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      The BAH (bromo-adjacent homology) domain: a link between DNA methylation, replication and transcriptional regulation

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      FEBS Letters
      Elsevier BV

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          Abstract

          Using sensitive methods of sequence analysis including hydrophobic cluster analysis, we report here a hitherto undescribed family of modules, the BAH (bromo-adjacent homology) family, which includes proteins such as eukaryotic DNA (cytosine-5) methyltransferases, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation. The BAH domain appears to act as a protein-protein interaction module specialized in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation.

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          Most cited references33

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          Prediction of protein secondary structure at better than 70% accuracy.

          We have trained a two-layered feed-forward neural network on a non-redundant data base of 130 protein chains to predict the secondary structure of water-soluble proteins. A new key aspect is the use of evolutionary information in the form of multiple sequence alignments that are used as input in place of single sequences. The inclusion of protein family information in this form increases the prediction accuracy by six to eight percentage points. A combination of three levels of networks results in an overall three-state accuracy of 70.8% for globular proteins (sustained performance). If four membrane protein chains are included in the evaluation, the overall accuracy drops to 70.2%. The prediction is well balanced between alpha-helix, beta-strand and loop: 65% of the observed strand residues are predicted correctly. The accuracy in predicting the content of three secondary structure types is comparable to that of circular dichroism spectroscopy. The performance accuracy is verified by a sevenfold cross-validation test, and an additional test on 26 recently solved proteins. Of particular practical importance is the definition of a position-specific reliability index. For half of the residues predicted with a high level of reliability the overall accuracy increases to better than 82%. A further strength of the method is the more realistic prediction of segment length. The protein family prediction method is available for testing by academic researchers via an electronic mail server.
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            A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei.

            Tissue-specific patterns of methylated deoxycytidine residues in the mammalian genome are preserved by postreplicative methylation of newly synthesized DNA. DNA methyltransferase (MTase) is here shown to associate with replication foci during S phase but to display a diffuse nucleoplasmic distribution in non-S phase cells. Analysis of DNA MTase-beta-galactosidase fusion proteins has shown that association with replication foci is mediated by a novel targeting sequence located near the N-terminus of DNA MTase. This sequence has the properties expected of a targeting sequence in that it is not required for enzymatic activity, prevents proper targeting when deleted, and, when fused to beta-galactosidase, causes the fusion protein to associate with replication foci in a cell cycle-dependent manner.
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              Hidden Markov models

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                Author and article information

                Journal
                FEBS Letters
                Elsevier BV
                00145793
                March 05 1999
                March 05 1999
                March 15 1999
                : 446
                : 1
                : 189-193
                Article
                10.1016/S0014-5793(99)00132-5
                10100640
                16674d9f-a921-4d8e-aa9a-0d365720b9fe
                © 1999

                http://doi.wiley.com/10.1002/tdm_license_1.1

                http://onlinelibrary.wiley.com/termsAndConditions#vor

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