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Comparative genomics using <Emphasis Type="Italic">Fugu</Emphasis> reveals insights into regulatory subfunctionalization 下载免费PDF全文
Background
A major mechanism for the preservation of gene duplicates in the genome is thought to be mediated via loss or modification of cis-regulatory subfunctions between paralogs following duplication (a process known as regulatory subfunctionalization). Despite a number of gene expression studies that support this mechanism, no comprehensive analysis of regulatory subfunctionalization has been undertaken at the level of the distal cis-regulatory modules involved. We have exploited fish-mammal genomic alignments to identify and compare more than 800 conserved non-coding elements (CNEs) that associate with genes that have undergone fish-specific duplication and retention. 相似文献2.
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Background
Embryonic development is coordinated by sets of cis-regulatory elements that are collectively responsible for the precise spatio-temporal organization of regulatory gene networks. There is little information on how these elements, which are often associated with highly conserved noncoding sequences, are combined to generate precise gene expression patterns in vertebrates. To address this issue, we have focused on Six3, an important regulator of vertebrate forebrain development. 相似文献4.
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Ryan B MacDonald Mélanie Debiais-Thibaud Kyle Martin Luc Poitras Boon-Hui Tay Byrappa Venkatesh Marc Ekker 《BMC evolutionary biology》2010,10(1):157
Background
The phylogenetic position of the elephant shark (Callorhinchus milii ) is particularly relevant to study the evolution of genes and gene regulation in vertebrates. Here we examine the evolution of Dlx homeobox gene regulation during vertebrate embryonic development with a particular focus on the forebrain. We first identified the elephant shark sequence orthologous to the URE2 cis -regulatory element of the mouse Dlx1/Dlx2 locus (herein named CmURE2). We then conducted a comparative study of the sequence and enhancer activity of CmURE2 with that of orthologous regulatory sequences from zebrafish and mouse. 相似文献8.
Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome 总被引:1,自引:0,他引:1
Background
Being the first noneutherian mammal sequenced, Monodelphis domestica (opossum) offers great potential for enhancing our understanding of the evolutionary processes that take place in mammals. This study focuses on the evolutionary relationships between conservation of noncoding sequences, cis-regulatory elements, and biologic functions of regulated genes in opossum and eight vertebrate species. 相似文献9.
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Background
Cis-regulatory modules are combinations of regulatory elements occurring in close proximity to each other that control the spatial and temporal expression of genes. The ability to identify them in a genome-wide manner depends on the availability of accurate models and of search methods able to detect putative regulatory elements with enhanced sensitivity and specificity. 相似文献11.
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Anna Pistocchi Germano Gaudenzi Silvia Carra Erica Bresciani Luca Del Giacco Franco Cotelli 《BMC developmental biology》2008,8(1):27
Background
Prox1, the vertebrate homolog of prospero in Drosophila melanogaster, is a divergent homeogene that regulates cell proliferation, fate determination and differentiation during vertebrate embryonic development. 相似文献14.
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Koji Doi Aeni Hosaka Toshifumi Nagata Kouji Satoh Kohji Suzuki Ramil Mauleon Michael J Mendoza Richard Bruskiewich Shoshi Kikuchi 《BMC plant biology》2008,8(1):20
Background
Information on more than 35 000 full-length Oryza sativa cDNAs, together with associated microarray gene expression data collected under various treatment conditions, has made it feasible to identify motifs that are conserved in gene promoters and may act as cis-regulatory elements with key roles under the various conditions. 相似文献16.
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Background
For the purposes of finding and aligning noncoding RNA gene- and cis-regulatory elements in multiple-genome datasets, it is useful to be able to derive multi-sequence stochastic grammars (and hence multiple alignment algorithms) systematically, starting from hypotheses about the various kinds of random mutation event and their rates. 相似文献20.