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

Abstract

In domestic mammals, cold stress decreases the survival rate of newborns and increases the cost of management. Brown adipose tissue (BAT) is the main thermogenic organ for cubs, and well-developed fetal BAT (FBAT) is beneficial for newborns to maintain core temperatures during the first several days of life. However, our knowledge of the epigenetic mechanisms during the early development of FBAT remains largely unknown. Rabbits (Oryctolagus cuniculus) are economically important domestic animals. In this study, a histological analysis shows that the tissue content, thermogenic capacity, and lipid content of FBAT dramatically increases from gestational day 21 (G21) to gestational day 24 (G24) in rabbits. RNA-seq, microRNA-seq (miRNA-seq), and the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) show that many genes, miRNAs, and chromatin-accessible regions (referred to as peaks) were identified as significantly changed from G21 to G24, respectively. The upregulated genes from G21 to G24 were significantly enriched in the mitochondrial metabolism and thermogenesis-related signal pathways. The integrated analysis of transcriptome and chromatin accessibility reveals that the peaks in the promoters have a more regulatory effect than peaks in other genomic elements on the expression of their nearby genes in FBATs. The upregulated genes that are associated with increased chromatin accessibility in the promoter regions are involved in the energy metabolism-related signaling pathways. The genes that have a greater tendency to be regulated by miRNAs than the chromatin accessibility in gene promoters are involved in the apelin, insulin, and endocytosis signaling pathways. Furthermore, genome-wide transcription factor (TF) footprinting analysis identifies early B-cell factor1 (EBF1) as playing a key role during early FBAT development. The carbon metabolism, citrate cycle, and PPAR signaling pathways are significantly enriched by the predicted EBF1-regulated cascade TF-network. In conclusion, our work provides a framework for understanding epigenetics regulatory mechanisms underlying the early development of FBAT and identifies potential TF involved in the early development of FBAT in rabbits.

The RNase III enzyme Dicer1 is essential for larval development in Bombyx mori

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“…For PITA, we set ddG ≤ −10 as the threshold by reference (Kertesz et al, 2007). For miRanda, referring to the setting (energy ≤ −15; Du et al, 2022), we reduced the energy option to ≤−30 in order to obtain more precise predictions and energy ≤7 (Parnell et al, 2011). For RNAhybrid, energy was set to ≤−30.…”

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“…BibiServ (https://bibiserv.cebitec.uni-bielefeld.de/rnahybrid/) com os seguintes parâmetros: threshold para energia livre mínima (MFE) < −15.0 kcal/mol(Li et al, 2021;Du et al, 2022), tamanho das seeds dos miRNAs variando…”