TINCR is not a non-coding RNA but encodes a protein component of cornified epidermal keratinocytes

Abstract

Long non-coding RNAs have been implicated in the regulation of a plethora of biological processes, yet it has been challenging to verify that they are truly not coding for proteins. Terminal differentiation-induced non-coding RNA (TINCR) is a 3.7-kilobase mRNA that is highly abundant in epidermal keratinocytes prior to cornification. Here, we report the presence of an evolutionarily conserved open reading frame in TINCR and the identification of peptides derived from this open reading frame in the proteome of human stratum corneum. Our results demonstrate that TINCR is a protein-coding RNA and suggest that the TINCR-encoded protein is involved in keratinocyte cornification.

Keywords: cornification; differentiation; epidermis; evolution; ubiquitin.

Figure 1

TINCR encodes an evolutionarily conserved protein. A, Schematic depiction of the protein‐coding role of TINCR. Exons are depicted as boxes with the open reading frame (ORF) shown in red. The coding region and the relative positions of so‐called “TINCR box” sequence motifs (white and black triangles) are indicated on the mRNA. B, Protein amounts in cornified envelopes and in the solubilized fraction of human stratum corneum are shown in units of intensity‐based absolute quantification (iBAQ). The values were obtained from Tables S2 and S3 of Reference Karim et al 2019.14 Proteins detected only in the cornified envelope fraction are marked by red arrows. C, Amino acid sequence alignment of TINCR proteins from phylogenetically diverse mammals and chicken. Exclusive unique peptides detected by mass spectrometry (MS)14 are indicated by red boxes in the human TINCR sequence. Numbers (n) of peptide hits are shown above the boxes. Grey shading indicates amino acid residues different from the human counterpart. Residues identical in all TINCR orthologs are indicated by asterisks below the alignment