methyltransferase regulates synaptic plasticity in the hippocampus. J Biol Chem 281:15763-15773
10. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A (2009) Conversion of 5- methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324:930-935
11. Kriaucionis S, Heintz N (2009) The nuclear DNA base 5- hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324:929-930
12. Szulwach KE, Li X, Li Y, Song CX, Wu H, Dai Q, Irier H, Upadhyay AK, Gearing M, Levey AI, Vasanthakumar A, Godley LA, Chang Q, Cheng X, He C, Jin P (2011) 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nat Neurosci 14:1607-1616
13. Wiers CE (2012) Methylation and the human brain: Towards a new discipline of imaging epigenetics. Eur Arch Psychiatry Clin Neurosci 262(3):271-273
14. Byrne JH (1987) Cellular analysis of associative learning. Physiol Rev 67:329-339
15. Carew TJ,Walters ET, Kandel ER (1981) Classical conditioning in a simple withdrawal reflex in Aplysia californica. J Neurosci 1:1426-1437
16. Carew TJ, Walters ET, Kandel ER (1981) Associative learning in Aplysia: Cellular correlates supporting a conditioned fear hypothesis. Science 211:501-504
17. Hawkins RD, Kandel ER, Bailey CH (2006) Molecular mechanisms of memory storage in Aplysia. Biol Bull 210:174-191
18. Hawkins RD, Schacher S (1989) Identified facilitator neurons L29 and L28 are excited by cutaneous stimuli used in dishabituation, sensitization, and classical conditioning of Aplysia. J Neurosci 9:4236-4245
19. Kandel ER (2001) The molecular biology of memory storage: A dialogue between genes and synapses. Science 294:1030-1038
20. Marinesco S, Kolkman KE, Carew TJ (2004) Serotonergic modulation in Aplysia. I. Distributed serotonergic network persistently activated by sensitizing stimuli. J Neurophysiol 92:2468-2486
21. Marinesco S, Wickremasinghe N, Carew TJ (2006) Regulation of behavioral and synaptic plasticity by serotonin release within local modulatory fields in the CNS of Aplysia. J Neurosci 26:12682-12693
22. Kandel ER (1976) Cellular basis of behavior. W.H. Freeman and Company, San Francisco
23. Kandel ER (1979) Behavioral biology of aplysia. W.H. Freeman and Company, San Francisco
24. Moroz LL (2011) Aplysia. Curr Biol 21: R60-R61
25. Iwamoto K, Bundo M, Ueda J, Oldham MC, Ukai W, Hashimoto E, Saito T, Geschwind DH, Kato T (2011) Neurons show distinctive DNA methylation profile and higher interindividual variations compared with non-neurons. Genome Res 21:688-696
26. Iwamoto K, Ueda J, Bundo M, Kojima T, Kato T (2011) Survey of the effect of genetic variations on gene expression in human prefrontal cortex and its application to genetics of psychiatric disorders. Neurosci Res 70:238-242
27. Gerdes R, Fieber LA (2006) Life history and aging of captive-reared California sea hares (Aplysia californica). J Am Assoc Lab Anim Sci 45:40-47
28. Stommes D, Fieber LA, Beno C, Gerdes R, Capo TR (2005) Temperature effects on growth, maturation, and lifespan of the california sea hare (Aplysia californica). Contemp Top Lab Anim Sci 44:31-35
29. Hirsch HR, Peretz B (1984) Survival and aging of a small laboratory population of a marine mollusc, Aplysia californica. Mech Ageing Dev 27:43-62
30. Antonov I, Ha T, Antonova I, Moroz LL, Hawkins RD (2007) Role of nitric oxide in classical conditioning of siphon withdrawal in Aplysia. J Neurosci 27:10993-11002
31. Rajasethupathy P, Fiumara F, Sheridan R, Betel D, Puthanveettil SV, Russo JJ, Sander C, Tuschl T, Kandel E (2009) Characterization of small RNAs in Aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREB. Neuron 63:803-817
32. Bailey CH, Kandel ER (2008) Synaptic remodeling, synaptic growth and the storage of long-Term memory in Aplysia. Prog Brain Res 169:179-198
33. MorozLL,KohnAB(2011)Parallel evolution of nitric oxide signaling: Diversity of synthesis and memory pathways. Front Biosci 16:2008-2051
34. Moroz LL, Edwards JR, Puthanveettil SV, Kohn AB, Ha T, Heyland A, Knudsen B, Sahni A, Yu F, Liu L, Jezzini S, Lovell P, Iannucculli W, Chen M, Nguyen T, Sheng H, Shaw R, Kalachikov S, Panchin YV, Farmerie W, Russo JJ, Ju J, Kandel ER (2006) Neuronal transcriptome of Aplysia: Neuronal compartments and circuitry. Cell 127:1453-1467
35. Moroz LL, Dahlgren RL, Boudko D, Sweedler JV, Lovell P (2005) Direct single cell determination of nitric oxide synthase related metabolites in identified nitrergic neurons. J Inorg Biochem 99:929-939
36. Moroz LL, Gillette R, Sweedler JV (1999) Single-cell analyses of nitrergic neurons in simple nervous systems. J Exp Biol 202(Pt 4): 333-341
37. Li L, Garden RW, Sweedler JV (2000) Singlecell MALDI: A new tool for direct peptide profiling. Trends Biotechnol 18:151-160
38. Li L, Sweedler JV (2008) Peptides in the brain: Mass spectrometry based measurement approaches and challenges. Annu Rev Anal Chem 1:451-493
39. Fuller RR, Moroz LL, Gillette R, Sweedler JV (1998) Single neuron analysis by capillary electrophoresis with fluorescence spectroscopy. Neuron 20:173-181
40. Liu L, van Groen T, Kadish I, Tollefsbol TO (2009) DNA methylation impacts on learning and memory in aging. Neurobiol Aging 30:549-560
41. Lovell P, Moroz LL (2006) The largest growth cones in the animal kingdom and dynamics of neuronal growth in cell culture of Aplysia. Integr Comp Biol 46:847-870
42. Jezzini SH, Bodnarova M, Moroz LL (2005) Two-color in situ hybridization in the CNS of Aplysia californica. J Neurosci Methods 149:15-25
43. Walters ET, Moroz LL (2009) Molluscan memory of injury: Evolutionary insights into chronic pain and neurological disorders. Brain Behav Evol 74:206-218
44. Tang F, Barbacioru C, Nordman E, Li B, Xu N, Bashkirov VI, Lao K, Surani MA (2010) RNASeq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5:516-535
45. Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch BB, Siddiqui A, Lao K, Surani MA (2009) mRNASeq whole-Transcriptome analysis of a single cell. Nat Methods 6(5):377-382
46. Islam S, Kjallquist U, Moliner A, Zajac P, Fan JB, Lonnerberg P, Linnarsson S (2011) Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res 21:1160-1167
47. Moroz LL, Kohn AB (2010) Do different neurons age differently? Direct genome-wide analysis of aging in single identified cholinergic neurons. Front Aging Neurosci 2:6. doi:10.3389/neuro.24.006.2010
48. Evrony GD, Cai X, Lee E, Hills LB, Elhosary PC, Lehmann HS, Parker JJ, Atabay KD, Gilmore EC, Poduri A, Park PJ, Walsh CA (2012) Single-neuron sequencing analysis of l1 retrotransposition and somatic mutation in the human brain. Cell 151:483-496
49. Kohn AB, Moroz TP, Barnes JP, Netherton M, Moroz LL (2013) Single-cell semiconductor sequencing. Trygve O, Tollefsbol (eds.). Biological Aging:Methods and Protocols,Methods in Mol Biol: Methods and Protocols, vol. 1048, doi:10.1007/978-1-62703-556-9-18, # Springer, New York, This volume
50. Nielsen C (2012) Animal Evolution: Interrelationships of the living phyla. Oxford University Press, Oxford
51. Valentine JW (2004) On the origin of phyla. The University of Chicago Press, Chicago
52. Srivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U, Kawashima T, Kuo A, Mitros T, Salamov A, Carpenter ML, Signorovitch AY, Moreno MA, Kamm K, Grimwood J, Schmutz J, Shapiro H, Grigoriev IV, Buss LW, Schierwater B, Dellaporta SL, Rokhsar DS (2008) The Trichoplax genome and the nature of placozoans. Nature 454:955-960
53. Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier ME,MitrosT, RichardsGS, ConacoC, Dacre M, Hellsten U, Larroux C, Putnam NH, Stanke M, Adamska M, Darling A, Degnan SM, Oakley TH, Plachetzki DC, Zhai Y, AdamskiM, Calcino A, Cummins SF, Goodstein DM,Harris C, Jackson DJ, Leys SP, Shu S, Woodcroft BJ, VervoortM,KosikKS,ManningG,DegnanBM, Rokhsar DS (2010) The Amphimedon queenslandica genome and the evolution of animal complexity. Nature 466:720-726
54. Zhang Y, Brown MR, Hyland C, Chen Y, Kronengold J, Fleming MR, Kohn AB, Moroz LL, Kaczmarek LK (2012) Regulation of neuronal excitability by interaction of fragile X mental retardation protein with slack potassium channels. J Neurosci 32:15318-15327
55. Moroz LL, Citarella M, Kohn AB (2012) Genome-wide analysis of plasticity-induced active DNA demethylation in memory-forming circuits: Insights from the Aplysia genome. Society for Neuroscience Meeting, Abstracts, New Orleans, 294.208/CCC233
56. Guan Z, Giustetto M, Lomvardas S, Kim JH, Miniaci MC, Schwartz JH, Thanos D, Kandel ER (2002) Integration of long-Term-memoryrelated synaptic plasticity involves bidirectional regulation of gene expression and chromatin structure. Cell 111:483-493
57. Lasek RJ, Dower WJ (1971) Aplysia californica: Analysis of nuclear DNA in individual nuclei of giant neurons. Science 172:278-280
58. Guo JU, Ma DK, Mo H, Ball MP, Jang MH, Bonaguidi MA, Balazer JA, Eaves HL, Xie B, Ford E, Zhang K, Ming GL, Gao Y, Song H (2011) Neuronal activity modifies the DNA methylation landscape in the adult brain. Nat Neurosci 14:1345-1351
59. Heyland A, Moroz LL (2006) Signaling mechanisms underlying metamorphic transitions in animals. Integr Comp Biol 46:743-759
60. Heyland A, Vue Z, Voolstra CR, Medina M, Moroz LL (2011) Developmental transcriptome of Aplysia californica. J Exp Zool B Mol Dev Evol 316B:113-134
61. Waddington CH (1956) Principles of Embryology. Allen & Unwin, New York