De Novo Reconstruction of Transcriptome Identified Long Non-Coding RNA Regulator of Aging-Related Brown Adipose Tissue Whitening in Rabbits

Abstract

Brown adipose tissues (BATs) convert to a “white-like” phenotype with age, which is also known as “aging-related BAT whitening (ARBW)”. Emerging evidence suggested that long non-coding RNAs (lncRNAs) were widely involved in adipose biology. Rabbit is an ideal model for studying the dynamics of ARBW. In this study, we performed histological analysis and strand-specific RNA-sequencing (ssRNA-seq) of rabbit interscapular adipose tissues (iATs). Our data indicated that the rabbit iATs underwent the ARBW from 0 days to 2 years and a total of 2281 novel lncRNAs were identified in the iATs. The classical rabbit BATs showed low lncRNA transcriptional complexity compared to white adipose tissues (WATs). A total of 631 differentially expressed lncRNAs (DELs) were identified in four stages. The signal pathways of purine metabolism, Wnt signaling pathway, peroxisome proliferator-activated receptor (PPAR) signaling pathway, cyclic guanosine monophosphate (cGMP)/cGMP-dependent protein kinase (cGMP-PKG) signaling pathway and lipid and atherosclerosis were significantly enriched by the DELs with unique expression patterns. A novel lncRNA that was highly expressed in the iATs of aged rabbits was validated to impair brown adipocyte differentiation in vitro. Our study provided a comprehensive catalog of lncRNAs involved in ARBW in rabbits, which facilitates a better understanding of adipose biology.

Integrated analysis of microRNAs, circular RNAs, long non-coding RNAs, and mRNAs revealed competing endogenous RNA networks involved in brown adipose tissue whitening in rabbits

“…In this study, the Tianfu Black rabbits (native species in Sichuan province of China) were raised at the breeding center of Sichuan Agricultural University, Ya’an, China. These rabbits were fed a standard diet as described in our previous study and water ad libitum [ 16 ]. The rabbits were euthanized by air injection into the ear vein.…”

“…Although the whole-transcriptome sequencing library contains both linear RNA and circRNAs, which led us to access the internal structures of circRNAs hardly, it could provide reliable back-splicing information to identify circRNAs [ 40 ]. In this study, the datasets of whole-transcriptome sequencing of the 12 samples were retrieved from our previous study [ 16 ] and were subjected to identification and quantification of circRNAs based on the back-splicing junction (BSJ) reads. Briefly, the clean reads of whole-transcriptome sequencing were mapped back to the rabbit genome using the non-splicing mode of Bowtie2 software (v2.4.5) [ 33 ].…”

“…While PPARA (a BAT-selective TF) could counter BAT whitening [ 15 ]. On the post-transcription level, our previous study has identified a set of long non-coding RNAs (lncRNAs) that were involved in the BAT whitening using whole-transcriptome sequencing [ 16 ]. Nevertheless, our knowledge of post-transcriptional regulation of BAT whitening remains at its infancy.…”

Dynamics of transcriptome and chromatin accessibility revealed sequential regulation of potential transcription factors during the brown adipose tissue whitening in rabbits

“…Given the large size and easy accessibility of infant BAT, rabbits exhibit great importance in revealing the whitening process of BAT. Our previous study characterized the morphology changes during BAT whitening in rabbits by using H&E staining and immunohistochemistry and found increased lipid accumulation and decreased proportion of classical brown adipocytes during BAT whitening ( Du et al, 2021 ). In this study, we performed RNA-sequencing (RNA-seq) and the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to investigate the dynamics and functions of the transcriptome and chromatin accessibility at four growth stages of rabbits.…”

Integrated Analysis of Transcriptome, microRNAs, and Chromatin Accessibility Revealed Potential Early B-Cell Factor1-Regulated Transcriptional Networks during the Early Development of Fetal Brown Adipose Tissues in Rabbits

“…Maintaining the chromatin accessibility of the binding sites of key genes was found to be essential for the thermogenesis of BAT [ 24 , 25 ]. In domestic animals, recent transcriptomic studies have revealed the RNA molecules regulating the postpartum development of BAT in goats [ 28 ], cattle [ 16 ], and rabbits [ 29 ]. Nevertheless, our knowledge of the regulatory mechanisms of epigenetic regulation during FBAT development, especially early FBAT development, remains largely unknown in domestic mammals.…”