Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences

Genome Research

Volumn 11, Issue 8, 2001, Pages 1335-1345

  Bergman, C M ^a   Kreitman, M ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ANIMAL CELL; ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DNA SEQUENCE; DNA STRUCTURE; DROSOPHILA; DROSOPHILA MELANOGASTER; DROSOPHILA VIRILIS; EVOLUTION; GENE DELETION; GENE FUNCTION; GENE INSERTION; GENE LOCUS; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CODE; GENETIC CONSERVATION; GENETIC PROCEDURES; GENETIC TRANSCRIPTION; INTRON; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; UNINDEXED SEQUENCE;

ANIMALS; CONSERVED SEQUENCE; DNA, INTERGENIC; DROSOPHILA MELANOGASTER; EVOLUTION, MOLECULAR; GENES, INSECT; GENOME; INTRONS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT;

ANIMALIA; DROSOPHILA MELANOGASTER; DROSOPHILA VIRILIS; MELANOGASTER;

EID: 0034883255     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.178701     Document Type: Article

References (66)

1. The genome sequence of Drosophila melanogaster
2. Unusual haplotype structure at the proximal breakpoint of In(2L)t in a natural population of Drosophila melanogaster
3. The hardwiring of development: Organization and function of genomic regulatory systems
4. Human and mouse gene structure: Comparative analysis and application to exon prediction
5. Interspecific nucleotide sequence comparisons used to identify regulatory and structural features of the Drosophila hsp82 gene
6. Regulatory elements and expression profiles
7. From DNA to diversity: Molecular genetics and the evolution of animal design
8. The correlation between intron length and recombination in Drosophila: Dynamic equilibrium between mutational and selective forces
9. The myogenic regulatory gene Mef2 is a direct target for transcriptional activation by Twist during Drosophila myogenesis
10. Intron-exon structures of eukaryotic model organisms
11. The evolution of regulatory genes and patterns in Drosophila
12. Active conservation of noncoding sequences revealed by three-way species comparisons
13. Searching for regulatory elements in human noncoding sequences
14. Discovery and modeling of transcriptional regulatory regions
15. D-mef2 is a target for Tinman activation during Drosophila heart development
16. Inferring pattern and process: Maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis
17. The causes of molecular evolution
18. The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment
19. Genome evolution: Between the nucleosome and the chromosome
20. A versatile vector set for animal transgenesis
21. A BAC-based physical map of the major autosomes of Drosophila melanogaster
22. Variation in the pattern of nucleotide substitution across sites
23. Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs
24. Distributions in statistics: Discrete distributions
25. A neuron-specific enhancer of the Drosophila dopa decarboxylase gene
26. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
27. Sequence conservation in the protein coding and intron regions of the engrailed transcription unit
28. Evolutionary conservation of homeodomain-binding sites and other sequences upstream and within the major transcription unit of the Drosophila segmentation gene engrailed
29. The neutral theory of molecular evolution
30. Phylogeny of Drosophila and related genera inferred from the nucleotide sequence of the Cu,Zn Sod gene
31. Conservation of regulatory elements controlling hairy pair-rule stripe formation
32. The making of a fly: The genetics of animal design
33. Twist-mediated activation of the NK-4 homeobox gene in the visceral mesoderm of Drosophila requires two distinct clusters of E-box regulatory elements
34. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons
35. Functional analysis of eve stripe 2 enhancer evolution in Drosophila: Rules governing conservation and change
36. Evidence for stabilizing selection in a eukaryotic cis-regulatory element
37. Enhanced graphic matrix analysis of nucleic acid and protein sequences
38. Homeotic response elements are tightly linked to tissue-specific elements in a transcriptional enhancer of the teashirt gene
39. A space-efficient algorithm for aligning large genomic sequences
40. Codon usage bias and base composition of nuclear genes in Drosophila
41. Intraspecific nuclear DNA variation in Drosophila
42. Synonymous substitution rates in Drosophila: Mitochondrial versus nuclear genes
43. The SV40 enhancer contains two distinct levels of organization
44. The bipartite D. melanogaster twist promoter is reorganized in D. virilis
45. High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups
46. Patterns of nucleotide substitution in Drosophila and mammalian genomes
47. Progress and prospects in evolutionary biology: The Drosophila model
48. Evidence for a high ancestral GC content in Drosophila
49. Gene targeting by homologous recombination in Drosophila
50. Systematic gain-of-function genetics in Drosophila
51. Molecular phylogeny and divergence times of drosophilid species
52. Evolutionary rates of insertion and deletion in noncoding nucleotide sequences of primates
53. Analysis of a fushi tarazu autoregulatory element: Multiple sequence elements contribute to enhancer activity
54. Pattern of selective constraint in C. elegans and C. briggsae genomes
55. Perspective: Evolutionary developmental biology and the problem of variation
56. Evolution of transcriptional regulation
57. Substitution-rate variation among sites and the estimation of transition bias
58. Human-mouse genome comparisons to locate regulatory sites
59. Organization of wing formation and induction of a wing-patterning gene at the dorsal/ventral compartment boundary
60. Structure and evolution of a pair-rule interaction element: Runt regulatory sequences in D. melanogaster and D. virilis
61. Smad proteins act in combination with synergistic and antagonistic regulators to target Dpp responses to the Drosophila mesoderm
62. Among-site rate variation and its impact on phylogenetic analyses
63. Maximum-likelihood models for combined analyses of multiple sequence data
64. Regulation of the twist target gene tinman by modular cis-regulatory elements during early mesoderm development
65. Bayesian adaptive sequence alignment algorithms