Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA261439 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Long non-coding RNAs (lncRNAs) are emerging as functional regulators of gene expression in many species1,2. However, aligning lncRNA-dependent phenotypes with their underlying molecular mechanisms remains challenging. The Polycomb Repressive Complex 1 (PRC1) family of the Polycomb Group (PcG) complexes interacts with lncRNAs and is essential for gene silencing during development. Despite the functional importance of PRC1, few specific lncRNAs that guide PRC1 activity are known3-5. We screened for human RNAs which co-precipitate with the PRC1-component BMI1, from a chromatin fraction. Knockdown of several of the lncRNA candidates perturbed PcG-regulated gene expression in vivo. In particular, we found that the PRC1-associated lncRNA CAT7 tunes PRC1 function during zebrafish and human development. During neuronal differentiation of human embryonic stem cells, CAT7 impacts expression and PcG-binding of the MNX1 locus, which encodes a master regulator of motor neuron development. During zebrafish development, human CAT7 functionally rescues defects caused by interference of the non-syntenic analog, zebrafish cat7 (zcat7.) Further, zcat7 genetically interacts with bmi1a/b during zebrafish embryogenesis. We propose that PRC1 acts in concert with specific lncRNAs, and that CAT7/zcat7 represent lncRNAs that convergently evolved to tune PRC1 repression at individual loci. We immunoprecipitated PRC1-interacting RNAs from a chromatin fraction using a technology called GRIP. We identified candidates in HeLa cells containing a 25% overexpression of FLAG-tagged murine Bmi1 (ectopic). Candidates were selected which were enriched in both Bmi1 and FLAG-Bmi1 GRIP versus input. Knockdown of 17 of these candidates was performed (vs a scramble control) and total RNA was sequenced 48 hours after knockdown. One candidate, CAT7 was also knocked down in developing (motor) neural cells (grown from human embryonic stem cells). We also performed ChIP targeting Polycomb proteins in the HeLa cells depleted for CAT7 or scramble controls.
2016-07-07 | GSE61549 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE32898: Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis [RNA_seq] GSE32899: Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis [ChIP_Seq] Refer to individual Series
2011-11-17 | E-GEOD-32900 | biostudies-arrayexpress
Project description:Polycomb repressive complexes 1 and 2 (PRC1 and 2) repress lineage inappropriate genes during development to maintain proper cellular identities. To reveal the function of a variant PRC1 containing PCGF1 (PCGF1-PRC1), we prepared PCGF1 interacting proteins by immunoprecipitation and characterized them by LC-MS/MS.
2023-05-13 | PXD033883 | JPOST Repository
Project description:First described in Drosophila melanogaster, planar cell polarity (PCP) is a developmental process essential for embryogenesis and development of polarized structures in Metazoans. This signaling pathway involves a set of evolutionarily conserved genes encoding transmembrane (Vangl, Frizzled, Celsr) and cytoplasmic (Prickle, Dishevelled) molecules. Vangl2 is of major importance in embryonic development as illustrated by its pivotal role during neural tube closure in human, mouse, Xenopus and zebrafish embryos. The regulated and poorly understood traffic of Vangl2 to the plasma membrane is a key event for its function in development. Here we identify a novel N-terminally extended isoform of Vangl2, termed Vangl2-Long that arises from the use of non-AUG start codon upstream of the coding region of canonical Vangl2. Vangl2-Long contains an evolutionarily conserved N-terminal 48 amino acid sequence bearing a signal for subcellular localization in the Golgi apparatus. Moreover, we provide data in Xenopus showing that Vangl2-Long is important for correct convergent extension movements and neural tube closure. These data describe a further level of complexity in Vangl2 expression, trafficking and function.
2024-04-09 | PXD021794 | Pride
Project description:Long non-coding control of pericyte function
| PRJNA358715 | ENA
Project description:Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis [RNA_seq]
| PRJNA154389 | ENA
Project description:Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis [ChIP_Seq]
| PRJNA154403 | ENA
Project description:Long non-coding RNAs (lncRNAs) have emerged as critical regulators of gene expression and chromatin modifications, with important functions in development and disease. Here we sought to identify and functionally characterize lncRNAs critical for vascular vertebrate development with significant conservation across species. Genome-wide transcriptomic analyses during human vascular lineage specification enabled the identification of three conserved novel lncRNAs: TERMINATOR, ALIEN and PUNISHER that are specifically expressed in pluripotent stem cells, mesoderm and endothelial cells, respectively. Gene expression profiling, alongside RNA immunoprecipitation coupled to mass spectrometry, revealed a wide range of new molecular networks and protein interactors related to post-transcriptional modifications for all three lncRNAs. Functional experiments in zebrafish and murine embryos, as well as differentiating human cells, confirmed a developmental-stage specific role for each lncRNA during vertebrate development. The identification and functional characterization of these three novel non-coding provide a comprehensive transcriptomic roadmap and shed new light on the molecular mechanisms underlying human vascular development. shRNA knock down of lncRNAs followed by microarray gene expression profiling
2015-05-15 | E-GEOD-54964 | biostudies-arrayexpress