MicroRNA transcriptome profiles during swine skeletal muscle development

Abstract

Background: MicroRNA (miR) are a class of small RNAs that regulate gene expression by inhibiting translation of protein encoding transcripts. To evaluate the role of miR in skeletal muscle of swine, global microRNA abundance was measured at specific developmental stages including proliferating satellite cells, three stages of fetal growth, day-old neonate, and the adult.

Results: Twelve potential novel miR were detected that did not match previously reported sequences. In addition, a number of miR previously reported to be expressed in mammalian muscle were detected, having a variety of abundance patterns through muscle development. Muscle-specific miR-206 was nearly absent in proliferating satellite cells in culture, but was the highest abundant miR at other time points evaluated. In addition, miR-1 was moderately abundant throughout developmental stages with highest abundance in the adult. In contrast, miR-133 was moderately abundant in adult muscle and either not detectable or lowly abundant throughout fetal and neonate development. Changes in abundance of ubiquitously expressed miR were also observed. MiR-432 abundance was highest at the earliest stage of fetal development tested (60 day-old fetus) and decreased throughout development to the adult. Conversely, miR-24 and miR-27 exhibited greatest abundance in proliferating satellite cells and the adult, while abundance of miR-368, miR-376, and miR-423-5p was greatest in the neonate.

Conclusion: These data present a complete set of transcriptome profiles to evaluate miR abundance at specific stages of skeletal muscle growth in swine. Identification of these miR provides an initial group of miR that may play a vital role in muscle development and growth.

Figure 1

Saturation plot of microRNA libraries. Saturation plots were created from the neonatal muscle sample to determine saturation of the signal as an indicator that abundance levels would remain constant as new results were added. A total of 5,000 observed miR were evaluated. The supply of unique singletons is represented by the small dashed line, while the known and unknown miR are represented by the solid black line and large dashed line, respectively.

Figure 2

Variation between microRNA libraries. Transcriptome profiles from samples at the same developmental state were compared within the three satellite cell libraries (2a), two individual adult biceps femoris libraries (2b), and two d 90 fetal biceps femoris libraries (2c). MicroRNA cDNA libraries for satellite cells (2a) were created from the pool of the 4th and 5th passage satellite cells and the 6th passage (6th passage, #1). A second library was created from a second flask of 6th passage stellite cells (6th passage, #2) to evaluate variation between satellite cells at the same passage. MicroRNA abundance is represented as number of individual miR tags observed per thousand tags evaluated.

Figure 3

MicroRNA transcriptome profiles. MicroRNA cDNA clone libraries were created from skeletal muscle during specific stages of swine development including satellite cells, d 60 (primary fiber development) of fetal development, d 90 (secondary fiber development) of fetal development, d 105 of fetal development, one day-old neonate and the adult. For the fetal samples, biceps femoris (BF) and longissimus dorsi (LD) were collected from female and male fetuses. Biceps femoris (BF) samples were collected for the one day-old neonate and the adult. MicroRNA abundance is represented as number of individual miR tags observed per thousand tags evaluated. Data for the satellite cells and adult muscle is presented as the average of multiple transcriptome libraries presented in Additional file 1.