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Reads - a Resource for Plant Non-coding Regulatory Sequence Analysis

Saima Shahid
Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka

Sabrina M. Elias
Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka

Sudip Biswas
Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka

Zeba I. Seraj
Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka

Abstract/ Executive Summary:

Identification and analysis of regulatory sequences that control gene expression can be greatly facilitated by database‐assisted bioinformatic approaches. READS (Regulatory Element Analysis Database) has been created as a web‐accessible freely available database of plant non‐coding regulatory sequences. It currently contains more than 300 known and putative promoters of constitutive as well as stress inducible genes belonging to diverse plants. The database has been manually curated with promoters collected mainly from scientific publications, thereafter cross‐referenced with other resources (NCBI database, PubMed, PubMed Central). A user‐friendly interface has been provided to allow easy access and analysis of data using different query options. A blast utility has also been provided, allowing users to search against all entries in the database. For each promoter, certain features such as expression data, GC content, core elements etc., were provided to assist in characterization of the regulatory sequences. To our knowledge, READS is the first plant promoter database that allows retrieval of sequences based on expression pattern. Thus the database can be utilized as a useful resource for identification of important putative regulatory cis‐elements in promoters by analysis of upstream regions of hundreds of coregulated or co‐expressed genes. Such knowledge can also be of use for identifying minimal or stress inducible promoters for effective transgene expression. We aim to provide the most up‐to‐date collection of promoters of well‐characterized stress inducible and constitutively expressed genes from many plant species. Hence, this resource will be updated regularly to incorporate new sequences. READs is available at http://www.pbtlabdu.net/READS/.

Keywords: Promoter database, Stress inducible, Constitutive, Gene expression, Cis-element

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Start Date:

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Program Area: Knowledge Management

Non-commodity: Performance

Objectives:

It is therefore highly desirable to build a more comprehensive plant promoter database for in silico analysis of regulatory elements and functional genomics research. There is also a great need for resources that will allow promoter mining from halophytes, which can survive in extreme conditions. READS has been developed as an attempt to address such challenges.

Methodology:

The majority of the data provided by READS has been curated manually. Stress inducible and constitutive genes were identified primarily through literature mining and available microarray expression data analysis. Differentially expressed genes in cold, drought, salinity stresses and abscisic acid application have been identified previously in rice using cDNA microarray and RNA gelblot analysis (Rabbani et al. 2003). In a more recent rice whole genome oligomer microarray experiment, drought and high salinity responsive genes in different organs were reported (Zhou et al. 2007). Data from these experiments were downloaded, and genes corresponding to stress responsive cDNA clones were identified by matching each cDNA sequence to a O. sativa cv. Japonica locus (MSU6 assembly), using the BLASTn search tool provided at the GRAMENE database (Liang et al. 2008). Information regarding the constitutive rice genes was obtained from a recently published report (Jiao et al. 2009), in which microarray experiments for 40 different cell types were performed. Briefly, putative constitutive genes were identified through statistical analysis (Lee et al. 2007) of microarray expression data based on the following criteria: (i) Ubiquitous expression and no more than two cell‐type nulls, and (ii) uniform expression and a difference between the highest third and lowest third of log‐transformed normalized value of < 2 (Jiao et al. 2009). Finally, promoter regions of all the stress‐inducible/constitutive rice genes (1 kbp upstream of the translational start site) were extracted, using the bulk data retrieval tool available at OryGenesDB (Droc et al. 2006). Experimentally characterized individual promoter sequences from rice landraces, barley and halophyte species with stress specific expression pattern reported in scientific literatures were extracted by searching the NCBI nucleotide database with corresponding GenBank accessions. Several promoters from salt tolerant rice landraces that have been characterized in the Plant Biotechnology Lab., University of Dhaka and whose sequences have been deposited at GenBank also constituted a part of the final dataset.

Source of Information: Plant Tissue Cult. & Biotech. 20(2): 211-223, 2010 (December)

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Achievement/Findings:

READS has also been developed to mine non‐coding regulatory sequences from halophytes, which can survive and grow in extreme conditions. To‐date, there is no publicly available promoter database for such purpose. Analysis of the regulatory regions of halophytes can be particularly significant to understand the dynamics of gene regulation in such organism and engineer crop plants tolerant to harsh environments. As genome sequences for halophytes are not available yet, the promoter data from such species in the current release of READS is limited. Nevertheless, continued efforts will be made to update the promoter sequences and expression data and other useful information. In future, promoters from additional plant species as well as tools for analyzing the data will be provided to enhance utility of the resource at READS. The manual curation section of the READS will also be made accessible to the community to enable improved annotation of non‐regulatory sequence

Knowledge Management: Journal