Identification of Long Non-coding RNAs Expressed During Early Adipogenesis

Abstract

Long non-coding RNAs (lncRNAs) are transcripts with a length of more than 200 nucleotides that lack protein-coding capacity. LncRNAs play important roles in the regulation of genes during many biological processes, development and disease progression, such as obesity. Obesity is an increasing health concern around the world. Although multiple studies linking lncRNAs and fully differentiated adipocytes have been published, the systematic analysis of those lncRNAs involved in early preadipocyte differentiation, when fate determination decisions are made, has not been reported. In order to fill this gap, we conducted strandspecific RNA-Seq on mouse 3T3-L1 preadipocyte cells and compared the expression profiles before and after early differentiation for 2 days. We identified 82 lncRNAs that significantly changed their expression after early differentiation, 98% of which were newly discovered in association with early adipogenesis. The most remarkable lncRNAs were U90926, Wincr1, Kcnq1ot1, Malat1 and Hotairm1. Expression patterns for these identified genes were also highly correlated with markers of adipogenesis, including PPAR, CEBP, FABP4 and FASN. Further analysis implies that many of those altered lncRNAs might coordinately inhibit Wnt/-catenin signaling pathway to promote preadipocyte differentiation. This work strongly suggests that lncRNAs are critical in the proliferation and differentiation of adipose tissue.

State-transition Modeling of Blood Transcriptome Predicts Disease Evolution and Treatment Response in Chronic Myeloid Leukemia

“…3B; Table S2). In addition to BCR::ABL, among the most upregulated DEGs, was Prrt4, encoding for a protein predicted to be an integral component of the cell membrane, and the lncRNA Gm6093, predicted to play a role in cell differentiation 20,21 . Among the most downregulated DEGs, we observed collagen and elastin encoding genes, in addition to Il33.…”

Transcriptome analysis of ciliary-dependent MCH signaling in differentiating 3T3-L1 pre-adipocytes

“…Total RNA from twelve samples were sent to the Center for Genome Research and Biocomputing (CGRB) at Oregon State University for library construction and stranded-specific sequencing on an Illumina HiSeq3000 as previously reported 19 . Library construction was described in detail by Shen et al 4 . Sequencing libraries were prepared with a WaferGen PrepXTM mRNA Strand-Specific Library Preparation Protocol (WaferGen Biosystem).…”

“…The remaining bases of 7–106 were kept for each read containing 100 bases. Further analysis followed the procedures as described by others 4 . Briefly, all the reads were mapped to mouse mm10 assembly with RefSeq gene annotation using STAR 19 .…”

“…Early in the differentiation process, Day 2 differentiating pre-adipocytes express a transient primary cilium that protrudes from the cell as an extension of the plasma membrane. This short-lived signaling structure may help to inhibit Wnt signaling, enabling adipogenesis to occur 3 , 4 . The primary cilium is therefore necessary for adipocyte development, since cells fail to fully differentiate in pre-adipocyte knock-out studies targeting the ciliary genes ift88 and kif3a 5 .…”