K-SPMM: a database of murine spermatogenic promoters modules & motifs

Abstract

Background: Understanding the regulatory processes that coordinate the cascade of gene expression leading to male gamete development has proven challenging. Research has been hindered in part by an incomplete picture of the regulatory elements that are both characteristic of and distinctive to the broad population of spermatogenically expressed genes.

Description: K-SPMM, a database of murine Spermatogenic Promoters Modules and Motifs, has been developed as a web-based resource for the comparative analysis of promoter regions and their constituent elements in developing male germ cells. The system contains data on 7,551 genes and 11,715 putative promoter regions in Sertoli cells, spermatogonia, spermatocytes and spermatids. K-SPMM provides a detailed portrait of promoter site components, ranging from broad distributions of transcription factor binding sites to graphical illustrations of dimeric modules with respect to individual transcription start sites. Binding sites are identified through their similarities to position weight matrices catalogued in either the JASPAR or the TRANSFAC transcription factor archives. A flexible search function allows sub-populations of promoters to be identified on the basis of their presence in any of the four cell-types, their association with a list of genes or their component transcription-factor families.

Conclusion: This system can now be used independently or in conjunction with other databases of gene expression as a powerful aid to research networks of co-regulation. We illustrate this with respect to the spermiogenically active protamine locus in which binding sites are predicted that align well with biologically foot-printed protein binding domains.

Availability: http://klab.med.wayne.edu/kspmm/

Figure 1

The system user-interface design. Panels [A-H] show the data available through a typical search strategy.

Figure 2

The module output for the promoter region of Protamine 2. The graphical output for Transfac PWMs is shown above the graphical and tabular output for JASPAR in which one potential binding domain has been highlighted. Regions noted as 1–5 have been added and correspond to the location of in vitro protected foot-printed sites proximate to the TSS [23]. An alternate representation of sequence conservation within the domain has been included from the vertebrate conservation track from the UCSC Genome Browser. This illustrates more fully the extent of alignment between conserved nucleotides and the predicted binding sequences, as such it is similar to the conservation data tabulated for four comparator species in the evidence table.