A study of the distribution of phylogenetically conserved blocks within clusters of mammalian homeobox genes

Abstract

Genome sequencing efforts of the last decade have produced a large amount of data, which has enabled whole-genome comparative analyses in order to locate potentially functional elements and study the overall patterns of phylogenetic conservation. In this paper we present a statistically based method for the characterization of these patterns in mammalian DNA sequences. We have applied this approach to the study of exceptionally well conserved homeobox gene clusters (Hox), based on an alignment of six species, and we have constructed a map of Hox cataloguing the conserved fragments, along with their locations in relation to the genes and other landmarks, sometimes showing unexpected layouts.

HLA Class I and II profiles in São Miguel Island (Azores): genetic diversity and linkage disequilibrium

“…The HLA data reported by Meyer et al [ 27 ] indicate a significant LD between all HLA loci in around 40 worldwide studied populations. The present research did not indicate large D' values and corroborates the results obtained by Service et al [ 28 ] and Branco et al [ 9 , 10 ], where the Azoreans have the lowest values of LD when compared with isolated and outbred populations.…”

“…These genetic data are crucial for the comprehension of the molecular ethiology and epidemiology of common diseases. In general, the data here presented corroborate previous works [ 3 , 6 - 10 ], where Azoreans including São Miguel islanders show high values of genetic diversity when compared to mainland Portugal and other European populations. This may be a direct consequence of the Azorean settlement, with a major contribution of mainland Portuguese (~60%) and, to a lesser extent, Flemish, Spanish, French, Italians, Germans, Scottish, Jews, Moors and blacks from Guinea, Cabo Verde and São Tomé.…”

“…São Miguel is the largest island of the Azores and is composed of 131,609 inhabitants (2001 Census, Portugal National Institute of Statistics). Several studies have been performed to characterize the genetic pool of the Azoreans [ 2 - 10 ]. These studies report a high genetic variability and heterogeneity of the Azorean population, explained by the settling history of the islands, where a major contribution of mainland Portugal individuals is evident.…”

Linear--Time Matching of Position Weight Matrices

“…Eukaryotic genes are generally regulated in complex ways, through networks of protein-DNA and protein-protein interactions, which direct chromatin remodeling, histone modifications, formation of transcriptional initiation complexes and RNA Polymerase elongation. The prevailing opinion, corroborated by some studies (Khambata-Ford et al, 2003;Young et al, 2003) but being increasingly questioned (Nelson et al, 2004;The ENCODE Project Consortium, 2007;Stojanovic, 2009) is that most of these interactions take place within a few hundred bases upstream of the transcription start sites. Even as regions important for the regulation of genes have been found at distal loci, around alternative first exons, in introns and sequences located downstream of the transcription start sites or even genes themselves, core promoter sites are still considered the most important for the gene expression.…”