BackgroundSkeletal muscle satellite cells (MSC) are crucial for postnatal growth and regeneration of skeletal muscle. An interaction exists between MSC and intramuscular preadipocytes (IMPA). This study is the first to investigate the effects of IMPA on MSC in chickens and unveil the molecular mechanisms by transcriptome analysis.ResultsPrimary MSC and IMPA were isolated from the pectoralis major muscle of 7-day-old chickens. After both cell types reached confluence, MSC were cultured alone or co-cultured with IMPA for 2 or 4 d. MSC treated for 2 d were subjected to RNA-seq. A total of 1653 known differentially expressed genes (DEG) were identified between co-cultured and mono-cultured MSC (|log2 FC| ≥ 1, FDR < 0.01). Based on Gene Ontology analysis, 48 DEG related to muscle development were screened, including the key genes MYOD1, MYOG, PAX7, and TMEM8C. The 44 DEG related to lipid deposition included the key genes CD36, FABP4, ACSBG2, CYP7A1 and PLIN2. Most of the DEG related to muscle development were downregulated in co-cultured MSC, and DEG related to lipid deposition were upregulated. Immunofluorescence of MHC supported IMPA impeding differentiation of MSC, and Oil Red O staining showed concurrent promotion of lipid deposition. Pathway analysis found that several key genes were enriched in JNK/MAPK and PPAR signaling, which may be the key pathways regulating differentiation and lipid deposition in MSC. Additionally, pathways related to cell junctions may also contribute to the effect of IMPA on MSC.ConclusionsThe present study showed that IMPA impeded differentiation of MSC while promoting their lipid deposition. Pathway analysis indicated that IMPA might inhibit differentiation via the JNK/MAPK pathway, and promote lipid deposition via the PPAR pathway. This study supplies insights into the effect of IMPA on MSC, providing new clues on exposing the molecular mechanisms underlying the interplay between skeletal muscle and intramuscular fat in chickens.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5209-5) contains supplementary material, which is available to authorized users.