Why so many noncoding nucleotides? The eukaryote genome as an epigenetic machine

Genetica

Volumn 115, Issue 1, 2002, Pages 105-129

  Zuckerkandl, Emile ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

C value paradox; Cell determination; Dispensability of sequences; Functional density; Gene interaction complexity; Introns; Position effect variegation; Transcriptional regulation

Indexed keywords

DNA, INTERGENIC; ENHANCER ELEMENTS (GENETICS); EUKARYOTIC CELLS; GENE EXPRESSION REGULATION; GENOME; INTRONS; MUTATION; PROMOTER REGIONS (GENETICS); SELECTION (GENETICS); SHORT INTERSPERSED NUCLEOTIDE ELEMENTS;

EUKARYOTA;

SPACER DNA;

ENHANCER REGION; EUKARYOTIC CELL; GENE EXPRESSION REGULATION; GENETIC SELECTION; GENETICS; GENOME; INTRON; MUTATION; PROMOTER REGION; REVIEW; SHORT INTERSPERSED REPEAT;

EID: 0036021705     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1016080316076     Document Type: Article

References (217)

1. Modulation of a transcription factor counteracts heterochromatic gene silencing in Drosophila
2. Mechanism of imprinting on mouse distal chromosome 7
3. Appropriate expression of the mouse H19 gene utilises three or more distinct enhancer regions spread over more than 130 kb
4. Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: The Lyon repeat hypothesis
5. The 10q25 neocentromere and its inactive progenitor have identical primary nucleotide sequence: Further evidence for epigenetic modification
6. Intervening sequences exhibit distinct vocabulary
7. Splice junctions follow a 205-vase ladder
8. Insulators and boundaries: Versatile regulatory elements in the eukaryotic genome
9. DNA amounts in two samples of angiosperm weeds
10. Genomic gigantism: DNA loss is slow in mountain grasshoppers
11. Van der Waals locks: Loop-n-lock structure of globular proteins
12. Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences
13. The isochore organization of the human genome
14. The human genome: Organization and evolutionary history
15. The rest is silence
16. LINES and Alus - The polyA connection
17. Enhancement of the nucleosomal pattern in sequences of lower complexity
18. Involvement of Alu sequences in the cell-specific regulation of transcription of the γ chain of Fc and T cell receptors
19. Evolutionary selection against change in many Alu repeat sequences interspersed through primate genomes
20. Quantitative study of Alu repeated sequences in primate genomes, yielding insight into their sources and evolution
21. DNA sequence insertion and evolutionary variation in gene regulation
22. Cases of ancient mobile element DNA insertions that now affect gene regulation
23. Mobile elements inserted in the distant past have taken on important functions
24. Nuclear structure, gene expression and development
25. Looping versus linking
26. A view through the clouds of imprinting
27. Irreversible gene expression model for control of development
28. Interactions of Drosophila Ultrabithorax regulatory regions with native and foreign promoters
29. The end of the LINE? Lack of recent L1 activity in a group of South American rodents
30. DNA repeats in the human genome
31. Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox
32. Skeletal DNA and the evolution of genome size
33. The skeletal function of non-genic nuclear DNA: New evidence from ancient cell chimaeras
34. A polycomb response element in the Ubx gene that determines an epigenetically inherited state of repression
35. Intron distribution in ancient paralogs supports random insertion and not random loss
36. Centromerization
37. Potential Alu function: Regulation of the activity of double-stranded RNA-activated kinase PKR
38. Protein kinases that phosphorylate eIF2 an eIF2B, and their role in eukaryotic cell translational control
39. Chromosome territories, nuclear architecture and gene regulation in mammalian cells
40. Genetic modification of heterochromatic association and nuclear organization in Drosophila
41. Large-scale chromosomal movements during interphase progression in Drosophila
42. Something from nothing: The evolution and utility of satellite repeats
43. Protective nucleosome centering at splice sites as suggested by sequence-directed mapping of the nucleosomes
44. Perturbation of nuclear architecture by long-distance chromosome interactions
45. Toward a resolution of the introns early/late debate: Only phase zero introns are correlated with the structure of ancient proteins
46. Intron-exon structures of eukaryotic model organisms
47. Efficient studies of long-distance Bmp5 gene regulation using bacterial artificial chromosomes
48. Centromere proteins and chromosome inheritance: A complex affaire
49. Origins and evolutionary relationships of retroviruses
50. Selfish genes, the phenotype paradigm and genome evolution
51. Expansion of transgene repeats cause heterochromatin formation and gene silencing in Drosophila
52. Transgene repeat arrays interact with distance heterochromatin and cause silencing in cis and trans
53. The vertebrate limb: A model system to study the Hox/HOM gene network during development and evolution
54. Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores
55. Transposing without ends: The non-LTR retrotransposable elements
56. Versatility of conviction: Heterochromatin as both a repressor and an activator of transcription
57. Nucleosome interactions with a human Alu element
58. Heterochromatin protein 1 binds transgene arrays
59. Chromatin as an essential part of the transcriptional mechanism
60. Chromatin structure and gene expression
61. Imprinting and the epigenetic asymmetry between parental genomes
62. To be or not to be active: The stochastic nature of enhancer action
63. A functional enhancer suppresses silencing of a transgene and prevents its localization close to centromeric heterochromatin
64. Locus control regions, chromatin activation and transcription
65. The biological properties and evolutionary dynamics of mammalian LINE-1 retrotransposons
66. Sequence-specific packaging of DNA in human sperm chromatin
67. Isolation of four core histones from human sperm chromatin representing a minor subset of somatic histones
68. Homeogene expression patterns and chromosomal imprinting
69. Drosophila nuclear proteins bind to regions of alternating C and T residues in gene promoters
70. The large-scale organization of the centromeric region in Beta species
71. Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma
72. The modulation of DNA content: Proximate causes and ultimate consequences
73. Chromatin interaction mechanism of transcriptional control in vivo
74. Limits of adaptation: The evolution of selective neutrality
75. Enhancement of reporter gene de novo methylation by DNA fragments from the α-fetoprotein control region
76. Spreading of transcriptional repressor SIR3 from telomeric heterochromatin
77. Molecular switches - The ON and OFF of bacterial phase variation
78. Epigenetic regulation of gene expression: The effect of altered chromatin structure from yeast to mammals
79. Position-effect variegation in Drosophila: Recent progress
80. Exploring and explaining epigenetic effects
81. Heterochromatic deposition of centromeric histone H3-like proteins
82. The centromere paradox: Stable inheritance with rapidly evolving DNA
83. Heterochromatin
84. 10-11 bp periodicities in complete genomes reflect protein structure and DNA folding
85. Protein dispensability and rate of evolution
86. Evolution of chromosome bands: Molecular ecology of noncoding DNA
87. Chromosome bands, their chromatin flavors, and their functional features
88. Chromatin self-organization by mutation bias
89. Structure of a polycomb response element and in vitro binding of polycomb group complexes containing GAGA factor
90. Specific binding sites for Pol III transcriptional repressor and Pol II transcription factor YY1 within the internucleosomal spacer region in primate Alu repetitive elements
91. Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure
92. Comparative genomic sequencing identifies novel tissue-specific enhancers and sequence elements for methylation-sensitive factors implicated in Igf2/H19 imprinting
93. Chromatin domains and nuclear compartments: Establishing sites of gene expression in eukaryotic nuclei
94. Origin and evolution of Alu repetitive elements
95. Free left arms as precursor molecules in the evolution of Alu sequences
96. Revision of consensus sequence of human Alu repeats - A review
97. Centric heterochromatin and the efficiency of achiasmate disjunction in Drosophila female meiosis
98. The case for epigenetic effects on centromere identity and function
99. Electron microscopic heteroduplex mapping identifies regions of the engrailed locus that are conserved between Drosophila melanogaster and Drosophila virilis
100. Evolutionary conservation of homeodomain-binding sites and other sequences upstream and within the major transcription unit of the Drosophila segmentation gene engrailed
101. Noncoding RNA genes in dosage compensation and imprinting
102. Silk worm Bm1 RA increases following cellular insults
103. Stress induction of Bm1 RNA in silk worm larvae: SINES, an unusual class of stress genes
104. Variation in nuclear DNA content across environmental gradients: A quantile regression analysis
105. Human and rodent DNA comparisons: A mosaic model of genomic evolution
106. Striking sequence similarity over almost 100 kilobases of human and mouse T-cell receptor DNA
107. Expression of transposon LINE-1 is relatively human-specific and function of the transcript may be proliferation-essential
108. Should scientists scrap the notion of junk DNA?
109. Nucleosome formation potential of exons, introns, and Alu repeats
110. Nucleosome formation potential of eukaryotic DNA: Calculation and promoter analysis
111. The phenomenon of position effect
112. A gene complex controlling segmentation in Drosophila
113. Physiological stresses increase mouse short interspersed element (SINE) RNA expression in vivo
114. Beyond the locus control region: New light on beta-globin locus regulation
115. Rat growth hormone gene introns stimulate nucleosome alignment in vitro and in transgenic mice
116. Alu transcripts: Cytoplasmic localisation and regulation by DNA methylation
117. Genomic imprinting and position-effect variegation in Drosophila melanogaster
118. LINE-1 elements and X chromosome inactivation: A function of junk DNA?
119. The Drosophila morphogenetic protein Bicoid binds DNA cooperatively
120. Acquisition and metastability of centromere identity and function: Sequence analysis of a human neocentromere
121. Alu sequences in the coding regions of mRNA: A source of protein variability
122. The age and evolution of non-LTR retrotransposable elements
123. Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses
124. Alu-family SINE RNA: Interacting proteins and pathways of expression
125. Nuclear architecture
126. The evolution of controlled multitasked gene networks: The role of introns and other noncoding RNAs in the development of complex organisms
127. A homologous protein-coding sequence in Drosophila homeotic genes and its conservation in other metazoans
128. Cellular mosaicism in the methylation and expression of hemizygous loci in the mouse
129. A conserved sequence motif in polycomb-response elements
130. Localized highly repetitive DNA sequences in vertebrate and invertebrate genomes
131. Analysis and significance of messenger RNA in human ejaculated spermatozoa
132. Chip, a widely expressed chromosomal protein required for segmentation and activity of a remote wing margin enhancer in Drosophila
133. Genome size and intron size in Drosophila
134. Transcriptional silencing by the polycomb protein in Drosophila embryos
135. Centromeres take flight: Alpha satellite and the quest for the human centromere
136. Relationship between the total size of exons and introns in protein-coding genes of higher eukaryotes
137. Clustered genes require extragenic territorial DNA sequences
138. Beginning of a notion of junk DNA
139. Transfer RNA-like structure of the human Alu family: Implications of its generation mechanism and possible functions
140. Selfish DNA: The ultimate parasite
141. Mapping polycomb-repressed domains in the bithorax complex using in vivo formaldehyde cross-linked chromatin
142. The role of polycomb group and trithorax group chromatin complexes in the maintenance of determined cell states
143. Evolutionary links between telomeres and transposable elements
144. Developmental roles for chromatin and chromosomal structure
145. Evolution of genome size: New approaches to an old problem
146. High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups
147. Evidence for DNA loss as a determinant of genome size
148. Mechanisms in Drosophila maintain patterns of gene expression
149. Recruitment of components of polycomb group chromatin complexes in Drosophila
150. A master sequence related to a free left Alu monomer (FLAM) at the origin of the B1 family in rodent genomes
151. Silent domains are assembled continuously from the telomere and are defined by promoter distance and strength, and by SIR3 dosage
152. Exon/intron structure of aldehyde dehydrogenase genes supports the 'introns-late' theory
153. Position dependent variegation of globin transgene expression in mice
154. Transcriptional control: Rheostat converted to on/off switch
155. Cell size predicts morphological complexity in the brains of frogs and salamanders
156. Genome size, secondary simplification, and the evolution of the brain in salamanders
157. Adenovirus type 2 preferentially stimulates polymerase III transcription of Alu elements by relieving repression: A potential role for chromatin
158. Genome imprinting: An overview
159. Alu: Structure, origin, evolution, significance and function of one-tenth of human DNA
160. Does SINE evolution preclude Alu function?
161. The evolution of interspersed repetitive DNA sequences in mammals and other vertebrates
162. Transcriptional regulation and transpositional selection of active SINE sequences
163. LINEs, SINEs and repetitive DNA: Non-LTR retrotransposons in plant genomes
164. Nuclear localization and histone acetylation: A pathway for chromatin opening and transcriptional activation of the human β-globin locus
165. Nuclear neighbors: The spatial and functional organization of genes and nuclear domains
166. Structural relationships among genes that control development: Sequence homology between Antennapedia, Ultrabithorax, and fushi tarazu loci of Drosophila
167. Ectopic HP1 promotes chromosome loops and variegated silencing in Drosophila
168. Pattern of selective constraint in C. elegans and C. briggsae
169. Selective constraint in intergenic regions of human and mouse genomes
170. Chromatin insulator elements block the silencing of a target gene by the Drosophila polycomb response element (PRE) but allow trans interactions between PREs on different chromosomes
171. Molecular mechanisms of cellular determination: Their relation to chromatin structure and parental imprinting
172. Interspersed repeats and other mementos of transposable elements in mammalian genomes
173. Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences
174. Structure of vertebrate genes: A statistical analysis implicating selection
175. Genetic conflicts and the evolutionary origin of genomic imprinting
176. Position-effect variegation in Drosophila
177. Testing the exon theory of genes: The evidence from protein structure
178. Co-localization of polycomb protein and GAGA factor on regulatory elements responsible for the maintenance of homeotic gene expression
179. The polycomb group protein complex of Drosophila melanogaster has different compositions at different target genes
180. A theory for developmental control by a program encoded in the genome
181. Reactivation of heritably silenced gene expression in mice
182. Members of the SRY family regulate the human LINE retrotransposons
183. Marginal fitness contributions of nonessential genes in yeast
184. Tightly regulated, developmentally specific expression of the first open reading frame from LINE-1 during mouse embryogenesis
185. The multiple codes of nucleotide sequences
186. Interfering contexts of regulatory sequence elements
187. Mechanisms of developmental control of transcription in the murine α- and β-globin loci
188. Drosophila telomeric transgenes provide insights on mechanisms of gene silencing
189. Transcriptional enhancers act in cis to suppress position-effect variegation
190. Heterochromatin and gene expression in Drosophila
191. Do all SINEs lead to LINEs?
192. Turned on by stress. Plant retrotransposons
193. Neocentromeres and human artificial chromosomes: An unnatural act
194. Biochemical evolution
195. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis
196. No footprints of primordial introns in a eukaryotic genome
197. Origin and evolution of retroelements based upon their reverse transcriptase sequences
198. Drosophila polycomb-group regulated chromatin inhibits the accessibility of a trans-activator to its target DNA
199. The centromere-kinetochore complex: A repeat subunit model
200. A possible role of 'inert' heterochromatin in cell differentiation. Action of and competition for 'locking' molecules
201. The appearance of new structures and functions in proteins during evolution
202. Evolutionary processes and evolutionary noise at the molecular level. I
203. Multilocus enzymes, gene regulation, and genetic sufficiency
204. A general function of noncoding polynucleotide sequences. Mass binding of transconformational proteins
205. Topological and quantitative relationships in evolving genomes
206. Polite DNA: Functional density and functional compatibility in genomes
207. Can large insertions and deletions between genes affect development?
208. Dispensability of parts of histones and the molecular clock
209. Molecular pathways of parallel evolution: I. Gene nexuses and their morphological correlates
210. Junk DNA and sectorial gene repression
211. Sectorial gene repression in the control of development
212. Intrinsically driven changes in gene interaction complexity. 1. Growth of regulatory complexes and increase in number of genes
213. Evolutionary divergence and convergence in proteins
214. Maintenance of function without selection: Alu sequences as cheap genes
215. Tracking heterochromatin