Here, we propose to elucidate the role of candidate lincRNAs during mammalian brain development using a unique resource of 20 mouse lincRNA knockout models that we have recently generated. We specifically focused on candidates we hypothesized, through previous studies, to play a role in neuronal development. Indeed 15 of the 20 candidates exhibit cell-type and brain specific expression patterns. More importantly, we have already observed lethality phenotypes and gross anatomical abnormalities during brain development in selected mutants.
We aim to explore the molecular and physiological underpinnings of the observed phenotypes as well as of others that we may encounter through this work. We propose to take a comprehensive and systematic approach to address the following questions: What are the spatial temporal dynamics of lincRNA expression in vivo during neuronal development and what gene pathways are regulated? (Aim 1). We will address these questions by leveraging a knock-in lacZ reporter to monitor lincRNA expression patterns and dynamics throughout brain development. We will address the second question through next generation RNA-sequencing studies between wild-type and knockout strains to identify specific genes and pathways regulated by lincRNAs in vivo. What are the physiological and molecular underpinnings of lethality and brain development phenotypes observed in selected lincRNA mutants? (Aim 2). Here, we will address this question through a battery of in vivo experiments to define perturbations to normal neuronal cell fate specification in selected mutants. We will focus first on three lincRNAs that have already shown brain specific phenotypes resulting in lethality and abnormalities of neurogenesis and one expressed in neuronal precursor cells. If time and resources allow we will expand these phenotypic studies to additional strains. How are lincRNAs working on a molecular and mechanistic level to ensure proper neuronal cell fate specification and viability? (Aim 3). Here, we use multifaceted and novel experimental protocols to define the specific regions of lincRNAs required to recover phenotypes. Moreover, we will identify lincRNA protein partners and how they interact to modulate cell fate decisions. The proposed research is driven by our vision, which seeks to unify experimental and computational genomics to push new frontiers in understanding the physiological and molecular regulatory roles of lincRNAs during neuronal development. Collectively, these studies will present the first phenotyping of lincRNA functional roles during neuronal development and will explore their biochemical mechanisms in vivo.

Public Health Relevance

Our research aims to understand a universal problem in human health: How does the same genome present in every cell take on alternate identities that orchestrate distinctive cell states and how are these states misregulated in diseases. We recently discovered a novel class of large intergenic non- coding RNAs (lincRNAs) that have the ability to regulate cellular identity. Here we aim to understand the in vivo relevance for lincRNAs in neuronal development. The ultimate goal of these innovative experimental and computational approaches is to develop novel RNA based therapeutics.

National Institute of Health (NIH)
National Institute of Mental Health (NIMH)
Research Project (R01)
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Molecular Neurogenetics Study Section (MNG)
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Panchision, David M
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Harvard University
Anatomy/Cell Biology
Schools of Arts and Sciences
United States
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Maass, Philipp G; Barutcu, A Rasim; Weiner, Catherine L et al. (2018) Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. Mol Cell 69:1039-1045.e3
Melé, Marta; Mattioli, Kaia; Mallard, William et al. (2017) Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs. Genome Res 27:27-37
Kelley, David R; Snoek, Jasper; Rinn, John L (2016) Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks. Genome Res 26:990-9
Groff, Abigail F; Sanchez-Gomez, Diana B; Soruco, Marcela M L et al. (2016) In Vivo Characterization of Linc-p21 Reveals Functional cis-Regulatory DNA Elements. Cell Rep 16:2178-2186
Hacisuleyman, Ezgi; Shukla, Chinmay J; Weiner, Catherine L et al. (2016) Function and evolution of local repeats in the Firre locus. Nat Commun 7:11021
Molyneaux, Bradley J; Goff, Loyal A; Brettler, Andrea C et al. (2015) DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex. Neuron 85:275-288
Goff, Loyal A; Groff, Abigail F; Sauvageau, Martin et al. (2015) Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A 112:6855-62