Literature DB >> 10984448

Active conservation of noncoding sequences revealed by three-way species comparisons.

I Dubchak1, M Brudno, G G Loots, L Pachter, C Mayor, E M Rubin, K A Frazer.   

Abstract

Human and mouse genomic sequence comparisons are being increasingly used to search for evolutionarily conserved gene regulatory elements. Large-scale human-mouse DNA comparison studies have discovered numerous conserved noncoding sequences of which only a fraction has been functionally investigated A question therefore remains as to whether most of these noncoding sequences are conserved because of functional constraints or are the result of a lack of divergence time.

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Year:  2000        PMID： 10984448      PMCID： PMC310906          DOI： 10.1101/gr.142200

Source DB:  PubMed          Journal:  Genome Res        ISSN： 1088-9051            Impact factor:   9.043


  8 in total

1.  Analysis of vertebrate SCL loci identifies conserved enhancers.

Authors:  B Göttgens; L M Barton; J G Gilbert; A J Bench; M J Sanchez; S Bahn; S Mistry; D Grafham; A McMurray; M Vaudin; E Amaya; D R Bentley; A R Green; A M Sinclair
Journal:  Nat Biotechnol       Date:  2000-02       Impact factor: 54.908

2.  Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome.

Authors:  R C Hardison; J Oeltjen; W Miller
Journal:  Genome Res       Date:  1997-10       Impact factor: 9.043

3.  Human and mouse gene structure: comparative analysis and application to exon prediction.

Authors:  S Batzoglou; L Pachter; J P Mesirov; B Berger; E S Lander
Journal:  Genome Res       Date:  2000-07       Impact factor: 9.043

4.  Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6.

Authors:  M A Ansari-Lari; J C Oeltjen; S Schwartz; Z Zhang; D M Muzny; J Lu; J H Gorrell; A C Chinault; J W Belmont; W Miller; R A Gibbs
Journal:  Genome Res       Date:  1998-01       Impact factor: 9.043

5.  Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons.

Authors:  G G Loots; R M Locksley; C M Blankespoor; Z E Wang; W Miller; E M Rubin; K A Frazer
Journal:  Science       Date:  2000-04-07       Impact factor: 47.728

6.  Large-scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains.

Authors:  J C Oeltjen; T M Malley; D M Muzny; W Miller; R A Gibbs; J W Belmont
Journal:  Genome Res       Date:  1997-04       Impact factor: 9.043

7.  A DNase I-hypersensitive site in the second intron of the murine IL-4 gene defines a mast cell-specific enhancer.

Authors:  G Henkel; D L Weiss; R McCoy; T Deloughery; D Tara; M A Brown
Journal:  J Immunol       Date:  1992-11-15       Impact factor: 5.422

8.  Striking sequence similarity over almost 100 kilobases of human and mouse T-cell receptor DNA.

Authors:  B F Koop; L Hood
Journal:  Nat Genet       Date:  1994-05       Impact factor: 38.330
  8 in total
  115 in total

1.  The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study.

Authors:  Anton Nekrutenko; Kateryna D Makova; Wen-Hsiung Li
Journal:  Genome Res       Date:  2002-01       Impact factor: 9.043

2.  High-resolution BAC-based map of the central portion of mouse chromosome 5.

Authors:  J Crabtree; T Wiltshire; B Brunk; S Zhao; J Schug; C J Stoeckert; M Bucan
Journal:  Genome Res       Date:  2001-10       Impact factor: 9.043

3.  Discovery of regulatory elements by a computational method for phylogenetic footprinting.

Authors:  Mathieu Blanchette; Martin Tompa
Journal:  Genome Res       Date:  2002-05       Impact factor: 9.043

Review 4.  The kangaroo genome. Leaps and bounds in comparative genomics.

Authors:  Matthew J Wakefield; Jennifer A Marshall Graves
Journal:  EMBO Rep       Date:  2003-02       Impact factor: 8.807

5.  Identification and characterization of multi-species conserved sequences.

Authors:  Elliott H Margulies; Mathieu Blanchette; David Haussler; Eric D Green
Journal:  Genome Res       Date:  2003-12       Impact factor: 9.043

6.  LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.

Authors:  Michael Brudno; Chuong B Do; Gregory M Cooper; Michael F Kim; Eugene Davydov; Eric D Green; Arend Sidow; Serafim Batzoglou
Journal:  Genome Res       Date:  2003-03-12       Impact factor: 9.043

7.  Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution.

Authors:  Hena Guo; Stephen P Moose
Journal:  Plant Cell       Date:  2003-05       Impact factor: 11.277

8.  Modeling DNA base substitution in large genomic regions from two organisms.

Authors:  Von Bing Yap; Terence P Speed
Journal:  J Mol Evol       Date:  2004-01       Impact factor: 2.395

9.  CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting.

Authors:  Eugene Berezikov; Victor Guryev; Ronald H A Plasterk; Edwin Cuppen
Journal:  Genome Res       Date:  2003-12-12       Impact factor: 9.043

10.  β-Catenin activates the HOXA10 and CDX4 genes in myeloid progenitor cells.

Authors:  Ling Bei; Chirag Shah; Hao Wang; Weiqi Huang; Rupali Roy; Elizabeth A Eklund
Journal:  J Biol Chem       Date:  2012-10-04       Impact factor: 5.157
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