Genomics

Dataset Information

356

Transcriptome-wide mapping of RNA binding sites of the RNA-binding protein Unkempt using iCLIP-seq


ABSTRACT: iCLIP experiments tomap the RNA binding sites of the RNA-binding protein Unkempt across the transcriptome in SH-SY5Y cells, HeLa cells with ectopic Unk expression and mouse E15 embryonic brain samples. Expression of Unk is normally largely restricted to the nervous system. We therefore mapped the binding sites in human SH-SY5Y and mouse E15 brain to detect its physiological binding sites (in SH-SY5Y, we also performed the RNAseq experiment upon Unk knockdown). HeLa cells on the other hand normally don't express Unk, but convert to neuron-like shape when the protein is ectopically expressed. So, here we hoped to identify those binding events (and hence target transcripts) that are critical for this morphological transformation.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Musculus  

SUBMITTER: Kathi Zarnack  

PROVIDER: E-MTAB-2279 | ArrayExpress | 2015-03-09

SECONDARY ACCESSION(S): ERP004684

REPOSITORIES: ArrayExpress, ENA

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Publications


Cellular morphology is an essential determinant of cellular function in all kingdoms of life, yet little is known about how cell shape is controlled. Here we describe a molecular program that controls the early morphology of neurons through a metazoan-specific zinc finger protein, Unkempt. Depletion of Unkempt in mouse embryos disrupts the shape of migrating neurons, while ectopic expression confers neuronal-like morphology to cells of different nonneuronal lineages. We found that Unkempt is a s  ...[more]

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