Dataset Information

The Samd9L gene: transcriptional regulation and tissue-specific expression in mouse development.

ABSTRACT: Normophosphatemic familial tumoral calcinosis (NFTC) is caused by mutations in the SAMD9 gene. This gene is absent in mouse, while there is a murine paralog, Samd9-like (Samd9L). To clarify the relationships between SAMD9 and SAMD9L, we investigated the transcriptional regulation and expression pattern of mouse Samd9L. An ?1.5-kb mouse Samd9L promoter fragment was cloned, and a series of 5' deletion constructs were linked to a luciferase reporter gene. All constructs showed significant activity in transfected epithelial cells and mouse fibroblasts, and the presence of regulatory cis-elements as close as 87?bp upstream of the transcription start site was identified. Ras-responsive element binding protein 1 (Rreb-1) was identified in this region by protein-DNA binding array. The expression of Samd9L was upregulated by calcitonin, and this was preceded by a significant increase in the expression of Rreb-1 mRNA. Quantitative real-time PCR analysis of Samd9L revealed near-ubiquitous expression, with the highest level in the kidney. Tissue-specific expression was also confirmed both by in situ ?-gal staining and quantitative enzymatic activity assay in a transgenic Samd9L(+/-) mouse in which the LacZ gene replaced exon 2 in the Samd9L gene. These findings assist in understanding the regulation of Samd9L in the context of its paralogous gene, SAMD9, which harbors mutations in NFTC.

SUBMITTER: Jiang Q

PROVIDER: S-EPMC3173943 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature

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The Samd9L gene: transcriptional regulation and tissue-specific expression in mouse development.

Jiang Qiujie Q Quaynor Benjamin B Sun Alex A Li Qiaoli Q Matsui Hirotaka H Honda Hiroaki H Inaba Toshiya T Sprecher Eli E Uitto Jouni J

The Journal of investigative dermatology 20110317 7

Normophosphatemic familial tumoral calcinosis (NFTC) is caused by mutations in the SAMD9 gene. This gene is absent in mouse, while there is a murine paralog, Samd9-like (Samd9L). To clarify the relationships between SAMD9 and SAMD9L, we investigated the transcriptional regulation and expression pattern of mouse Samd9L. An ∼1.5-kb mouse Samd9L promoter fragment was cloned, and a series of 5' deletion constructs were linked to a luciferase reporter gene. All constructs showed significant activity ...[more]

PMID: 21412262

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Project description:BackgroundTranscription factors (TFs) are proteins that can bind to DNA sequences and regulate gene expression. Many TFs are master regulators in cells that contribute to tissue-specific and cell-type-specific gene expression patterns in eukaryotes. Maize has been a model organism for over one hundred years, but little is known about its tissue-specific gene regulation through TFs. In this study, we used a network approach to elucidate gene regulatory networks (GRNs) in four tissues (leaf, root, SAM and seed) in maize. We utilized GENIE3, a machine-learning algorithm combined with large quantity of RNA-Seq expression data to construct four tissue-specific GRNs. Unlike some other techniques, this approach is not limited by high-quality Position Weighed Matrix (PWM), and can therefore predict GRNs for over 2000 TFs in maize.ResultsAlthough many TFs were expressed across multiple tissues, a multi-tiered analysis predicted tissue-specific regulatory functions for many transcription factors. Some well-studied TFs emerged within the four tissue-specific GRNs, and the GRN predictions matched expectations based upon published results for many of these examples. Our GRNs were also validated by ChIP-Seq datasets (KN1, FEA4 and O2). Key TFs were identified for each tissue and matched expectations for key regulators in each tissue, including GO enrichment and identity with known regulatory factors for that tissue. We also found functional modules in each network by clustering analysis with the MCL algorithm.ConclusionsBy combining publicly available genome-wide expression data and network analysis, we can uncover GRNs at tissue-level resolution in maize. Since ChIP-Seq and PWMs are still limited in several model organisms, our study provides a uniform platform that can be adapted to any species with genome-wide expression data to construct GRNs. We also present a publicly available database, maize tissue-specific GRN (mGRN, https://www.bio.fsu.edu/mcginnislab/mgrn/ ), for easy querying. All source code and data are available at Github ( https://github.com/timedreamer/maize_tissue-specific_GRN ).

Dataset Information

The Samd9L gene: transcriptional regulation and tissue-specific expression in mouse development.

Publications

The Samd9L gene: transcriptional regulation and tissue-specific expression in mouse development.

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