Finding regulatory sequences

DNA regulatory sequences control gene expression by forming DNA-protein complex with specific DNA binding protein. A major task of studies of gene regulation is to identify DNA regulatory sequences in genome-wide. Especially with the rapid pace of genome project, the function of DNA regulatory sequences becomes one of the focuses in functional genome era. Several approaches for screening and characterizing DNA regulatory sequences emerged one by one, from initial low-throughput methods to high-throughput strategies. Even though at present bioinformatics tools facilitate the process of screening regulatory fragments, the most reliable results will come from experimental test. This article highlights some experimental methods for the identification of regulatory sequences. A brief review of the history and procedures for selection methods are provided. Tendency as well as limitation and extension of these methods are also presented.     

Algorithms for isolating regulatory signals in DNA sequences]

An algorithm is proposed for extracting regulatory signals from DNA sequences. The algorithm complexity is nearly quadratic. The results of testing the algorithm on artificial and natural sequences are presented.     

Possible molecular detent in the DNA structure at regulatory sequences

A common feature that appears in a number of DNA sites where proteins interact is the sequence GTG/CAC. In the lac operator this sequence leads to a region with a higher imino proton exchange rate well below the optical melting temperature. It is suggested that this reflects a structural feature recognized by proteins that bind specific sites on the DNA molecule.     

Repetitive plasmid sequences generate DNA fingerprinting patterns in mammals

Bacterial plasmids with stringently regulated copy numbers have directly repeated DNA sequences, termed iterons, in the vicinity of their replication origins. These sequences bind a specific protein exerting a key role in the initiation of plasmid replication. Plasmids P1, pSC101 and RFS1010 have different iteron sequences and belong to three different incompatibility groups. Used as DNA probes each of these plasmids generates specific patterns in mammals similar to those obtained by the DNA fingerprinting technique. The iteron-containing regions were identified as the part of the plasmids responsible for those patterns by using polymerase chain reaction (PCR) amplified DNA segments that contained the iteron regions as probes.     

Investigating extended regulatory regions of genomic DNA sequences.

MOTIVATION: Despite the growing volume of data on primary nucleotide sequences, the regulatory regions remain a major puzzle with regard to their function. Numerous recognising programs considering a diversity of properties of regulatory regions have been developed. The system proposed here allows the specific contextual, conformational and physico-chemical properties to be revealed based on analysis of extended DNA regions. RESULTS: The Internet-accessible computer system RegScan, designed to analyse the extended regulatory regions of eukaryotic genes, has been developed. The computer system comprises the following software: (i) programs for classification dividing a set of promoters into TATA-containing and TATA-less promoters and promoters with and without CpG islands; (ii) programs for constructing (a) nucleotide frequency profiles, (b) sequence complexity profiles and (c) profiles of conformational and physico-chemical properties; (iii) the program for constructing the sets of degenerate oligonucleotide motifs of a specified length; and (iv) the program searching for and visualising repeats in nucleotide sequences. The system has allowed us to demonstrate the following characteristic patterns of vertebrate promoter regions: the TATA box region is flanked by regions with an increased G+C content and increased bending stiffness, the TATA box content is asymmetric and promoter regions are saturated with both direct and inverted repeats. AVAILABILITY: The computer system RegScan is available via the Internet at http://www.mgs.bionet.nsc. ru/Systems/RegScan, http://www.cbil.upenn.edu/mgs/systems/r egscan/.     

pBR322 contains glucocorticoid regulatory element DNA consensus sequences

A computer search of the pBR322 DNA sequence identified five sites matching reported glucocorticoid regulatory element (GRE) DNA consensus sequences and three related sites. A pBR322 DNA fragment containing one GRE site was shown to bind immobilized HeLa S3 cell glucocorticoid receptor and to compete for receptor binding in a competitive binding assay. Conversely, a pBR322 DNA fragment devoid of GRE sites showed barely detectable interaction with glucocorticoid receptor in either of these assays. These results demonstrate the importance of GRE consensus sequences in glucocorticoid receptor interactions with DNA, and further identify a cause for high background binding observed when pBR322 DNA is used as a negative control in studies of glucocorticoid receptor-DNA interactions.     

EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences

Background  

Understanding gene regulatory networks has become one of the central research problems in bioinformatics. More than thirty algorithms have been proposed to identify DNA regulatory sites during the past thirty years. However, the prediction accuracy of these algorithms is still quite low. Ensemble algorithms have emerged as an effective strategy in bioinformatics for improving the prediction accuracy by exploiting the synergetic prediction capability of multiple algorithms.     

Recognition of characteristic patterns in sets of functionally equivalent DNA sequences

An algorithm has been developed for the identification of unknownpatterns which are distinctive for a set of short DNA sequencesbelieved to be functionally equivalent. A pattern is definedas being a string, containing fully or partially specified nucleotidesat each position of the string. The advantage of this ‘vague’definition of the pattern is that it imposes minimum constraintson the characterization of patterns. A new feature of the approachdeveloped here is that it allows a ‘fair’ simultaneoustesting of patterns of all degrees of degeneracy. This analysisis based on an evaluation of inhomogeneity in the empiricaloccurrence distribution of any such pattern within a set ofsequences. The use of the nonparametric kernel density estimationof Parzen allows one to assess small disturbances among thesequence alignments. The method also makes it possible to identifysequence subsets with different characteristic patterns. Thisalgorithm was implemented in the analysis of patterns characteristicof sets of promoters, terminators and splice junction sequences.The results are compared with those obtained by other methods. Received on November 17, 1986; accepted on June 15, 1987     

Finding gene-expression patterns in bacterial biofilms

The production of biofilms by bacteria is a lifestyle that is thought to require or involve a differential gene expression compared with that of planktonic bacteria. Recently, we have witnessed a change of focus from the simple hunt for hypothetical essential biofilm genes to the identification of late and more complex biofilm functions. However, finding common bacterial biofilm gene-expression patterns through global expression analysis remains difficult. Owing to the apparently minimal overlap between functions involved in biofilm formation by different bacteria, exploring the biofilm lifestyle could prove to be a case-by-case task for which global approaches show their limits.     

Polymorphism in regulatory gene sequences

The extensive polymorphism revealed in non-coding gene-regulatory sequences, particularly in the immune system, suggests that this type of genetic variation is functionally and evolutionarily far more important than has been suspected, and provides a lead to new therapeutic strategies.