Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome.

Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome. Research Abstract Details 

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Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome. Abstract Text:

Shaun Mahony,David L Corcoran,Eleanor Feingold,Panayiotis V Benos,

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. RESULTS: Analysis of 145 intergenic microRNA and all protein coding genes revealed that the upstream sequences of the former are up to twice as conserved as the latter among mammals, except in the first 500 base pairs, where the conservation is similar. Comparison of promoter conservation in 513 protein coding genes and related transcription factor binding sites (TFBSs) showed that 41% of the known human TFBSs are located in the 6.7% of promoter regions that are conserved between human and opossum. Some core biologic processes exhibited significantly fewer conserved TFBSs in human-opossum comparisons, suggesting greater functional divergence. A new measure of efficiency in multigenome phylogenetic footprinting (base regulatory potential rate [BRPR]) shows that including human-opossum conservation increases specificity in finding human TFBSs. CONCLUSION: Opossum facilitates better estimation of promoter conservation and TFBS turnover among mammals. The fact that substantial TFBS numbers are located in a small proportion of the human-opossum conserved sequences emphasizes the importance of marsupial genomes for phylogenetic footprinting-based motif discovery strategies. The BRPR measure is expected to help select genome combinations for optimal performance of these algorithms. Finally, although the etiology of the microRNA upstream increased conservation remains unknown, it is expected to have strong implications for our understanding of regulation of their expression.

Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome. Publishing Authors By Initials

S Mahony,DL Corcoran,E Feingold,PV Benos,

For similar animals: chordata: vertebrates research abstracts see: animals: chordata: vertebrates research

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Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Genome biology

VOLUME: 8

Page Numbers: R84

Journal Abbreviation: Genome Biol.

ISSN: 1465-6914

DAY: 3

MONTH: 12

YEAR: 2007

Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome. Information

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LANGUAGE: eng

NlmUniqueID: 100960660

Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome. Keywords Mesh Terms:

KEYWORDS: Vertebrates

MESH TERMS: metabolism

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Substance Name: Transcription Factors

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Grant and Affiliation Information for Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome.

AFFILIATION: Department of Computational Biology, School of Medicine, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15260, USA. shaun.mahony@ccbb.pitt.edu

Country: England

AGENCY: United States NCRR

GRANT: RR014214

ACRONYM: RR

MEDLINETA: Genome Biol

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