lncRNA expression in the auditory forebrain during postnatal development

Abstract

The biological processes governing brain development and maturation depend on complex patterns of gene and protein expression, which can be influenced by many factors. One of the most overlooked is the long noncoding class of RNAs (lncRNAs), which are known to play important regulatory roles in an array of biological processes. Little is known about the distribution of lncRNAs in the sensory systems of the brain, and how lncRNAs interact with other mechanisms to guide the development of these systems. In this study, we profiled lncRNA expression in the mouse auditory forebrain during postnatal development at time points before and after the onset of hearing (P7, P14, P21, adult). First, we generated lncRNA profiles of the primary auditory cortex (A1) and medial geniculate body (MG) at each age. Then, we determined the differential patterns of expression by brain region and age. These analyses revealed that the lncRNA expression profile was distinct between both brain regions and between each postnatal age, indicating spatial and temporal specificity during maturation of the auditory forebrain. Next, we explored potential interactions between functionally-related lncRNAs, protein coding RNAs (pcRNAs), and associated proteins. The maturational trajectories (P7 to adult) of many lncRNA – pcRNA pairs were highly correlated, and predictive analyses revealed that lncRNA-protein interactions tended to be strong. A user-friendly database was constructed to facilitate inspection of the expression levels and maturational trajectories for any lncRNA or pcRNA in the database. Overall, this study provides an in-depth summary of lncRNA expression in the developing auditory forebrain and a broad-based foundation for future exploration of lncRNA function during brain development.

Porcine endemic diarrhea virus infection regulates long noncoding RNA expression

“…This effect may be due to the time and spatial-temporal expression of lncRNAs. The expression of lncRNAs can be affected by many factors, such as cell type, tissue type, development stage, culture time and stimulants (Cabili et al, 2011;Gaiti et al, 2015;Guo et al, 2016;Hart and Goff, 2016;Pauli et al, 2012;Peng et al, 2010;Zhao et al, 2016). The reasons for this effect can be explained as above.…”

Adenosine A1 Receptor mRNA Expression by Neurons and Glia in the Auditory Forebrain

“…Rapid upregulation during this period has been noted in other brain regions (Rivkees, ). In addition, we found that expression of several neurotransmitter receptors (e.g., M 1 R) and numerous coding and noncoding genes known to be involved in critical periods plasticity were in flux during this time interval, suggesting that activity‐dependent mechanisms may alter expression among networks of genes (Hackett et al, ; Guo et al, ; Hackett et al, ).…”

“…The time course of these effects parallels the maturational trajectory of adenosine receptor expression in the mouse auditory forebrain. In previous work, we generated whole genome transcriptome profiles of A1 and MG, highlighting expression trajectories for over 200 gene families at key stages during postnatal development in mice (P7, P14, P21, adult) (Hackett et al, ; Guo et al, ). For the adenosine receptor family, Adora1 transcript expression was dominant in A1 and MG, compared to very low expression of Adora2a and Adora2b (Fig.…”

Understanding the Role of lncRNAs in Nervous System Development

“…Techniques such as customized microarrays for lncRNAs, serial analysis of gene expression (SAGE), and RNA-Seq analysis of primary nervous system tissue have identified thousands of lncRNAs expressed in the nervous system of multiple species [19, 20, 22, 23, 30, 46–50, 61, 76–78]. Additionally, highly cell and tissue-specific lncRNAs can be identified by expression profiling of micro-dissected or sorted tissue and/or cell populations.…”

“…Large-scale efforts, including the Allen Brain Atlas, have begun to examine both the spatial and temporal expression of individual lncRNAs [22, 81]. Additional studies have complemented these large-scale efforts, focusing on more discrete cell populations, including the primary auditory cortex and medial geniculate body [76] or restricted numbers of lncRNAs including, but not limited to, linc-RBE [82], linc-00320 [83], Dio3os [84], Evf 1 [85, 86], and Evf2 [87]. Other studies have observed changes in brain lncRNA expression that are associated with genetic mutants in neurological and psychiatric diseases [88–94] and pharmacological treatments [95, 96] in the brain.…”