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Mol Cell. 2016 Oct 6;64(1):37-50. doi: 10.1016/j.molcel.2016.08.010. Epub 2016 Sep 8.

A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage.

Author information

1
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
2
Los Alamos National Laboratory, Theoretical Biology and Biophysics Group, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87544, USA.
3
Undergraduate Research Opportunities Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
4
Los Alamos National Laboratory, Theoretical Biology and Biophysics Group, Los Alamos, NM 87545, USA; Pacific Northwest National Laboratory, Environmental Molecular Sciences Laboratory, Richmond, WA 99354, USA.
5
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: lboyer@mit.edu.

Abstract

Long non-coding RNAs (lncRNAs) are an emerging class of transcripts that can modulate gene expression; however, their mechanisms of action remain poorly understood. Here, we experimentally determine the secondary structure of Braveheart (Bvht) using chemical probing methods and show that this ∼590 nt transcript has a modular fold. Using CRISPR/Cas9-mediated editing of mouse embryonic stem cells, we find that deletion of 11 nt in a 5' asymmetric G-rich internal loop (AGIL) of Bvht (bvhtdAGIL) dramatically impairs cardiomyocyte differentiation. We demonstrate a specific interaction between AGIL and cellular nucleic acid binding protein (CNBP/ZNF9), a zinc-finger protein known to bind single-stranded G-rich sequences. We further show that CNBP deletion partially rescues the bvhtdAGIL mutant phenotype by restoring differentiation capacity. Together, our work shows that Bvht functions with CNBP through a well-defined RNA motif to regulate cardiovascular lineage commitment, opening the door for exploring broader roles of RNA structure in development and disease.

KEYWORDS:

Braveheart; CNBP; SHAPE; cardiac; long non-coding RNA

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PMID:
27618485
DOI:
10.1016/j.molcel.2016.08.010
[Indexed for MEDLINE]
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