Localization of the horse (&lt;i&gt;Equus caballu&lt;/i&gt;&lt;i&gt;s&lt;/i&gt;) α-globin gene complex to chromosome 13 by luorescence in situ hybridization

Oakenfull, E. Ann; Buckle, Veronica J.; Clegg, J. B.

doi:10.1159/000133456

Cited by 16 publications

(5 citation statements)

References 8 publications

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“…It has been shown previously that the α globin clusters of several species (e.g. man, rabbit and horse), lie in a telomeric position (18)(19)(20). In man, the α cluster commonly lies only 150 kb from the 16p telomere (allele A) (18).…”

Section: Overall Comparison Of the Extended Sequencesmentioning

confidence: 99%

Comparative genome analysis delimits a chromosomal domain and identifies key regulatory elements in the alpha globin cluster

Flint

Tufarelli

Peden

et al. 2001

Human Molecular Genetics

154

149

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We have cloned, sequenced and annotated segments of DNA spanning the mouse, chicken and pufferfish alpha globin gene clusters and compared them with the corresponding region in man. This has defined a small segment ( approximately 135-155 kb) of synteny and conserved gene order, which may contain all of the elements required to fully regulate alpha globin gene expression from its natural chromosomal environment. Comparing human and mouse sequences using previously described methods failed to identify the known regulatory elements. However, refining these methods by ranking identity scores of non-coding sequences, we found conserved sequences including the previously characterized alpha globin major regulatory element. In chicken and pufferfish, regions that may correspond to this element were found by analysing the distribution of transcription factor binding sites. Regions identified in this way act as strong enhancer elements in expression assays. In addition to delimiting the alpha globin chromosomal domain, this study has enabled us to develop a more sensitive and accurate routine for identifying regulatory elements in the human genome.

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Section: Overall Comparison Of the Extended Sequencesmentioning

confidence: 99%

Comparative genome analysis delimits a chromosomal domain and identifies key regulatory elements in the alpha globin cluster

Flint

Tufarelli

Peden

et al. 2001

Human Molecular Genetics

154

149

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“…The ␣-globin cluster in the rabbit (24) and horse (25) are also known to lie close to telomeric regions. Here, we found telomeric repeats upstream of the ␣ cluster in 8 of 16 species analyzed, suggesting that, in many species, it is located or originated close to a telomere; a clear exception occurs in the mouse and rat clusters, which contain no telomeric repeats and lie at interstitial chromosomal locations (26,27).…”

Section: A Region Of Conserved Synteny Maintained Throughout 500 My Ofmentioning

confidence: 99%

Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences

Hughes

Cheng

Ventress

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

135

130

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An important step toward improving the annotation of the human genome is to identify cis-acting regulatory elements from primary DNA sequence. One approach is to compare sequences from multiple, divergent species. This approach distinguishes multispecies conserved sequences (MCS) in noncoding regions from more rapidly evolving neutral DNA. Here, we have analyzed a region of Ϸ238kb containing the human ␣ globin cluster that was sequenced and͞or annotated across the syntenic region in 22 species spanning 500 million years of evolution. Using a variety of bioinformatic approaches and correlating the results with many aspects of chromosome structure and function in this region, we were able to identify and evaluate the importance of 24 individual MCSs. This approach sensitively and accurately identified previously characterized regulatory elements but also discovered unidentified promoters, exons, splicing, and transcriptional regulatory elements. Together, these studies demonstrate an integrated approach by which to identify, subclassify, and predict the potential importance of MCSs.conserved noncoding elements ͉ gene regulation ͉ globin gene ͉ comparative genomics W ith the development of multiple computational algorithms and appropriate biological data, it is now possible to detect coding sequences relatively efficiently and accurately from primary DNA sequence (1). By contrast, it is still difficult to identify and assign function to noncoding sequences that include critical cisacting regulatory elements such as promoters, enhancers, silencers, locus control elements, nuclear matrix attachment sites, and origins of replication. A promising approach is to search for conserved orthologous noncoding sequences from multiple, evolutionarily diverse species (2-8), so-called multispecies conserved sequences (MCSs). However, at present, it is not established how best to design and carry out such searches. Furthermore, even when complete, it is not clear how to evaluate and prioritize MCSs for functional analysis.An important issue is to know which species to include in searches for MCSs. When comparing the sequences of distantly related species [e.g., birds and mammals, which diverged 310 million years (my) ago], cis elements may have diverged too much to be easily identified. By contrast, when comparing more closely related species (e.g., rodents and primates, which diverged 64-74 my ago), it may be difficult to distinguish between sequence homology resulting from a slow rate of evolution and the conservation of functionally important cis elements. Nevertheless, it is becoming clear that analyzing multiple species in different combinations adds significant power to the identification of functionally important cis-acting sequences (2, 3).Even when MCS can be unequivocally identified, there is often no way to judge how sensitive the searches have been. Do these routines overcall or undercall regulatory elements? Furthermore, the true functional significance of MCSs often remains untested and͞or unknown because there is u...

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“…Since mid-1990s (Oakenfull et al 1993, Godard et al 1997, 1998, Raudsepp et al 1999), FISH has been the primary approach used to map gene-specific and microsatellite markers in the horse (Godard et al 2000, Lear et al 2001, Lindgren et al 2001, 2002a,b, Chowdhary et al 2002, 2003, Milenkovic et al 2002, Brinkmeyer-Langford et al 2005, GustafsonSeabury et al 2005, Perrocheau et al 2005). The availability of the CHORI-241 BAC library and the isolation of BAC clones for a large assortment of loci have been instrumental in facilitating their chromosomal localizations.…”

Section: Cytogenetic Mapmentioning

confidence: 99%

The Horse Genome Derby: racing from map to whole genome sequence

Chowdhary

Raudsepp

2008

Chromosome Res

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The map of the horse genome has undergone unprecedented expansion during the past six years. Beginning from a modest collection of approximately 300 mapped markers scattered on the 31 pairs of autosomes and the X chromosome in 2001, today the horse genome is among the best-mapped in domestic animals. Presently, high-resolution linearly ordered gene maps are available for all autosomes as well as the X and the Y chromosome. The approximately 4350 mapped markers distributed over the approximately 2.68 Gbp long equine genome provide on average 1 marker every 620 kb. Among the most remarkable developments in equine genome analysis is the availability of the assembled sequence (EquCab2) of the female horse genome and the generation approximately 1.5 million single nucleotide polymorphisms (SNPs) from diverse breeds. This has triggered the creation of new tools and resources like the 60K SNP-chip and whole genome expression microarrays that hold promise to study the equine genome and transcriptome in ways not previously envisaged. As a result of these developments it is anticipated that, during coming years, the genetics underlying important monogenic traits will be analyzed with improved accuracy and speed. Of larger interest will be the prospects of dissecting the genetic component of various complex/multigenic traits that are of vital significance for equine health and welfare. The number of investigations recently initiated to study a multitude of such traits hold promise for improved diagnostics, prevention and therapeutic approaches for horses.

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Localization of the horse (<i>Equus caballu</i><i>s</i>) α-globin gene complex to chromosome 13 by luorescence in situ hybridization

Abstract: The α-globin gene complex in Equus caballus has been mapped by fluorescence in situ hybridization to the telomeric region of the long arm of chromosome 13. This is the first equine gene to be mapped to this chromosome.

Cited by 16 publications

References 8 publications

Comparative genome analysis delimits a chromosomal domain and identifies key regulatory elements in the alpha globin cluster

Comparative genome analysis delimits a chromosomal domain and identifies key regulatory elements in the alpha globin cluster

Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences

The Horse Genome Derby: racing from map to whole genome sequence

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