Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA312346 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3175173_1.fastq.gz | Fastqsanger.gz | |||
| SRR3175173_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:Genomic approaches have predicted hundreds of thousands of tissue specific cis-regulatory sequences, but the determinants critical to their function and evolutionary history are mostly unknown1-4. Here, we systematically decode a set of brain enhancers active in the zona limitans intrathalamica (zli), a signaling center essential for vertebrate forebrain development via the secreted morphogen, Sonic hedgehog (Shh)5,6. We apply a de novo motif analysis tool to identify six position-independent sequence motifs together with their cognate transcription factors that are essential for zli enhancer activity and Shh expression in the mouse embryo. Using knowledge of this regulatory lexicon, we discover novel Shh zli enhancers in mice, and a functionally equivalent element in hemichordates, indicating an ancient origin of the Shh zli regulatory network that predates the chordate phylum. These findings establish a paradigm for delineating functionally conserved enhancers in the absence of overt sequence homologies, and over extensive evolutionary distances. Gene expression profiles from the mouse zona limitans intrathalamica (ZLI) region at E10.5
2016-03-25 | E-GEOD-78005 | biostudies-arrayexpress
Project description:Genomic approaches have predicted hundreds of thousands of tissue specific cis-regulatory sequences, but the determinants critical to their function and evolutionary history are mostly unknown1-4. Here, we systematically decode a set of brain enhancers active in the zona limitans intrathalamica (zli), a signaling center essential for vertebrate forebrain development via the secreted morphogen, Sonic hedgehog (Shh)5,6. We apply a de novo motif analysis tool to identify six position-independent sequence motifs together with their cognate transcription factors that are essential for zli enhancer activity and Shh expression in the mouse embryo. Using knowledge of this regulatory lexicon, we discover novel Shh zli enhancers in mice, and a functionally equivalent element in hemichordates, indicating an ancient origin of the Shh zli regulatory network that predates the chordate phylum. These findings establish a paradigm for delineating functionally conserved enhancers in the absence of overt sequence homologies, and over extensive evolutionary distances.
2016-03-25 | GSE78005 | GEO
Project description:Deciphering the cis-regulatory architecture of mammalian photoreceptors
| PRJNA124083 | ENA
Project description:The brain regulatory program predates central nervous system evolution
| PRJNA903823 | ENA
Project description:The SNF1-related protein kinase 2 (SnRK2) pathway is central to abiotic stress signaling in land plants; however, its evolutionary origin and ancestral functions remain poorly understood. Here, we identify and characterize a functional SnRK2 signaling module in the unicellular green alga Chlamydomonas reinhardtii. We demonstrate that the algal isoform SnRK2.7 is essential for osmotic stress tolerance, providing a pre- abscisic acid (ABA) model system for characterizing SnRK2 signaling. Functional analysis reveals that SnRK2.7 exhibits key regulatory elements conserved in land plant SnRK2s, but also displays lineage-specific features: it is required for general cellular viability in algae and localizes to the contractile vacuole—an osmoregulatory organelle lost during streptophyte evolution. Notably, SnRK2.7 phosphorylates PP2C3, a clade A protein phosphatase, revealing an ancestral regulatory logic distinct from that in angiosperms, where PP2Cs functions upstream, dephosphorylating SnRK2 proteins. Together with MAPKKK3, a B1/B3-RAF kinase, these proteins form an evolutionarily ancient SnRK2 signaling module. Our findings reveal that a sophisticated SnRK2 pathway predates both the evolution of ABA signaling and plant terrestrialization, implying key regulatory innovations that emerged during chlorophyte-streptophyte divergence.
2026-07-02 | PXD072844 | Pride
Project description:The hypothalamus predates the origin of vertebrates
| PRJNA699670 | ENA
Project description:Hybrid mice reveal parent-of-origin and cis- and trans-regulatory effects in the retina
| PRJNA258520 | ENA
Project description:The mouse X-inactivation center (Xic) locus represents a powerful model for understanding the links between genome architecture and gene regulation, with the non-coding genes Xist and Tsix showing opposite developmental expression patterns while being organized as an overlapping sense/antisense unit. The Xic is organized into two topologically associating domains (TADs) but the role of this architecture in orchestrating cis-regulatory information remains elusive. To explore this, we generated genomic inversions within the Xic that swap the Xist/Tsix transcriptional unit and place their promoters in each other’s TAD. We found that this led to a switch in their expression dynamics: Xist became precociously and ectopically up-regulated, both in male and female pluripotent cells, while Tsix expression aberrantly persisted during differentiation. The topological partitioning of the Xic is thus critical to ensure proper developmental timing of X-inactivation. Our study illustrates how genomic architecture can hardwire the potential for mammalian developmental regulation by cis-regulatory landscapes.
2019-05-27 | GSE111205 | GEO
Project description:The evolution of tetrapod limbs from fish fins enabled the conquest of land by vertebrates and thus represents a key step in evolution. Despite the use of comparative gene expression analyses, critical aspects of this transformation remain controversial, in particularly the origin of digits. Hoxa and Hoxd genes are essential for the specification of the different limb segments and their functional abrogation leads to large truncations of the appendages. Here we show that the selective transcription of mouse Hoxa genes in proximal and distal limbs is related to a bimodal higher order chromatin structure, similar to that reported for Hoxd genes, thus revealing a generic regulatory strategy implemented by both gene clusters during limb development. We found the same bimodal chromatin architecture in fish embryos, indicating that the regulatory strategy used to pattern tetrapod limbs predates the divergence between fish and tetrapods. However, when assessed in mice, both fish regulatory domains triggered transcription in proximal, rather than distal limb territories, supporting an evolutionary scenario whereby digits arose as true tetrapod novelties through genetic retrofitting of a preexisting bimodal chromatin framework. We discuss the possibility to consider regulatory circuitries, rather than expression patterns, as essential parameters to define evolutionary synapomorphies. Circular Chromosome Conformation Capture (4C seq) at the mouse HoxA and HoxD loci in proximal and distal forelimbs and forebrain at E12.5 and at the zebrafish HoxAa, HoxAb and HoxDa loci in 5 dpf whole embryos.
2014-01-21 | E-GEOD-47644 | biostudies-arrayexpress