| References |
|
|
Arbiza L,
Dopazo J and
Dopazo H
(2006a)
Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome.
PLoS Computational Biology
2:
e38.
|
|
|
Arbiza L,
Duchi S,
Montaner D et al.
(2006b)
Selective pressures at a codon-level predict deleterious mutations in human disease genes.
Journal of Molecular Biology
358:
1390–1404.
|
|
|
Batada NN and
Hurst LD
(2007)
Evolution of chromosome organization driven by selection for reduced gene expression noise.
Nature Genetics
39:
945–949.
|
|
|
Bejerano G,
Pheasant M,
Makunin I et al.
(2004)
Ultraconserved elements in the human genome.
Science
304:
1321–1325.
|
|
|
Bird A
(2002)
DNA methylation patterns and epigenetic memory.
Genes & Development %R 10.1101/gad.947102
16:
6–21.
|
|
|
Bird CP,
Stranger BE and
Dermitzakis ET
(2006)
Functional variation and evolution of non-coding DNA.
Current Opinion in Genetics & Development
16:
559–564.
|
|
|
Bird CP,
Stranger BE,
Liu M et al.
(2007)
Fast-evolving noncoding sequences in the human genome.
Genome Biology
8:
R118.
|
|
|
Castillo-Davis CI,
Mekhedov SL,
Hartl DL et al.
(2002)
Selection for short introns in highly expressed genes.
Nature Genetics
31:
415–418.
|
|
|
Chamary JV and
Hurst LD
(2004)
Similar rates but different modes of sequence evolution in introns and at exonic silent sites in rodents: evidence for selectively driven codon usage.
Molecular Biology and Evolution
21:
1014–1023.
|
|
|
Chan RY,
Boudreau-Lariviere C,
Angus LM,
Mankal FA and
Jasmin BJ
(1999)
An intronic enhancer containing an N-box motif is required for synapse- and tissue-specific expression of the acetylcholinesterase gene in skeletal muscle fibers.
Proceedings of the National Academy of Sciences of the USA
96:
4627–4632.
|
|
|
Comeron JM and
Kreitman M
(2000)
The correlation between intron length and recombination in Drosophila. Dynamic equilibrium between mutational and selective forces.
Genetics
156:
1175–1190.
|
|
|
Dermitzakis ET,
Reymond A and
Antonarakis SE
(2005)
Conserved non-genic sequences – an unexpected feature of mammalian genomes.
Nature Reviews. Genetics
6:
151–157.
|
|
|
Drake JA,
Bird C,
Nemesh J et al.
(2006)
Conserved noncoding sequences are selectively constrained and not mutation cold spots.
Nature Genetics
38:
223–227.
|
|
|
Duffy DL,
Montgomery GW,
Chen W et al.
(2007)
A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variation.
American Journal of Human Genetics
80:
241–252.
|
|
|
Duret L,
Mouchiroud D and
Gautier C
(1995)
Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores.
Journal of Molecular Evolution
40:
308–317.
|
|
|
Eisenberg E and
Levanon EY
(2003)
Human housekeeping genes are compact.
Trends in Genetics
19:
362–365.
|
|
|
Eyre-Walker A
(1993)
Recombination and mammalian genome evolution.
Proceedings. Biological Sciences
252:
237–243.
|
|
|
Fraser P and
Bickmore W
(2007)
Nuclear organization of the genome and the potential for gene regulation.
Nature
447:
413–417.
|
|
|
Gaffney DJ and
Keightley PD
(2006)
Genomic selective constraints in murid noncoding DNA.
PLoS Genetics
2:
e204.
|
|
|
Gazave E,
Marques-Bonet T,
Fernando O,
Charlesworth B and
Navarro A
(2007)
Patterns and rates of intron divergence between humans and chimpanzees.
Genome Biology
8:
R21.
|
|
|
Haddrill PR,
Charlesworth B,
Halligan DL and
Andolfatto P
(2005)
Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content.
Genome Biology
6:
R67.
|
|
|
Hawkins JD
(1988)
A survey on intron and exon lengths.
Nucleic Acids Research
16:
9893–9908.
|
|
|
Henkel G,
Weiss DL,
McCoy R et al.
(1992)
A DNase I-hypersensitive site in the second intron of the murine IL-4 gene defines a mast cell-specific enhancer.
Journal of Immunology
149:
3239–3246.
|
|
|
Hill WG and
Robertson A
(1968)
The effects of inbreeding at loci with heterozygote advantage.
Genetics
60:
615–628.
|
|
|
Hural JA,
Kwan M,
Henkel G,
Hock MB and
Brown MA
(2000)
An intron transcriptional enhancer element regulates IL-4 gene locus accessibility in mast cells.
Journal of Immunology
165:
3239–3249.
|
|
|
Johnson JM,
Edwards S,
Shoemaker D and
Schadt EE
(2005)
Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments.
Trends in Genetics
21:
93–102.
|
|
|
Jonsson JJ,
Foresman MD,
Wilson N and
McIvor RS
(1992)
Intron requirement for expression of the human purine nucleoside phosphorylase gene.
Nucleic Acids Research
20:
3191–3198.
|
|
|
Kampa D,
Cheng J,
Kapranov P et al.
(2004)
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22.
Genome Research
14:
331–342.
|
|
|
Keightley PD and
Gaffney DJ
(2003)
Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents.
Proceedings of the National Academy of Sciences of the USA
100:
13402–13406.
|
|
|
Keightley PD,
Lercher MJ and
Eyre-Walker A
(2005)
Evidence for widespread degradation of gene control regions in hominid genomes.
PLoS Biology
3:
e42.
|
|
|
Kim SY and
Pritchard JK
(2007)
Adaptive evolution of conserved noncoding elements in mammals.
PLoS Genetics
3:
1572–1586.
|
|
|
Krawczak M,
Thomas NS,
Hundrieser B et al.
(2007)
Single base-pair substitutions in exon–intron junctions of human genes: nature, distribution, and consequences for mRNA splicing.
Human Mutation
28:
150–158.
|
|
|
Lander ESLM,
Linton B,
Birren C et al.
(2001)
Initial sequencing and analysis of the human genome.
Nature
409:
860–921.
|
|
|
Le Hir H,
Nott A and
Moore MJ
(2003)
How introns influence and enhance eukaryotic gene expression.
Trends in Biochemical Sciences
28:
215–220.
|
|
|
Levy S,
Hannenhalli S and
Workman C
(2001)
Enrichment of regulatory signals in conserved non-coding genomic sequence.
Bioinformatics
17:
871–877.
|
|
|
Majewski J and
Ott J
(2002)
Distribution and characterization of regulatory elements in the human genome.
Genome Research
12:
1827–1836.
|
|
|
Marais G,
Nouvellet P,
Keightley PD and
Charlesworth B
(2005)
Intron size and exon evolution in Drosophila.
Genetics
170:
481–485.
|
|
|
Mattick JS and
Gagen MJ
(2001)
The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms.
Molecular Biology and Evolution
18:
1611–1630.
|
|
|
Mattick JS and
Makunin I
(2006)
Non-coding RNA.
Human Molecular Genetics
15:
R17–R29.
|
|
|
Mattick JS and
Makunin IV
(2005)
Small regulatory RNAs in mammals.
Human Molecular Genetics
14(1):
R121–R132.
|
|
|
McCullough AJ and
Berget SM
(1997)
G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection.
Molecular and Cellular Biology
17:
4562–4571.
|
|
|
McVean GA,
Myers SR,
Hunt S et al.
(2004)
The fine-scale structure of recombination rate variation in the human genome.
Science
304:
581–584.
|
|
|
Mikkelsen TS,
Hillier LW,
Eichler EE et al.
(2005)
Initial sequence of the chimpanzee genome and comparison with the human genome.
Nature
437:
69–87.
|
|
|
Oshima RG,
Abrams L and
Kulesh D
(1990)
Activation of an intron enhancer within the keratin 18 gene by expression of c-fos and c-jun in undifferentiated F9 embryonal carcinoma cells.
Genes and Development
4:
835–848.
|
|
|
Palmiter RD,
Sandgren EP,
Avarbock MR,
Allen DD and
Brinster RL
(1991)
Heterologous introns can enhance expression of transgenes in mice.
Proceedings of the National Academy of Sciences of the USA
88:
478–482.
|
|
|
Pollard KS,
Salama SR,
King B et al.
(2006)
Forces shaping the fastest evolving regions in the human genome.
PLoS Genetics
2.
|
|
|
Ponting CP and
Lunter G
(2006)
Signatures of adaptive evolution within human non-coding sequence.
Human Molecular Genetics
15(2):
R170–R175.
|
|
|
Pozzoli U,
Menozzi G,
Comi GP et al.
(2007)
Intron size in mammals: complexity comes to terms with economy.
Trends in Genetics
23:
20–24.
|
|
|
Prendergast JG,
Campbell H,
Gilbert N et al.
(2007)
Chromatin structure and evolution in the human genome.
BMC Evolutionary Biology
7:
72.
|
|
|
Presgraves DC
(2006)
Intron length evolution in Drosophila.
Molecular Biology and Evolution
23:
2203–2213.
|
|
|
Rohrer J and
Conley ME
(1998)
Transcriptional regulatory elements within the first intron of Bruton's tyrosine kinase.
Blood
91:
214–221.
|
|
|
Saxonov S,
Berg P and
Brutlag DL
(2006)
A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters.
Proceedings of the National Academy of Sciences of the USA
103:
1412–1417.
|
|
|
Seoighe C,
Gehring C and
Hurst LD
(2005)
Gametophytic selection in Arabidopsis thaliana supports the selective model of intron length reduction.
PLoS Genetics
1:
e13.
|
|
|
Sironi M,
Menozzi G,
Comi GP et al.
(2005a)
Fixation of conserved sequences shapes human intron size and influences transposon-insertion dynamics.
Trends in Genetics
21:
484–488.
|
|
|
Sironi M,
Menozzi G,
Comi GP et al.
(2005b)
Analysis of intronic conserved elements indicates that functional complexity might represent a major source of negative selection on non-coding sequences.
Human Molecular Genetics
14:
2533–2546.
|
|
|
Sorek R and
Ast G
(2003)
Intronic sequences flanking alternatively spliced exons are conserved between human and mouse.
Genome Research
13:
1631–1637.
|
|
|
Takai D and
Jones PA
(2002)
Comprehensive analysis of CpG islands in human chromosomes 21 and 22.
Proceedings of the National Academy of Sciences of the USA
99:
3740–3745.
|
|
|
Tishkoff SA,
Reed FA,
Ranciaro A et al.
(2007)
Convergent adaptation of human lactase persistence in Africa and Europe.
Nature Genetics
39:
31–40.
|
|
|
Vinogradov AE
(2006)
“Genome design” model: evidence from conserved intronic sequence in human–mouse comparison.
Genome Research
16:
347–354.
|
|
|
Wong GKS,
Passey DA,
Huang YZ,
Yang ZY and
Yu J
(2000)
Is “junk” DNA mostly intron DNA?
Genome Research
10:
1672–1678.
|
|
|
Woolfe A,
Goodson M,
Goode DK et al.
(2005)
Highly conserved non-coding sequences are associated with vertebrate development.
PLoS Biology
3:
e7.
|
| Further Reading |
|
|
Rodriguez-Trelles F,
Tarrio R and
Ayala FJ
(2006)
Origin and evolution of spliceosomal introns.
Annual Review of Genetics
40:
47–76.
|
|
|
Roy T and
Gilbert T
(2006)
The evolution of spliceosomal introns: patterns, puzzles and progress.
Nature Reviews. Genetics
7:
211–221.
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