1
|
Göttgens B, Barton LM, Gilbert JG, Bench AJ, Sanchez MJ, Bahn S, Mistry S, Grafham D, McMurray A, Vaudin M, Amaya E, Bentley DR, Green AR, Sinclair AM. Analysis of vertebrate SCL loci identifies conserved enhancers. Nat Biotechnol 2000; 18:181-6. [PMID: 10657125 DOI: 10.1038/72635] [Citation(s) in RCA: 140] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 01/26/2023]
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.
Collapse
|
Comparative Study |
25 |
140 |
2
|
Sinclair AM, Göttgens B, Barton LM, Stanley ML, Pardanaud L, Klaine M, Gering M, Bahn S, Sanchez M, Bench AJ, Fordham JL, Bockamp E, Green AR. Distinct 5' SCL enhancers direct transcription to developing brain, spinal cord, and endothelium: neural expression is mediated by GATA factor binding sites. Dev Biol 1999; 209:128-42. [PMID: 10208748 DOI: 10.1006/dbio.1999.9236] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/24/2022]
Abstract
The SCL gene encodes a basic helix-loop-helix transcription factor with a pivotal role in the development of endothelium and of all hematopoietic lineages. SCL is also expressed in the central nervous system, although its expression pattern has not been examined in detail and its function in neural development is unknown. In this article we present the first analysis of SCL transcriptional regulation in vivo. We have identified three spatially distinct regulatory modules, each of which was both necessary and sufficient to direct reporter gene expression in vivo to three different regions within the normal SCL expression domain, namely, developing endothelium, midbrain, and hindbrain/spinal cord. In addition we have demonstrated that GATA factor binding sites are essential for neural expression of the SCL constructs. The midbrain element was particularly powerful and axonal lacZ expression revealed the details of axonal projections, thus implicating SCL in the development of occulomotor, pupillary, or retinotectal pathways. The neural expression pattern of the SCL gene was highly conserved in mouse, chicken, and zebrafish embryos and the 5' region of the chicken SCL locus exhibited a striking degree of functional conservation in transgenic mice. These data suggest that SCL performs critical functions in neural development. The regulatory elements identified here provide important tools for analyzing these functions.
Collapse
|
|
26 |
91 |
3
|
Göttgens B, Barton LM, Chapman MA, Sinclair AM, Knudsen B, Grafham D, Gilbert JGR, Rogers J, Bentley DR, Green AR. Transcriptional regulation of the stem cell leukemia gene (SCL)--comparative analysis of five vertebrate SCL loci. Genome Res 2002; 12:749-59. [PMID: 11997341 PMCID: PMC186570 DOI: 10.1101/gr.45502] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 01/04/2001] [Accepted: 03/19/2002] [Indexed: 12/25/2022]
Abstract
The stem cell leukemia (SCL) gene encodes a bHLH transcription factor with a pivotal role in hematopoiesis and vasculogenesis and a pattern of expression that is highly conserved between mammals and zebrafish. Here we report the isolation and characterization of the zebrafish SCL locus together with the identification of three neighboring genes, IER5, MAP17, and MUPP1. This region spans 68 kb and comprises the longest zebrafish genomic sequence currently available for comparison with mammalian, chicken, and pufferfish sequences. Our data show conserved synteny between zebrafish and mammalian SCL and MAP17 loci, thus suggesting the likely genomic domain necessary for the conserved pattern of SCL expression. Long-range comparative sequence analysis/phylogenetic footprinting was used to identify noncoding conserved sequences representing candidate transcriptional regulatory elements. The SCL promoter/enhancer, exon 1, and the poly(A) region were highly conserved, but no homology to other known mouse SCL enhancers was detected in the zebrafish sequence. A combined homology/structure analysis of the poly(A) region predicted consistent structural features, suggesting a conserved functional role in mRNA regulation. Analysis of the SCL promoter/enhancer revealed five motifs, which were conserved from zebrafish to mammals, and each of which is essential for the appropriate pattern or level of SCL transcription.
Collapse
|
Comparative Study |
23 |
78 |
4
|
Göttgens B, Gilbert JG, Barton LM, Grafham D, Rogers J, Bentley DR, Green AR. Long-range comparison of human and mouse SCL loci: localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences. Genome Res 2001; 11:87-97. [PMID: 11156618 PMCID: PMC311011 DOI: 10.1101/gr.153001] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 06/20/2000] [Accepted: 10/12/2000] [Indexed: 11/24/2022]
Abstract
Long-range comparative sequence analysis provides a powerful strategy for identifying conserved regulatory elements. The stem cell leukemia (SCL) gene encodes a bHLH transcription factor with a pivotal role in hemopoiesis and vasculogenesis, and it displays a highly conserved expression pattern. We present here a detailed sequence comparison of 193 kb of the human SCL locus to 234 kb of the mouse SCL locus. Four new genes have been identified together with an ancient mitochondrial insertion in the human locus. The SCL gene is flanked upstream by the SIL gene and downstream by the MAP17 gene in both species, but the gene order is not collinear downstream from MAP17. To facilitate rapid identification of candidate regulatory elements, we have developed a new sequence analysis tool (SynPlot) that automates the graphical display of large-scale sequence alignments. Unlike existing programs, SynPlot can display the locus features of more than one sequence, thereby indicating the position of homology peaks relative to the structure of all sequences in the alignment. In addition, high-resolution analysis of the chromatin structure of the mouse SCL gene permitted the accurate positioning of localized zones accessible to restriction endonucleases. Zones known to be associated with functional regulatory regions were found to correspond precisely with peaks of human/mouse homology, thus demonstrating that long-range human/mouse sequence comparisons allow accurate prediction of the extent of accessible DNA associated with active regulatory regions.
Collapse
|
Comparative Study |
24 |
72 |
5
|
Göttgens B, Broccardo C, Sanchez MJ, Deveaux S, Murphy G, Göthert JR, Kotsopoulou E, Kinston S, Delaney L, Piltz S, Barton LM, Knezevic K, Erber WN, Begley CG, Frampton J, Green AR. The scl +18/19 stem cell enhancer is not required for hematopoiesis: identification of a 5' bifunctional hematopoietic-endothelial enhancer bound by Fli-1 and Elf-1. Mol Cell Biol 2004; 24:1870-83. [PMID: 14966269 PMCID: PMC350551 DOI: 10.1128/mcb.24.5.1870-1883.2004] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/20/2022] Open
Abstract
Analysis of cis-regulatory elements is central to understanding the genomic program for development. The scl/tal-1 transcription factor is essential for lineage commitment to blood cell formation and previous studies identified an scl enhancer (the +18/19 element) which was sufficient to target the vast majority of hematopoietic stem cells, together with hematopoietic progenitors and endothelium. Moreover, expression of scl under control of the +18/19 enhancer rescued blood progenitor formation in scl(-/-) embryos. However, here we demonstrate by using a knockout approach that, within the endogenous scl locus, the +18/19 enhancer is not necessary for the initiation of scl transcription or for the formation of hematopoietic cells. These results led to the identification of a bifunctional 5' enhancer (-3.8 element), which targets expression to hematopoietic progenitors and endothelium, contains conserved critical Ets sites, and is bound by Ets family transcription factors, including Fli-1 and Elf-1. These data demonstrate that two geographically distinct but functionally related enhancers regulate scl transcription in hematopoietic progenitors and endothelial cells and suggest that enhancers with dual hematopoietic-endothelial activity may represent a general strategy for regulating blood and endothelial development.
Collapse
|
Research Support, Non-U.S. Gov't |
21 |
72 |
6
|
Barton LM, Gottgens B, Gering M, Gilbert JG, Grafham D, Rogers J, Bentley D, Patient R, Green AR. Regulation of the stem cell leukemia (SCL) gene: a tale of two fishes. Proc Natl Acad Sci U S A 2001; 98:6747-52. [PMID: 11381108 PMCID: PMC34424 DOI: 10.1073/pnas.101532998] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 11/07/2000] [Indexed: 11/18/2022] Open
Abstract
The stem cell leukemia (SCL) gene encodes a tissue-specific basic helix-loop-helix (bHLH) protein with a pivotal role in hemopoiesis and vasculogenesis. Several enhancers have been identified within the murine SCL locus that direct reporter gene expression to subdomains of the normal SCL expression pattern, and long-range sequence comparisons of the human and murine SCL loci have identified additional candidate enhancers. To facilitate the characterization of regulatory elements, we have sequenced and analyzed 33 kb of the SCL genomic locus from the pufferfish Fugu rubripes, a species with a highly compact genome. Although the pattern of SCL expression is highly conserved from mammals to teleost fish, the genes flanking pufferfish SCL were unrelated to those known to flank both avian and mammalian SCL genes. These data suggest that SCL regulatory elements are confined to the region between the upstream and downstream flanking genes, a region of 65 kb in human and 8.5 kb in pufferfish. Consistent with this hypothesis, the entire 33-kb pufferfish SCL locus directed appropriate expression to hemopoietic and neural tissue in transgenic zebrafish embryos, as did a 10.4-kb fragment containing the SCL gene and extending to the 5' and 3' flanking genes. These results demonstrate the power of combining the compact genome of the pufferfish with the advantages that zebrafish provide for studies of gene regulation during development. Furthermore, the pufferfish SCL locus provides a powerful tool for the manipulation of hemopoiesis and vasculogenesis in vivo.
Collapse
|
research-article |
24 |
43 |
7
|
Barton LM, Göttgens B, Green AR. The stem cell leukaemia (SCL) gene: a critical regulator of haemopoietic and vascular development. Int J Biochem Cell Biol 1999; 31:1193-207. [PMID: 10582347 DOI: 10.1016/s1357-2725(99)00082-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 01/08/2023]
|
Review |
26 |
13 |
8
|
Göttgens B, Gilbert JG, Barton LM, Aparicio S, Hawker K, Mistry S, Vaudin M, King A, Bentley D, Elgar G, Green AR. The pufferfish SLP-1 gene, a new member of the SCL/TAL-1 family of transcription factors. Genomics 1998; 48:52-62. [PMID: 9503016 DOI: 10.1006/geno.1997.5162] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/24/2022]
Abstract
The SCL/TAL-1 gene encodes a basic helix-loop-helix (bHLH) transcription factor essential for the development of all hemopoietic lineages and also acts as a T-cell oncogene. Four related genes have been described in mammals (LYL-1, TAL-2, NSCL1, and NSCL2), all of which exhibit a high degree of sequence similarity to SCL/TAL-1 in the bHLH domain and two of which (LYL-1 and TAL-2) have also been implicated in the pathogenesis of T-cell acute lymphoblastic leukemia. In this study we describe the identification and characterization of a pufferfish gene termed SLP-1, which represents a new member of this gene family. The genomic structure and sequence of SLP-1 suggests that it forms a subfamily with SCL/TAL-1 and LYL-1 and is most closely related to SCL/TAL-1. However, unlike SCL/TAL-1, SLP-1 is widely expressed. Sequence analysis of a whole cosmid containing SLP-1 shows that SLP-1 is flanked upstream by a zinc finger gene and a fork-head-domain gene and downstream by a heme-oxygenase and a RING finger gene.
Collapse
|
|
27 |
12 |
9
|
Abstract
We describe here Tdr2, a new class of Tc1-like transposons in zebrafish. Tdr2 was identified from the genomic sequence of a zebrafish PAC (P1 artificial chromosome) clone, and fragments of Tdr2 were found in several zebrafish EST (expressed sequence tag) sequences. Predicted translation of the Tdr2 transposase gene showed that it was most closely related to Caenorhabditis elegans Tc3A, suggesting an ancient origin of the Tdr2 transposon. Tdr2 spans 1. 1kb and is flanked by inverted repeats of approx. 100bp. The 5' repeat is itself composed of an inverted repeat, raising the possibility of the formation of a cruciform DNA structure. Tdr2 transposons may facilitate the development of novel transposon-based tools for the genetic analysis of zebrafish.
Collapse
|
|
26 |
11 |
10
|
John C, Reeve NF, Free RC, Williams AT, Ntalla I, Farmaki AE, Bethea J, Barton LM, Shrine N, Batini C, Packer R, Terry S, Hargadon B, Wang Q, Melbourne CA, Adams EL, Bee CE, Harrington K, Miola J, Brunskill NJ, Brightling CE, Barwell J, Wallace SE, Hsu R, Shepherd DJ, Hollox EJ, Wain LV, Tobin MD. Cohort Profile: Extended Cohort for E-health, Environment and DNA (EXCEED). Int J Epidemiol 2019; 48:678-679j. [PMID: 31062032 PMCID: PMC6659362 DOI: 10.1093/ije/dyz073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Accepted: 03/26/2019] [Indexed: 12/22/2022] Open
|
research-article |
6 |
4 |
11
|
John C, Reeve NF, Free RC, Williams AT, Ntalla I, Farmaki AE, Bethea J, Barton LM, Shrine N, Batini C, Packer R, Terry S, Hargadon B, Wang Q, Melbourne CA, Adams EL, Bee CE, Harrington K, Miola J, Brunskill NJ, Brightling CE, Barwell J, Wallace SE, Hsu R, Shepherd DJ, Hollox EJ, Wain LV, Tobin MD. Cohort profile: Extended Cohort for E-health, Environment and DNA (EXCEED). Int J Epidemiol 2019; 48:1734. [PMID: 31365084 PMCID: PMC6857747 DOI: 10.1093/ije/dyz175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/05/2022] Open
|
Published Erratum |
6 |
3 |
12
|
|
Case Reports |
21 |
2 |
13
|
Barton LM, Green AR. Management of resistance to lymphoblastoid interferon alpha in chronic myeloid leukaemia. Br J Haematol 1998; 103:1208-9. [PMID: 9886345 DOI: 10.1046/j.1365-2141.1998.1161c.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/20/2022]
|
Case Reports |
27 |
|