13 research outputs found
Discovering sequences with potential regulatory characteristics
AbstractWe developed a computational model to explore the hypothesis that regulatory instructions are context dependent and conveyed through specific ‘codes’ in human genomic DNA. We provide examples of correlation of computational predictions to reported mapped DNase I hypersensitive segments in the HOXA locus in human chromosome 7. The examples show that statistically significant 9-mers from promoter regions may occur in sequences near and upstream of transcription initiation sites, in intronic regions, and within intergenic regions. Additionally, a subset of 9-mers from coding sequences appears frequently, as clusters, in regulatory regions dispersed in noncoding regions in genomic DNA. The results suggest that the computational model has the potential of decoding regulatory instructions to discover candidate transcription factor binding sites and to discover candidate epigenetic signals that appear in both coding and regulatory regions of genes
Gene regulation : methods and protocols / edited by Minou Bina.
Includes bibliographical references and index.xv, 401 p.
DNA Sequencing Strategies: Automated and Advanced Approaches Edited by Wilhelm Ansorge, Hartmut Voss, and Jürgen Zimmermann (EMBL, Heidelberg). Wiley: New York. 1996. xiv + 202 pp. $39.95. ISBN 0-471-13683-2.
Datasets on The Genomic Positions of The MLL1 Morphemes, The ZFP57 Binding Site, and ZFBS-Morph Overlaps in The Build mm9 of The Mouse Genome
While MLL1 activates gene expression in most tissues, ZFP57 represses transcription. MLL1 selectively interacts with a group of nonmethylated DNA sequences known as the MLL1 morphemes. ZFP57 associates with a methylated hexamer (ZFBS), dispersed in the genomic DNA segments known as Imprinted Control Regions (ICRs) and germline Differentially Methylated Regions (gDMRs), to maintain allele-specific gene repression. We have identified a set of composite DNA elements (ZFBS-Morph overlaps) that provides the sequence context of ZFBS in the canonical ICRs/gDMRs. This report provides tables listing the nucleotide sequences of the MLL1 morphemes and ZFBS-Morph overlaps. The report also offers links to the data repository at Purdue University, for downloading the positions of the MLL1 morphemes, the ZFP57 binding site, and the ZFBS-Morph overlaps in the mouse genome