BLNCR is a long non-coding RNA adjacent to integrin beta-1 that is rapidly lost during epidermal progenitor cell differentiation

Sabine E J Tanis,Elif Senem Köksal,Jessie A G L Van Buggenum,Klaas W Mulder

doi:10.1038/s41598-018-37251-w

Abstract

As our understanding of transcriptional regulation improves so does our appreciation of its complexity. Both coding and (long) non-coding RNAs provide cells with multiple levels of control and thereby flexibility to adapt gene expression to the environment. However, few long non-coding RNAs (lncRNAs) have been studied in human epidermal stem cells. Here, we characterized the expression of 26 lncRNAs in human epidermal keratinocytes, 7 of which we found to be dynamically expressed during differentiation. We performed in depth analysis of a lncRNA located proximal to the epidermal stem cell marker integrin beta-1 (ITGB1) and transcribed in the opposite direction. We dubbed this gene Beta1-adjacent long non-coding RNA, or BLNCR, and found that its expression is regulated by p63 and AP1 transcription factors. Furthermore, BLNCR expression is regulated downstream the integrin and EGF signaling pathways that are key to epidermal stem cell maintenance. Finally, we found that BLNCR expression is rapidly reduced upon induction of differentiation, preceding the down regulation of integrin beta-1 expression. These dynamics closely mirror the loss of proliferative and adhesion capacity of epidermal stem cells in colony formation assays. Together, these results suggest that loss of BLNCR expression marks the switch from a proliferative state towards terminal differentiation in human epidermal stem cells.

Highlights

Historically research has predominantly focused on protein encoding genes, it is evident that non-coding RNAs play important roles in the regulation of many, if not all, biological processes
We found that integrin beta-1 (ITGB1) and BLNCR are closely spaced genes that are transcribed from opposite strands of the DNA and that the p63 and AP-1 transcription factors are involved in regulating their expression
To explore other long non-coding RNAs (lncRNAs) that may be functionally relevant in this system, we selected 26 lncRNAs that were identified in primary human keratinocytes in the context of the GENCODE consortium[1]

Summary

Introduction

Historically research has predominantly focused on protein encoding genes, it is evident that non-coding RNAs play important roles in the regulation of many, if not all, biological processes. LncRNAs have been implicated in many developmental processes ranging from dosage compensation (e.g. Xist), imprinting (e.g. Kcnq[1], Airn), neuronal development (e.g. Peril, Evf) and stem cell differentiation of neuronal, cardiac, epidermal, endodermal, endothelial and hematopoietic cells[2] Their involvement in various types of cancer and other pathologies highlight the importance of identifying and characterizing these transcripts[3]. The high renewal rate of the epidermal layer requires tight regulation of gene expression programs governing proliferation and differentiation in human epidermal stem cells These cells are anchored to the basement membrane by integrin subunits and are released upon initiation of differentiation, enabling them to traverse several stages of differentiation to eventually be sloughed from the surface of the epidermis. We identified BLNCR as a new epidermal progenitor cell marker that is rapidly down regulated upon induction of differentiation, potentially marking early events of epidermal stem cell differentiation

Methods

Results

Conclusion