Vanin genes are clustered (human 6q22-24 and mouse 10A2B1) and encode isoforms of pantetheinase ectoenzymes
Florent MartinFabrice MalergueGiuseppina PitariJean Marc PhilippeSamantha PhilipsClaude ChabretSamuel GranjeaudMarie‐Geneviève MattéiAndrew J. MungallPhilippe NaquetFranck Galland
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This article illustrates the use of the Encyclopedia of DNA Elements (ENCODE) resource to generate or refine hypotheses from genomic data on disease and other phenotypic traits. First, the goals and history of ENCODE and related epigenomics projects are reviewed. Second, the rationale for ENCODE and the major data types used by ENCODE are briefly described, as are some standard heuristics for their interpretation. Third, the use of the ENCODE resource is examined. Standard use cases for ENCODE, accessing the ENCODE resource, and accessing data from related projects are discussed. Although the focus of this article is the use of ENCODE data, some of the same approaches can be used with data from other projects.
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The ENCODE (Encyclopedia of DNA Elements) project, started in 2003, is a consortium of 442 scientists from around the world working together to assign a function to the DNA that does not encode genes. ENCODE used 147 different cell types and many different research techniques to achieve their goal. On September 5, 2012, ENCODE released the initial results of their study. The purpose of this review is to summarize a fraction of ENCODE’s results.
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This chapter contains sections titled: Introduction α Isoforms β Isoforms Physiological Role of Na,K-ATPase Isoforms Duplication and Divergence of α and β Isoform Genes Enzymatic Properties of α and β Isoform Genes Differential Expression of α and β Isoform Genes Non-transport Function of the Na,K-ATPase In Vivo Studies of Differential Isoform Function Gene Knock-out of the β2 Isoform Gene Replacement of the β2 Isoform with β1 Overexpression of the α2 Isoform Gene Knock-out of the α1 and α2 Isoform Genes Model for Differential Function of the α1 Isoform and the α2, α3 and α4 Isoforms Na,K-ATPase Isoforms and Disease Migraine Headache and the α2 Isoform Acknowledgments References
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In its first production phase, The ENCODE Project Consortium (ENCODE) has generated thousands of genome-scale data sets, resulting in a genomic “parts list” that encompasses transcripts, sites of transcription factor binding, and other functional features that now number in the millions of distinct elements. These data are reshaping many long-held beliefs concerning the information content of the human and other complex genomes, including the very definition of the gene. Here I discuss and place in context many of the leading findings of ENCODE, as well as trends that are shaping the generation and interpretation of ENCODE data. Finally, I consider prospects for the future, including maximizing the accuracy, completeness, and utility of ENCODE data for the community.
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A bstract : The Na,K‐ATPase is composed of two subunits, α and β, and each subunit consists of multiple isoforms. In the case of α, four isoforms, α1, α2, α3, and α4 are present in mammalian cells. The distribution of these isoforms is tissue‐ and developmental‐specific, suggesting that they may play specific roles, either during development or coupled to specific physiological processes. In order to understand the functional properties of each of these isoforms, we are using gene targeting, where animals are produced lacking either one copy or both copies of the corresponding gene or have a modified gene. To date, we have produced animals lacking the α1 and α2 isoform genes. Animals lacking both copies of the α1 isoform gene are not viable, while animals lacking both copies of the α2 isoform gene make it to birth, but are either born dead or die very soon after. In the case of animals lacking one copy of the α1 or α2 isoform gene, the animals survive and appear healthy. Heart and EDL muscle from animals lacking one copy of the α2 isoform exhibit an increase in force of contraction, while there is reduced force of contraction in both muscles from animals lacking one copy of the α1 isoform gene. These studies indicate that the α1 and α2 isoforms carry out different physiological roles. The α2 isoform appears to be involved in regulating Ca 2+ transients involved in muscle contraction, while the α1 isoform probably plays a more generalized role. While we have not yet knocked out the α3 or α4 isoform genes, studies to date indicate that the α4 isoform is necessary to maintain sperm motility. It is thus possible that the α2, α3, and α4 isoforms are involved in specialized functions of various tissues, helping to explain their tissue‐ and developmental‐specific regulation.
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A new encode/decode scheme of OCDMA—films encode/decoder is proposed. The principle of films encode/decoder is analyzed. The system structure of films encode/decoder is given. It can also be seen that all optical CDMA encode/decode can be realized by the proposed system of films encode/decoder.At the same time, the OCDMA encode/decoder can be integrated easily.It can also made the access be controlled easily.
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The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in the human and mouse genomes. Data generated by the ENCODE consortium are freely accessible at the ENCODE portal (https://www.encodeproject.org/), which is developed and maintained by the ENCODE Data Coordinating Center (DCC). Since the initial portal release in 2013, the ENCODE DCC has updated the portal to make ENCODE data more findable, accessible, interoperable and reusable. Here, we report on recent updates, including new ENCODE data and assays, ENCODE uniform data processing pipelines, new visualization tools, a dataset cart feature, unrestricted public access to ENCODE data on the cloud (Amazon Web Services open data registry, https://registry.opendata.aws/encode-project/) and more comprehensive tutorials and documentation.
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