Transcriptome map of mouse isochores

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Arhondakis, Stilianos ^a   Frousios, Kimon ^b   Iliopoulos, Costas S ^b,c   Pissis, Solon P ^b   Tischler, German ^d   Kossida, Sophia ^a  

^a BIOMEDICAL RESEARCH FOUNDATION   (Greece)

^b KING'S COLLEGE LONDON   (United Kingdom)

^c CURTIN UNIVERSITY   (Australia)

^d UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; TRANSCRIPTOME;

ANIMAL TISSUE; ARTICLE; BRAIN TISSUE; CONTROLLED STUDY; DNA BASE COMPOSITION; DNA SEQUENCE; EVOLUTIONARY ADAPTATION; GENE EXPRESSION PROFILING; GENE LOCATION; GENE MAPPING; GENETIC CONSERVATION; ISOCHORE; LIVER PARENCHYMA; MAMMALIAN GENETICS; MOUSE; MULTIGENE FAMILY; MUSCLE TISSUE; NONHUMAN; ANIMAL; BRAIN; C57BL MOUSE; GENETICS; GENOME; LIVER; METABOLISM; MUSCLE; SEQUENCE ANALYSIS;

MAMMALIA;

ANIMALS; BASE COMPOSITION; BRAIN; GENOME; ISOCHORES; LIVER; MICE; MICE, INBRED C57BL; MUSCLES; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 80054074407     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-511     Document Type: Article

References (49)

1. Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F. The mosaic genome of warm--blooded vertebrates. Science 1985, 228:953-958. 10.1126/science.4001930, 4001930.
2. Bernardi G. Structural and Evolutionary Genomics: Natural Selection in Genome Evolution 2005, Elsevier Science Publishers Ltd.
3. Costantini M, Clay O, Auletta F, Bernardi G. Isochore Map of Human Chromosomes. Genome Research 2006, 16:536-541. 10.1101/gr.4910606, 1457033, 16597586.
4. Bernardi G. The neoselectionist Theory of Genome Evolution. PNAS 2007, 104(20):8385-8390. 10.1073/pnas.0701652104, 1866311, 17494746.
5. Costantini M, Cammarano R, Bernardi G. The evolution of isochore patterns in vertebrate genomes. BMC Genomics 2008, 10:146.
6. Wu C, Li W. Evidence for higher rates of nucleotide substitution in rodents than in man. PNAS 1985, 82:1741-1745. 10.1073/pnas.82.6.1741, 397348, 3856856.
7. Gu X, Li W. Higher rates of amino acids substitution in rodents than in human. Mol Phylogenet Evol 1992, 1:211-214. 10.1016/1055-7903(92)90017-B, 1342937.
8. Holliday R. Understanding Ageing 1995, Cambridge University Press, Cambridge, U.K.
9. Eyre-Walker A, Hurst LD. The evolution of isochores. Nature Reviews Genetics 2001, 2(7):549-555. 10.1038/35080577, 11433361.
10. Galtier N, Piganeau G, Mouchiroud D, Duret L. GC-Content Evolution in Mammalian Genomes: The Biased Gene Conversion Hypothesis. Genetics 2001, 159(2):907-911. 1461818, 11693127.
11. Duret L, Galtier N. Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes. Annual Review of Genomics and Human Genetics 2009, 10:285-311. 10.1146/annurev-genom-082908-150001, 19630562.
12. Chojnowski J, Franklin J, Katsu Y, et al. Patterns of Vertebrate Isochore Evolution Revealed by Comparison of Expressed Mammalian, Avian, and Crocodilian Genes. Journal of Molecular Evolution 2007, 65(3):259-266. 10.1007/s00239-007-9003-2, 17674077.
13. Duret L. Evolution of synonymous codon usage in metazoans. Current Opinion in Genetics & Development 2002, 12(6):640-649. 10.1016/S0959-437X(02)00353-2, 21963082.
14. Konu O, Li M. Correlations between mRNA expression levels and GC contents of coding and untranslated regions of genes in rodents. Journal of Molecular Evolution 2002, 54:35-41. 10.1007/s00239-001-0015-z, 11734896.
15. Versteeg R, van Schaik B, van Batenburg M, et al. The human transcriptome map reveals extremes in gene dentistry, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. Genome Research 2003, 13(9):1998-2004. 10.1101/gr.1649303, 403669, 12915492.
16. Vinogradov A. Isochores and tissue specificity. Nucleic Acids Research 2003, 31(17):5212-5220. 10.1093/nar/gkg699, 212799, 12930973.
17. Arhondakis S, Auletta F, Torelli G, D'Onofrio G. Base composition and expression level of human genes. Gene 2004, 325:165-169.
18. Comeron J. Selective and Mutational Patterns Associated With Gene Expression in Humans: Influences on Synonymous Composition and Intron Presence. Genetics 2004, 167(3):1293-1304. 10.1534/genetics.104.026351, 1470943, 15280243.
19. Semon M, Mouchiroud D, Duret L. Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance. Human Molecular Genetics 2005, 14(3):421-427.
20. Vinogradov A. Dualism of gene GC content and CpG pattern in regard to expression in the human genome: Magnitude versus breadth. Trends in Genetics 2005, 21(12):639-643. 10.1016/j.tig.2005.09.002, 16202472.
21. Arhondakis S, Clay O, Bernardi G. Compositional properties of human cDNA libraries: Practical implications. FEBS Letters 2006, 580(24):5772-5778. 10.1016/j.febslet.2006.09.034, 17022979.
22. Arhondakis S, Clay O, Bernardi G. GC level and expression of human coding sequences. Biochemical and Biophysical Research Communications 2008, 367(3):542-545. 10.1016/j.bbrc.2007.12.155, 18177737.
23. Mahmud A, Amore G, Bernardi G. Compositional Genome Contexts Affect Gene Expression Control in Sea Urchin Embryo. PLoS ONE 2008, 3(12):e4025. 10.1371/journal.pone.0004025, 2603317, 19112499.
24. Caron H, van Schaik B, van der Mee M, et al. The Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains. Science 2001, 291(5507):1289-1292. 10.1126/science.1056794, 11181992.
25. Lercher M, Urrutia A, Pavlicek A, Hurst L. A unification of mosaic structures in the human genome. Human Molecular Genetics 2003, 12(19):2411-2415. 10.1093/hmg/ddg251, 12915446.
26. Mouchiroud D, D'Onofrio G, Aissani B, et al. The distribution of genes in the human genome. Gene 1991, 100:181-187.
27. Zoubak S, Clay O, Bernardi G. The gene distribution of the human genome. Gene 1996, 174:95-102. 10.1016/0378-1119(96)00393-9, 8863734.
28. Mijalski T, Harder A, Halder T, et al. Identification of coexpressed gene clusters in a comparative analysis. PNAS 2005, 102(24):8621-8626. 10.1073/pnas.0407672102, 1143582, 15939889.
29. Singer G, Lloyd A, Huminiecki L, Wolfe K. Clusters of Co-expressed Genes in Mammalian Genomes Are Conserved by Natural Selection. Molecular Biology and Evolution 2005, 22(3):767-775.
30. Wang Z, Gerstein M, Snyder M. RNA-seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 2009, 10:57-63. 10.1038/nrg2484, 2949280, 19015660.
31. Metzker M. Sequencing technologies -- the next generation. Nature Reviews Genetics 2010, 11:31-46. 10.1038/nrg2626, 19997069.
32. Ozsolak F, Milos P. RNA sequencing: advances, challenges and opportunities. Nature Reviews Genetics 2011, 12(2):87-98. 10.1038/nrg2934, 3031867, 21191423.
33. Dalca A, Brudno M. Genome variation discovery with high-throughput sequencing data. Briefings in Bioinformatics 2010, 11:bbp058-14.
34. Ng S, Buckingham K, Lee C, et al. Exome sequencing identifies the cause of a mendelian disorder. Nature Genetics 2010, 42:30-35. 10.1038/ng.499, 2847889, 19915526.
35. Wu T, Nacu S. Fast and SNP--tolerant detection of complex variants and splicing in short reads. Bioinformatics 2010, 26(7):873-881. 10.1093/bioinformatics/btq057, 2844994, 20147302.
36. Xiang H, Zhu J, Chen Q, et al. Single--base resolution methylome of the silkworm reveals a sparse epigenomic map. Nature Biotechnology 2010, 28(5):516-520. 10.1038/nbt.1626, 20436463.
37. Mortazavi A, Williams B, McCue K, et al. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nature Methods 2008, 5(7):621-628. 10.1038/nmeth.1226, 18516045.
38. Kikuta H, Laplante M, Navratilova P, et al. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Research 2007, 17(5):545-555. 10.1101/gr.6086307, 1855176, 17387144.
39. Navratilova P, Becker T. Genomic regulatory blocks in vertebrates and implications in human disease. Briefings in Functional Genomics & Proteomics 2009, 8(4):333-342. 10.1093/bfgp/elp019, 21987714.
40. Hiratani I, Leskovar A, Gilbert D. Differentiation--induced replication-timing changes are restricted to AT--rich/long interspersed nuclear element (LINE)--rich isochores. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(48):16861-16866. 10.1073/pnas.0406687101, 534734, 15557005.
41. Ren L, Gao G, Zhao D, et al. Developmental stage related patterns of codon usage and genomic GC content: Searching for evolutionary fingerprints with models of stem cell differentiation. Genome Biology 2007, 8(3).
42. Clay O, Bernardi G. GC3 of Genes Can Be Used as a Proxy for Isochore Base Composition: A Reply to Elhaik et al. Molecular Biology and Evolution 2011, 28:21-23. 10.1093/molbev/msq222, 20817719.
43. UCSC Genome Browser 2011, UCSC Genome Browser., http://genome.ucsc.edu
44. Frousios K, Iliopoulos CS, Mouchard L, et al. REAL: an efficient REad ALigner for next generation sequencing reads. Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology 2010, 154-159. New York, NY, USA: ACM, BCB '10,.
45. REad ALigner (REAL) 2011, REad ALigner (REAL)., http://www.inf.kcl.ac.uk/pg/real/
46. Navarro G, Raffinot M. Flexible Pattern Matching in Strings: Practical On-Line Search Algorithms for Texts and Biological Sequences 2002, Cambridge University Press.
47. Langmead B, Trapnell C, Pop M, Salzberg S. Ultrafast and memory--efficient alignment of short DNA sequences to the human genome. Genome Biology 2009, 10(3):R25+. 2690996, 19261174.
48. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24(5):btn025-714.
49. National Center for Biotechnology Information (NCBI) 2011, National Center for Biotechnology Information (NCBI)., ftp://ftp.ncbi.nlm.nih.gov