Collaborative interactions of heterogenous ribonucleoproteins contribute to transcriptional regulation of sterol metabolism in mice

Abstract

Heterogeneous nuclear ribonucleoproteins (hnRNPs) are a group of functionally versatile proteins that play critical roles in the biogenesis, cellular localization and transport of RNA. Here, we outline a role for hnRNPs in gene regulatory circuits controlling sterol homeostasis. Specifically, we find that tissue-selective loss of the conserved hnRNP RALY enriches for metabolic pathways. Liver-specific deletion of RALY alters hepatic lipid content and serum cholesterol level. In vivo interrogation of chromatin architecture and genome-wide RALYbinding pattern reveal insights into its cooperative interactions and mode of action in regulating cholesterogenesis. Interestingly, we find that RALY binds the promoter region of the master metabolic regulator Srebp2 and show that it directly interacts with coactivator Nuclear Transcription Factor Y (NFY) to influence cholesterogenic gene expression. Our work offers insights into mechanisms orchestrating selective promoter activation in metabolic control and a model by which hnRNPs can impact health and disease states.

Transcriptional regulation of N6-methyladenosine orchestrates sex-dimorphic metabolic traits

“…For lipidomics analysis, 50–100 mg of frozen liver were homogenized in cold phosphate-buffered saline (PBS) using the Omni Bead Ruptor Elite with 2 mL homogenizer tube system (Omni, 19–628D) for 3 cycles of 10 s each at 5 m/s with a 10 s dwell time between cycles 49 . A total of 3–6 mg of homogenized material were applied to a modified Bligh and Dyer extraction.…”

“…ATAC-seq was optimized in liver after several modifications from original Buenstero et al protocol 49 . A total of 100 mg of frozen liver were grinded to fine powder using cellcrusher and 1 mL of ice cold nuclei isolation buffer was added (20 mM Tris-HCl, 50 mM EDTA, 5 mM spermidine, 0.15 mM spermine, 0.1% mercaptoethanol, 40% glycerol, pH 7.5, mM EGTA, and 60 mM KCl).…”

“…A total of 75,000 nuclei pellet were used for transposase reaction. The rest of the protocol followed that described by Buenstero 49 . ATAC-Seq libraries were prepared using the Nextera Tn5 Transposase and DNA library preparation kit (Illumina) as described 49 .…”

“…The rest of the protocol followed that described by Buenstero 49 . ATAC-Seq libraries were prepared using the Nextera Tn5 Transposase and DNA library preparation kit (Illumina) as described 49 . Libraries were single-end sequenced (50 bp) on an Illumina HiSeq 2000.…”

Downregulation of a Dorsal Root Ganglion‐Specifically Enriched Long Noncoding RNA is Required for Neuropathic Pain by Negatively Regulating RALY‐Triggered Ehmt2 Expression

“…This transcriptional activation may require nuclear transcription factor Y, as a recent study reported that RALY directly interacted with this transcription factor to influence cholesterogenic gene expression. [ 51 ] CCI produced DS‐lncRNA downregulation, RALY upregulation, and the increases of RALY interaction with RNP II or the Ehmt2 gene promoter and of RNP II interaction with the Ehmt2 gene promoter in injured DRG. Given that rescuing DRG DS‐lncRNA downregulation not only attenuated these increased interactions but also reversed the CCI‐induced decrease in the binding of RALY to DS‐lncRNA , our results suggest that DS‐lncRNA may compete with RNP II and the Ehmt2 gene promoter to bind to RALY (Figure 9 ).…”