Location of Repository

Genetics: Polymorphisms, Epigenetics, and Something In Between

By Keith A. Maggert


At its broadest sense, to say that a phenotype is epigenetic suggests that it occurs without changes in DNA sequence, yet is heritable through cell division and occasionally from one organismal generation to the next. Since gene regulatory changes are oftentimes in response to environmental stimuli and may be retained in descendent cells, there is a growing expectation that one's experiences may have consequence for subsequent generations and thus impact evolution by decoupling a selectable phenotype from its underlying heritable genotype. But the risk of this overbroad use of “epigenetic” is a conflation of genuine cases of heritable non-sequence genetic information with trivial modes of gene regulation. A look at the term “epigenetic” and some problems with its increasing prevalence argues for a more reserved and precise set of defining characteristics. Additionally, questions arising about how we define the “sequence independence” aspect of epigenetic inheritance suggest a form of genome evolution resulting from induced polymorphisms at repeated loci (e.g., the rDNA or heterochromatin)

Topics: Review Article
Publisher: Hindawi Publishing Corporation
OAI identifier: oai:pubmedcentral.nih.gov:3335516
Provided by: PubMed Central
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • http://www.pubmedcentral.nih.g... (external link)
  • Suggested articles



    1. (2000). A .R .L o h ea n dP .A .R o b e r t s ,“ E v o l u t i o no fD N Ai nh e t -erochromatin: the Drosophila melanogaster sibling species subgroup as a resource,”
    2. (2004). A forgotten debate: is selenocysteine the 21st amino acid?”
    3. (2011). A Genome-Wide survey of imprinted genes in rice seeds reveals imprintingGenetics
    4. (2004). A programmed strand-specific and modified nick in S. pombe constitutes a novel type of chromosomal imprint,”
    5. (2011). a r e d e s ,A .T .B r a n c o ,D .L .H a r t l ,K .A .M a g g e r t ,a n d B. Lemos, “Ribosomal dna deletions modulate genomewide gene expression: ”rDNA-sensitive” genes and natural variation,”
    6. (1985). A two-stage model for the control of rDNA magnification,”
    7. (2000). Acquisition and metastability of centromere identity and function: sequence analysis of a human neocentromere,”
    8. (2001). Adaptive evolution of Cid, a centromere-specific histone in
    9. (2004). Centromeric chromatin exhibits a histone modification pattern that is distinct from both euchromatin and heterochromatin,”
    10. (1976). Characterization of Drosophila chromatin. I. Staining and decondensation with
    11. (1976). Characterization of Drosophila heterochromatin.
    12. (1934). Chromosome constitution and behavior in eversporting and mottling in drosophila melanogaster,”
    13. (2001). Clark,“IdentificationoffivenewgenesontheYchromosome of Drosophila melanogaster,”
    14. (2002). Conflict begets complexity: the evolution of centromeres,”
    15. Conserved (CT)n.(GA)n repeats in the non-coding regions at the Gpdh locus are binding sites for the GAGA factor in Drosophila melanogaster and its sibling species,”
    16. (2006). DEMETER DNA glycosylase establishes MEDEA polycomb gene selfimprinting by allele-specific demethylation,”
    17. (2005). Drosophila : A Laboratory Handbook,
    18. (2007). Drosophila TIFIA is required for ribosome synthesis and cell growth and is regulated by the TOR pathway,”
    19. (1998). Dynamics of the sub-nuclear distribution of Modulo and the regulation of position-effect variegation by nucleolus in
    20. (2008). Epigenetic control of rDNA loci in response to intracellular energy status,”
    21. (2010). Epigenetic effects of polymorphic Y chromosomes modulate chromatin components, immune response, and sexual conflict,”
    22. (2011). Epigenetic patterns maintained in early Caenorhabditis elegans embryos can be established by gene activity in the parental germ cells,”
    23. (2008). Epigenetic regulation of heterochromatic
    24. (2008). Epigenetic regulation of retrotransposons within the nucleolus of
    25. (1975). Evidence for heterogeneity in heterochromatin of
    26. (2009). Expression of I-CreI endonuclease generates deletions within the rDNA
    27. (2003). Extrachromosomal circular DNA of tandemly repeated genomic sequences in
    28. (1997). F r i t z e ,K .V e r s c h u e r e n ,R .S t r i c h ,a n dR .E .E s p o s i t o , “DirectevidenceforSIR2modulationofchromatinstructure in yeast rDNA,”
    29. (1991). Fine mapping of satellite DNA sequences along the Y chromosome of Drosophila melanogaster: relationships between satellite sequences and fertility factors,”
    30. (2008). Genomic architecture and inheritance of human ribosomal RNA gene clusters,”
    31. (1999). Genomic imprinting and position-effect variegation
    32. (2011). Genomic imprinting: the emergence of an epigenetic paradigm,”
    33. (2007). H3K9 methylation and RNA interference regulate nucleolar organization and repeated
    34. (2007). Heritable germline epimutation is not the same as transgenerational epigenetic inheritance,”
    35. (2009). Heterochromatic genome stability requires regulators of histone
    36. (2008). HP1: a functionally multifaceted protein,”
    37. (2001). Initial sequencing and analysis of the human genome,”
    38. (1981). Isolation of dominant suppressor mutations for position-effect variegation in Drosophila melanogaster,”
    39. (2011). J.Seguin et al.,“High-Resolution analysis of parent-of-origin allelic expression in the Arabidopsis endosperm,”PLoSGenetics,vol.7,no.6,ArticleIDe1002126,
    40. (2001). K.WeilerandB.Wakimoto,“Suppressionofheterochromatic gene variegation can be used to distinguish and characterize E(var) genes potentially important for chromosome structure
    41. (2005). L.Li,A.Orian,R.N.Eisenman,andB.A.Edgar, “Myc-dependent regulation of ribosomal RNA synthesis during Drosophila development,”
    42. (2007). Large-scale polymorphism of heterochromatic repeats in the
    43. (1993). Mapping simple repeated DNA sequences
    44. (2005). Mechanisms and control of rapid genomic changes in flax,”
    45. (2002). Modification of position-effect variegation by competition for binding to Drosophila satellites,”
    46. (2008). Molecular landscape of modified histones in Drosophila heterochromatic genes and euchromatin-heterochromatin transition zones,”
    47. (1997). Molecular structure of a functional Drosophila centromere,”
    48. (1986). Multiplicity of satellite DNA sequences
    49. Mutants affecting position-effect heterochromatinization
    50. (2000). N a k a y a m a ,A .J .S .K l a r ,a n dS .I .S .G r e w a l ,“ A chromodomain protein, Swi6, perform imprinting functions infissionyeast duringmitosisandmeiosis,”
    51. (2011). Novel nucleolar pathway connecting intracellular energy status withp53activation,”
    52. (1991). Nucleolus organizer-suppressed position-effect variegation
    53. (2010). Nutritional control of gene expression in Drosophila larvae via TOR, Myc and a novel cis-regulatory element,”
    54. (2010). o u l o n ,B .J .W e s t m a n ,S .H u t t e n ,F .M .B o i s v e r t ,a n dA .I .
    55. (1986). omme,“Differentialeliminationof rDNAgenesinbobbedmutantsofDrosophilamelanogaster,” Molecular and Cellular Biology,
    56. (1999). Orientation of DNA replication establishes mating-type switching pattern in S.
    57. (1990). Partial reversion at the bobbed locus of Drosophila melanogaster,”
    58. (2008). Polymorphic Y chromosomes harbor cryptic variation with manifold functional consequences,”
    59. (1992). Position effect variegation and chromatin proteins,”
    60. (1989). Position effect variegation in Drosophila melanogaster: relationship between suppression effect and the amount of
    61. (1994). Raff,R .K e l l u m ,a n dB .A l b e rt s ,“T h eD r o s o p h i l aG A G A transcription factor is associated with specific regions of heterochromatin throughout the cell cycle,”
    62. (2011). Rapamycin increases rDNA stability by enhancing association of
    63. (1990). Regulation of fission yeast mating-type interconversion by chromosome imprinting,”
    64. (1980). Repeated genes in eukaryotes,”
    65. (2009). Retrotransposon silencing and telomere integrity in somatic cells
    66. (1989). Ribosomal DNA and Stellate gene copy number variation on the Y chromosome of Drosophila melanogaster,”
    67. (2009). Ribosomal DNA contributes to global chromatin regulation,”
    68. (1977). Sequence arrangement of the rDNA
    69. (2008). SIRT1 redistribution on chromatin promotes genomic stability but alters gene expression during aging,”
    70. (1991). Specific DNA alterations associated with the environmental induction of heritable changes in flax,”
    71. (2003). SU(VAR)3-9 is a conserved key function in heterochromatic gene silencing,”
    72. (2011). Sutcliffe et al., “Alterations in nucleolar structure and gene expression programs in prostatic neoplasia are driven by the MYC oncogene,”
    73. (2010). Systematic protein location mapping reveals five principal chromatin types
    74. The 1.688 repetitive DNA of Drosophila:concerted evolution at different genomic scales and association with genes,” Molecular Biology and Evolution.I n press.
    75. (2001). The activation of a neocentromere in Drosophila requires proximity to an endogenous centromere,”
    76. (2002). The AT-hook protein D1 is essential for Drosophila melanogaster development and is implicated in position-effect variegation,”
    77. (2011). The CCCTC-binding factor (CTCF) of drosophila contributes to the regulation of the ribosomal DNA and nucleolar stability,”
    78. (1999). The economics of ribosome biosynthesis in yeast,”TrendsinBiochemicalSciences,vol.24,no.11,pp.437– 440,
    79. (2008). The epigenetics of rRNA genes: from molecular to chromosome biology,”
    80. (1989). The genetics of position - effect variegation modifying loci
    81. (1992). The Genome of Drosophila Melanogaster,
    82. (1984). The rare transcripts of interrupted rRNA genes in Drosophila melanogaster are processed or degraded during synthesis,”
    83. (2005). The Schizosaccharomyces pombe imprint—Nick or ribonucleotide(s),”
    84. (1977). The structural organization of ribosomal DNA
    85. (2002). The Y chromosome of Drosophila melanogaster exhibits chromosome-wide imprinting,”
    86. (2007). Transcription elongation by RNA polymerase I is linked to efficient rRNAGenetics
    87. (2008). Transgenerational epigenetic effects,”
    88. (1974). Unequal mitotic sister chromatid exchange as the mechanism of ribosomal RNA gene magnification,”
    89. (2001). V e n t e r ,M .D .A d a m s ,E .W .M y e r se ta l .
    90. (2000). Varied expression of a Y-linked P[W+] insert due to imprinting
    91. (1969). Visualization of nucleolar genes,”
    92. (2009). What the nucleolus says to a tumour pathologist,”
    93. (2010). Y not a dead end: epistatic interactions between Y-linked regulatory polymorphisms and genetic background affect global gene expression

    To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.