Analysis of vertebrate SCL loci identifies conserved enhancers

Berthold Göttgens; Linda M. Barton; James G R Gilbert; Anthony J. Bench; Maria José Sanchez; Sabine Bahn; Shailesh Mistry; Darren Grafham; Amanda McMurray; Mark Vaudin; Enrique Amaya; David R. Bentley; Anthony R. Green

doi:10.1038/72635

Analysis of vertebrate SCL loci identifies conserved enhancers

Berthold Göttgens, Linda M. Barton, James G R Gilbert, Anthony J. Bench, Maria José Sanchez, Sabine Bahn, Shailesh Mistry, Darren Grafham, Amanda McMurray, Mark Vaudin, Enrique Amaya, David R. Bentley, Anthony R. Green

Research output: Contribution to journal › Article › peer-review

Abstract

The SCL gene encodes a highly conserved bHLH transcription factor with a pivotal role in hemopoiesis and vasculogenesis. We have sequenced and analyzed 320 kb of genomic DNA composing the SCL loci from human, mouse, and chicken. Long-range sequence comparisons demonstrated multiple peaks of human/mouse homology, a subset of which corresponded precisely with known SCL enhancers. Comparisons between mammalian and chicken sequences identified some, but not all, SCL enhancers. Moreover, one peak of human/mouse homology (+23 region), which did not correspond to a known enhancer, showed significant homology to an analogous region of the chicken SCL locus. A transgenic Xenopus reporter assay was established and demonstrated that the +23 region contained a new neural enhancer. This combination of long-range comparative sequence analysis with a high-throughput transgenic bioassay provides a powerful strategy for identifying and characterizing developmentally important enhancers.

Original language	English
Pages (from-to)	181-186
Number of pages	5
Journal	Nature biotechnology
Volume	18
Issue number	2
DOIs	https://doi.org/10.1038/72635
Publication status	Published - Feb 2000

Keywords

Comparative genomics
SCL
Xenopus transgenics

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title = "Analysis of vertebrate SCL loci identifies conserved enhancers",

abstract = "The SCL gene encodes a highly conserved bHLH transcription factor with a pivotal role in hemopoiesis and vasculogenesis. We have sequenced and analyzed 320 kb of genomic DNA composing the SCL loci from human, mouse, and chicken. Long-range sequence comparisons demonstrated multiple peaks of human/mouse homology, a subset of which corresponded precisely with known SCL enhancers. Comparisons between mammalian and chicken sequences identified some, but not all, SCL enhancers. Moreover, one peak of human/mouse homology (+23 region), which did not correspond to a known enhancer, showed significant homology to an analogous region of the chicken SCL locus. A transgenic Xenopus reporter assay was established and demonstrated that the +23 region contained a new neural enhancer. This combination of long-range comparative sequence analysis with a high-throughput transgenic bioassay provides a powerful strategy for identifying and characterizing developmentally important enhancers.",

keywords = "Comparative genomics, SCL, Xenopus transgenics",

author = "Berthold G{\"o}ttgens and Barton, {Linda M.} and Gilbert, {James G R} and Bench, {Anthony J.} and Sanchez, {Maria Jos{\'e}} and Sabine Bahn and Shailesh Mistry and Darren Grafham and Amanda McMurray and Mark Vaudin and Enrique Amaya and Bentley, {David R.} and Green, {Anthony R.}",

year = "2000",

month = feb,

doi = "10.1038/72635",

language = "English",

volume = "18",

pages = "181--186",

journal = "Nature biotechnology",

issn = "1546-1696",

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T1 - Analysis of vertebrate SCL loci identifies conserved enhancers

AU - Göttgens, Berthold

AU - Barton, Linda M.

AU - Gilbert, James G R

AU - Bench, Anthony J.

AU - Sanchez, Maria José

AU - Bahn, Sabine

AU - Mistry, Shailesh

AU - Grafham, Darren

AU - McMurray, Amanda

AU - Vaudin, Mark

AU - Amaya, Enrique

AU - Bentley, David R.

AU - Green, Anthony R.

PY - 2000/2

Y1 - 2000/2

N2 - The SCL gene encodes a highly conserved bHLH transcription factor with a pivotal role in hemopoiesis and vasculogenesis. We have sequenced and analyzed 320 kb of genomic DNA composing the SCL loci from human, mouse, and chicken. Long-range sequence comparisons demonstrated multiple peaks of human/mouse homology, a subset of which corresponded precisely with known SCL enhancers. Comparisons between mammalian and chicken sequences identified some, but not all, SCL enhancers. Moreover, one peak of human/mouse homology (+23 region), which did not correspond to a known enhancer, showed significant homology to an analogous region of the chicken SCL locus. A transgenic Xenopus reporter assay was established and demonstrated that the +23 region contained a new neural enhancer. This combination of long-range comparative sequence analysis with a high-throughput transgenic bioassay provides a powerful strategy for identifying and characterizing developmentally important enhancers.

AB - The SCL gene encodes a highly conserved bHLH transcription factor with a pivotal role in hemopoiesis and vasculogenesis. We have sequenced and analyzed 320 kb of genomic DNA composing the SCL loci from human, mouse, and chicken. Long-range sequence comparisons demonstrated multiple peaks of human/mouse homology, a subset of which corresponded precisely with known SCL enhancers. Comparisons between mammalian and chicken sequences identified some, but not all, SCL enhancers. Moreover, one peak of human/mouse homology (+23 region), which did not correspond to a known enhancer, showed significant homology to an analogous region of the chicken SCL locus. A transgenic Xenopus reporter assay was established and demonstrated that the +23 region contained a new neural enhancer. This combination of long-range comparative sequence analysis with a high-throughput transgenic bioassay provides a powerful strategy for identifying and characterizing developmentally important enhancers.

KW - Comparative genomics

KW - SCL

KW - Xenopus transgenics

U2 - 10.1038/72635

DO - 10.1038/72635

M3 - Article

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SN - 1546-1696

VL - 18

SP - 181

EP - 186

JO - Nature biotechnology

JF - Nature biotechnology

IS - 2

ER -

Analysis of vertebrate SCL loci identifies conserved enhancers

Abstract

Keywords

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