Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage

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Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage. / Sanges, Remo; Kalmar, Eva; Claudiani, Pamela; D'Amato, Maria; Muller, Ferenc; Stupka, Elia.

In: Genome Biol, Vol. 7, No. 7, 2006, p. R56.

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Sanges, Remo ; Kalmar, Eva ; Claudiani, Pamela ; D'Amato, Maria ; Muller, Ferenc ; Stupka, Elia. / Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage. In: Genome Biol. 2006 ; Vol. 7, No. 7. pp. R56.

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@article{016de24be7cc437b93b169dde9564f01,
title = "Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage",
abstract = "BACKGROUND: All vertebrates share a remarkable degree of similarity in their development as well as in the basic functions of their cells. Despite this, attempts at unearthing genome-wide regulatory elements conserved throughout the vertebrate lineage using BLAST-like approaches have thus far detected noncoding conservation in only a few hundred genes, mostly associated with regulation of transcription and development.RESULTS: We used a unique combination of tools to obtain regional global-local alignments of orthologous loci. This approach takes into account shuffling of regulatory regions that are likely to occur over evolutionary distances greater than those separating mammalian genomes. This approach revealed one order of magnitude more vertebrate conserved elements than was previously reported in over 2,000 genes, including a high number of genes found in the membrane and extracellular regions. Our analysis revealed that 72% of the elements identified have undergone shuffling. We tested the ability of the elements identified to enhance transcription in zebrafish embryos and compared their activity with a set of control fragments. We found that more than 80% of the elements tested were able to enhance transcription significantly, prevalently in a tissue-restricted manner corresponding to the expression domain of the neighboring gene.CONCLUSION: Our work elucidates the importance of shuffling in the detection of cis-regulatory elements. It also elucidates how similarities across the vertebrate lineage, which go well beyond development, can be explained not only within the realm of coding genes but also in that of the sequences that ultimately govern their expression.",
keywords = "Algorithms, Animals, Enhancer Elements, Genetic, Evolution, Molecular, Promoter Regions, Genetic, Regulatory Sequences, Nucleic Acid, Sister Chromatid Exchange, Vertebrates, Zebrafish",
author = "Remo Sanges and Eva Kalmar and Pamela Claudiani and Maria D'Amato and Ferenc Muller and Elia Stupka",
year = "2006",
doi = "10.1186/gb-2006-7-7-r56",
language = "English",
volume = "7",
pages = "R56",
journal = "Genome Biology",
issn = "1474-7596",
publisher = "BioMed Central",
number = "7",

}

RIS

TY - JOUR

T1 - Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage

AU - Sanges, Remo

AU - Kalmar, Eva

AU - Claudiani, Pamela

AU - D'Amato, Maria

AU - Muller, Ferenc

AU - Stupka, Elia

PY - 2006

Y1 - 2006

N2 - BACKGROUND: All vertebrates share a remarkable degree of similarity in their development as well as in the basic functions of their cells. Despite this, attempts at unearthing genome-wide regulatory elements conserved throughout the vertebrate lineage using BLAST-like approaches have thus far detected noncoding conservation in only a few hundred genes, mostly associated with regulation of transcription and development.RESULTS: We used a unique combination of tools to obtain regional global-local alignments of orthologous loci. This approach takes into account shuffling of regulatory regions that are likely to occur over evolutionary distances greater than those separating mammalian genomes. This approach revealed one order of magnitude more vertebrate conserved elements than was previously reported in over 2,000 genes, including a high number of genes found in the membrane and extracellular regions. Our analysis revealed that 72% of the elements identified have undergone shuffling. We tested the ability of the elements identified to enhance transcription in zebrafish embryos and compared their activity with a set of control fragments. We found that more than 80% of the elements tested were able to enhance transcription significantly, prevalently in a tissue-restricted manner corresponding to the expression domain of the neighboring gene.CONCLUSION: Our work elucidates the importance of shuffling in the detection of cis-regulatory elements. It also elucidates how similarities across the vertebrate lineage, which go well beyond development, can be explained not only within the realm of coding genes but also in that of the sequences that ultimately govern their expression.

AB - BACKGROUND: All vertebrates share a remarkable degree of similarity in their development as well as in the basic functions of their cells. Despite this, attempts at unearthing genome-wide regulatory elements conserved throughout the vertebrate lineage using BLAST-like approaches have thus far detected noncoding conservation in only a few hundred genes, mostly associated with regulation of transcription and development.RESULTS: We used a unique combination of tools to obtain regional global-local alignments of orthologous loci. This approach takes into account shuffling of regulatory regions that are likely to occur over evolutionary distances greater than those separating mammalian genomes. This approach revealed one order of magnitude more vertebrate conserved elements than was previously reported in over 2,000 genes, including a high number of genes found in the membrane and extracellular regions. Our analysis revealed that 72% of the elements identified have undergone shuffling. We tested the ability of the elements identified to enhance transcription in zebrafish embryos and compared their activity with a set of control fragments. We found that more than 80% of the elements tested were able to enhance transcription significantly, prevalently in a tissue-restricted manner corresponding to the expression domain of the neighboring gene.CONCLUSION: Our work elucidates the importance of shuffling in the detection of cis-regulatory elements. It also elucidates how similarities across the vertebrate lineage, which go well beyond development, can be explained not only within the realm of coding genes but also in that of the sequences that ultimately govern their expression.

KW - Algorithms

KW - Animals

KW - Enhancer Elements, Genetic

KW - Evolution, Molecular

KW - Promoter Regions, Genetic

KW - Regulatory Sequences, Nucleic Acid

KW - Sister Chromatid Exchange

KW - Vertebrates

KW - Zebrafish

U2 - 10.1186/gb-2006-7-7-r56

DO - 10.1186/gb-2006-7-7-r56

M3 - Article

C2 - 16859531

VL - 7

SP - R56

JO - Genome Biology

JF - Genome Biology

SN - 1474-7596

IS - 7

ER -