Supporting data for characterization of non-coding RNAs associated with the Neuronal growth regulator 1 (NEGR1) adhesion protein

Long non-coding RNAs and microRNAs control gene expression to determine central nervous system development and function. Neuronal growth regulator 1 (NEGR1) is a cell adhesion molecule that plays an important role in neurite outgrowth during neuronal development and its precise expression is crucial for correct brain development. The data described here is related to the research article titled “A long non-coding RNA, BC048612 and a microRNA, miR-203 coordinate the gene expression of Neuronal growth regulator 1 (NEGR1) adhesion protein” [1]. This data article contains detailed bioinformatics analysis of genetic signatures at the Negr1 gene locus retrieved from the UCSC genome browser. This approach could be adopted to identify putative regulatory non-coding RNAs in other tissues and diseases.


a b s t r a c t
Long non-coding RNAs and microRNAs control gene expression to determine central nervous system development and function. Neuronal growth regulator 1 (NEGR1) is a cell adhesion molecule that plays an important role in neurite outgrowth during neuronal development and its precise expression is crucial for correct brain development. The data described here is related to the research article titled "A long non-coding RNA, BC048612 and a microRNA, miR-203 coordinate the gene expression of Neuronal growth regulator 1 (NEGR1) adhesion protein" [1]. This data article contains detailed bioinformatics analysis of genetic signatures at the Negr1 gene locus retrieved from the UCSC genome browser. This approach could be adopted to identify putative regulatory non-

Value of the data
This data provides a comprehensive in silico analysis of the genetic signatures and expression pattern of long non-coding RNAs associated with the Negr1 gene.
This data is useful in understanding the regulatory relationship between non-coding RNA gene expression and Negr1 gene expression.
The methodology provided can be used to postulate regulatory relationships between long noncoding RNAs and proximal genes.
This approach could be adopted to identify putative regulatory non-coding RNAs in other tissues and diseases which could be evaluated with further functional studies.

Data
The data in this article describes the initial in silico analysis carried out on the Negr1 gene locus for genetic signatures and expression patterns of long non-coding RNAs in proximity to the Negr1 gene [1] (Figs. 1 and 2, Table 1). The proposed interaction between the BC048612 lncRNA and microRNA-203 were validated using qPCR (Fig. 3).
Further interrogation of the BC048612 lncRNA and Negr1 gene transcription start sites as well as putative regulatory transcription factors was carried out (Fig. 2). RegRNA [10] was employed to predict transcription factor binding sites proximal to the transcription start sites (Fig. 2).

Determination of effect of lncRNA expression on miR-203 levels
To determine if there is any interaction between the BC048612 lncRNA and miR-203, the BC048612 sequence was analyzed for putative binding sites for miR-203. RegRNA analysis did not Refseq number for each transcript is indicated. CpG islands overlapping with the promoter are also indicated. Transcription start site of each transcript on the promoter sequence is denoted by letters in bold in specific colours with corresponding arrows denoting transcription direction. Putative Sp1 binding sites (red arrows) as determined by RegRNA [10] are mapped on the Negr1 promoter. Table 1 Negr1 mRNA, lncRNAs (AK083124 and BC048612) expression, DNA hypomethylation status, H3K4m3 and H3K27m3 histone modification data in 8 week old mouse cortex, cerebellum, heart and liver extracted from the UCSC Genome Browser [2][3][4][5][6][7][8][9] on the Mouse July 2007 (NCBI37/mm9) assembly. Detailed information is presented in Fig. 1. N.A.: data not available.

Negr1 mRNA expression
LncRNAs expression DNA hypomethylation H3K4m3 H3K27m3 predict any miR-203 binding sites on the BC048612 lncRNA [10]. Further verification of the effect of BC048612 lncRNA expression on miR-203 levels was carried out by quantifying miR-203 expression in both lncRNA knockdown (Fig. 3A) and over expression of lncRNA (Fig. 3B) in primary neuronal cultures. Primary neuronal cultures on Day 6 were transfected with LNA™ GapmeR against the BC048612 lncRNA or mammalian expression vector (pcDNA4/TO/myc His A) containing BC048612 (pc_BC048612 LncRNA). The cells were harvested 48 h after transfection and total cellular RNA was extracted for quantification of miR-203 expression levels.