Characterization of the hypothalamic transcriptome in response to food deprivation reveals global changes in long noncoding RNA, and cell cycle response genes

Abstract

The hypothalamus integrates energy balance information from the periphery using different neuronal subtypes within each of the hypothalamic areas. However, the effects of prandial state on global mRNA, microRNA and long noncoding (lnc) RNA expression within the whole hypothalamus are largely unknown. In this study, mice were given either a 24-h fast, or ad libitum access to food. RNA samples were analyzed by microarray, and then a subset was confirmed using quantitative real-time PCR (QPCR). A total of 540 mRNAs were either up-or downregulated with food deprivation. Since gene ontology enrichment analyses identified several categories of mRNAs related to cell cycle processes, ten cell-cycle-related genes were further analyzed using QPCR with six confirmed to be significantly up-regulated and one downregulated in response to 24-h fasting. While 22 independent microRNAs were differentially expressed by microarray, secondary analysis by QPCR failed to confirm significant changes with fasting. There were 622 lncRNAs identified as differentially expressed, and of three tested by QPCR, two were confirmed. Overall, this is the first time that expression of hypothalamic lncRNAs has been shown to be responsive to food deprivation. In addition, this study is the first to identify a list of lncRNAs with high expression in RNA extracted from hypothalamus. Individual contributions from specific miRNA, lncRNA and mRNAs to the food deprivation response can now be further studied at the physiological and biochemical levels.

A molecular conundrum involving hypothalamic responses to and roles of long non-coding RNAs following food deprivation

“…There is only one study where the adult expression patterns of hypothalamic lncRNAs under energy availability stress were studied, and that comes from our laboratory 67 . Using Affymetrix exon arrays of WT ad lib fed and fasted mice, we identified over 12,000 lncRNA transcripts in the hypothalamus, 622 of which were differentially-regulated in response to 24-hour fasting.…”

“…AK038506 was upregulated by approximately 3-fold in fasted compared to ad lib fed mice, while AK049914 showed a nearly 6-fold increase. At the time when writing the original paper 67 , there was no significant homology for AK038506 using a genomic blast, but a new Blast analysis, using a less stringent approach and a ref-seq genomic blast, revealed 99% overlap of 99% of the 1933 nucleotide sequence with two different sequences. The first is the RasAl2 gene on mouse chromosome 1, with homology within an intron between exons 8 and 9.…”

“…The other hypothalamic lncRNA increased with fasting was AK049914, blasts to a region that sits between exons 3 and 4 of the ApoD gene 67 . The ApoD gene, whose protein product is a component of high-density lipoproteins, is upregulated by fasting 70 , suggesting that the placement of a fasting-regulated lncRNA might not be coincidental.…”

“…As the study on WT and N2KO mice was done in the 129Sv/J strain, compared to the C57Bl/6 strained using in our published paper 67 , we were also able to compare expression of lncRNA between strains, and in response to fasting. As shown in Table 2, using statistical criteria of P-value ≤0.05, fold change of ≥ 1.5, and more than 2 identified probes for analysis, a total of 386 lncRNAs were found to be differentially regulated by food deprivation in C57Bl/6 with 305 of those up-regulated and 81 down-regulated by a 24-hour fast.…”

Lnc-IL7R promotes the growth of fibroblast-like synoviocytes through interaction with enhancer of zeste homolog 2 in rheumatoid arthritis

“…Dysregulation of lncRNA has been identified to be associated with human diseases, including inflammation and cancer (13)(14)(15). The abnormal expression of lncRNA may contribute to disease initiation and progression through regulating expression of the gene products (16,17). A recent study has reported that differentiation and activation of immune cells are associated with lncRNAs, which have an essential role in autoimmune diseases, including RA (18).…”