In the present study, researchers extensively characterized lncRNA expression in mesenchymal cells during commitment and differentiation to the osteoblast lineage using a whole transcriptome sequencing approach (RNA-Seq)

Osteogenesis is a complex biological process that requires mesenchymal stem cell differentiation through the osteoblast lineage together with the precise timing of developmental signaling cascades, expression of transcriptional regulators of genes producing a bone matrix, and promoting mineral deposition.

In mammals, while 75% of the genome is transcribed, only 2% encodes proteins. In addition to the messenger RNA (mRNA) transcribed genes, a large part of the osteoblast genome is represented by numerous classes of noncoding RNAs, among which are the well studied microRNAs that function in regulating protein translation. 

The role of microRNAs in cell fate determination of mesenchymal stem cells: balancing adipogenesis and osteogenesis. BMB It is becoming increasingly apparent that the group of long noncoding RNAs (lncRNAs) contribute significantly to the regulation of gene expression.

mMSCs were isolated from bone marrow of 8-week transgenic male mice and differentiated over 21 days. RNA was isolated four stages of differentiation: undifferentiated (day0), commitment (day7), extracellular matrix (ECM) deposition (day14) and mineralization (day21).

Expression patterns of known osteoblast marker genes confirmed data quality at the differentiation time points. From this analysis, we identified 12,391 mRNAs and 1,438 annotated lncRNAs expressed during mMSC osteoblast differentiation.

Differential expression of mRNAs and lncRNAs in mMSCs was analyzed and 3,100 mRNAs and 462 lncRNAs were identified as being differentially expressed (fold-change >2-fold; FDR adjusted p-value <0.05).

Clustering of the differentially expressed mRNAs showed distinct profiles across development. Cluster 1 consisted of mRNAs that exhibit increased expression with differentiation.

Osteoblast marker genes

An examination of mRNAs in this cluster revealed several known osteoblast marker genes and GO analysis identified this cluster to be enriched in genes associated with ossification, skeletal development, and mineralization.

 Using mouse primary mesenchymal stromal cells (mMSC), they identified 1438 annotated lncRNAs expressed during MSC differentiation, 462 of which are differentially expressed.

Researchers performed guilt-by-association analysis using lncRNA and mRNA expression profiles to identify lncRNAs influencing MSC commitment and differentiation. These findings open novel dimensions for exploring lncRNAs in regulating the normal bone formation and in skeletal disorders.