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BLSSpeller to discover novel regulatory motifs in maize.

ABSTRACT: With the decreasing cost of sequencing and availability of larger numbers of sequenced genomes, comparative genomics is becoming increasingly attractive to complement experimental techniques for the task of transcription factor (TF) binding site identification. In this study, we redesigned BLSSpeller, a motif discovery algorithm, to cope with larger sequence datasets. BLSSpeller was used to identify novel motifs in Zea mays in a comparative genomics setting with 16 monocot lineages. We discovered 61 motifs of which 20 matched previously described motif models in Arabidopsis. In addition, novel, yet uncharacterized motifs were detected, several of which are supported by available sequence-based and/or functional data. Instances of the predicted motifs were enriched around transcription start sites and contained signatures of selection. Moreover, the enrichment of the predicted motif instances in open chromatin and TF binding sites indicates their functionality, supported by the fact that genes carrying instances of these motifs were often found to be co-expressed and/or enriched in similar GO functions. Overall, our study unveiled several novel candidate motifs that might help our understanding of the genotype to phenotype association in crops.

SUBMITTER: Rahmani RS

PROVIDER: S-EPMC9358016 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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BLSSpeller to discover novel regulatory motifs in maize.

Rahmani Razgar Seyed RS Decap Dries D Fostier Jan J Marchal Kathleen K

DNA research : an international journal for rapid publication of reports on genes and genomes 20220601 4

With the decreasing cost of sequencing and availability of larger numbers of sequenced genomes, comparative genomics is becoming increasingly attractive to complement experimental techniques for the task of transcription factor (TF) binding site identification. In this study, we redesigned BLSSpeller, a motif discovery algorithm, to cope with larger sequence datasets. BLSSpeller was used to identify novel motifs in Zea mays in a comparative genomics setting with 16 monocot lineages. We discovere ...[more]

PMID: 35904558

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Project description:BackgroundStreptomyces coelicolor is a bacterium with a vast repertoire of metabolic functions and complex systems of cellular development. Its genome sequence is rich in genes that encode regulatory proteins to control these processes in response to its changing environment. We wished to apply a recently published bioinformatic method for identifying novel regulatory sequence signals to gain new insights into regulation in S. coelicolor.ResultsThe method involved production of position-specific weight matrices from alignments of over-represented words of DNA sequence. We generated 2497 weight matrices, each representing a candidate regulatory DNA sequence motif. We scanned the genome sequence of S. coelicolor against each of these matrices. A DNA sequence motif represented by one of the matrices was found preferentially in non-coding sequences immediately upstream of genes involved in polysaccharide degradation, including several that encode chitinases. This motif (TGGTCTAGACCA) was also found upstream of genes encoding components of the phosphoenolpyruvate phosphotransfer system (PTS). We hypothesise that this DNA sequence motif represents a regulatory element that is responsive to availability of carbon-sources. Other motifs of potential biological significance were found upstream of genes implicated in secondary metabolism (TTAGGTtAGgCTaACCTAA), sigma factors (TGACN19TGAC), DNA replication and repair (ttgtCAGTGN13TGGA), nucleotide conversions (CTACgcNCGTAG), and ArsR (TCAGN12TCAG). A motif found upstream of genes involved in chromosome replication (TGTCagtgcN7Tagg) was similar to a previously described motif found in UV-responsive promoters.ConclusionsWe successfully applied a recently published in silico method to identify conserved sequence motifs in S. coelicolor that may be biologically significant as regulatory elements. Our data are broadly consistent with and further extend data from previously published studies. We invite experimental testing of our hypotheses in vitro and in vivo.

Project description:IntroductionThe neuron-specific K-Cl cotransporter KCC2 maintains low intracellular chloride levels, which are crucial for fast GABAergic and glycinergic neurotransmission. KCC2 also plays a pivotal role in the development of excitatory glutamatergic neurotransmission by promoting dendritic spine maturation. The cytoplasmic C-terminal domain (KCC2-CTD) plays a critical regulatory role in the molecular mechanisms controlling the cotransporter activity through dimerization, phosphorylation, and protein interaction.MethodsTo identify novel CTD regulatory motifs, we used the Mu transposon-based mutagenesis system to generate a library of KCC2 mutants with 5 amino acid insertions randomly distributed within the KCC2-CTD. We determined the insertion positions in 288 mutants by restriction analysis and selected clones with a single insertion site outside known KCC2 regulatory motifs. We analyzed the subcellular distribution of KCC2-CTD mutants in cultured cortical neurons using immunocytochemistry and selected ten mutants with ectopic expression patterns for detailed characterization.ResultsA fluorescent Cl--transport assay in HEK293 cells revealed mutants with both reduced and enhanced Cl--extrusion activity, which overall correlated with their glycosylation patterns. Live-cell immunostaining analysis of plasma membrane expression of KCC2-CTD mutants in cultured cortical neurons corroborated the glycosylation data. Furthermore, the somatodendritic chloride gradient in neurons transfected with the KCC2-CTD mutants correlated with their Cl--extrusion activity in HEK293 cells. Gain- and loss-of-function mutant positions were analyzed using available KCC2 cryo-EM structures.DiscussionTwo groups of mutants were identified based on 3D structural analysis. The first group, located near the interface of transmembrane and cytoplasmic domains, may affect interactions with the N-terminal inhibitory peptide regulating KCC2 activity. The second group, situated on the external surface of the cytoplasmic domain, may disrupt interactions with regulatory proteins. Analyzing CTD mutations that modulate KCC2 activity enhances our understanding of its function and is essential for developing novel anti-seizure therapies.

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BLSSpeller to discover novel regulatory motifs in maize.

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BLSSpeller to discover novel regulatory motifs in maize.

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