Chromatin accessibility in canine stromal cells and its implications for canine somatic cell reprogramming

Stem Cells Translational Medicine

Matthew L. Settles¹  Pablo J. Ross²  Maria Questa³  Robert J. Jimenez³  Veronica Lopez‐Cervantes³  Charles K. Crawford³  Maryam Moshref³  Amir Kol³ 

[1] Bioinformatics Core Facility University of California Davis Davis California USA;Department of Animal Science University of California Davis Davis California USA;Department of Pathology, Microbiology and Immunology School of Veterinary Medicine, University of California Davis Davis California USA;

关键词: ATAC‐Seq, cellular reprogramming;    chromatin;    dogs;    induced pluripotent stem cells (iPSC);    regenerative medicine;   

DOI  :  10.1002/sctm.20-0278

来源: DOAJ

【 摘 要 】

Abstract Naturally occurring disease in pet dogs is an untapped and unique resource for stem cell‐based regenerative medicine translational research, given the many similarities and complexity such disease shares with their human counterparts. Canine‐specific regulators of somatic cell reprogramming and pluripotency maintenance are poorly understood. While retroviral delivery of the four Yamanaka factors successfully reprogrammed canine embryonic fibroblasts, adult stromal cells remained resistant to reprogramming in spite of effective viral transduction and transgene expression. We hypothesized that adult stromal cells fail to reprogram due to an epigenetic barrier. Here, we performed assay for transposase‐accessible chromatin using sequencing (ATAC‐seq) on canine stromal and pluripotent stem cells, analyzing 51 samples in total, and establishing the global landscape of chromatin accessibility before and after reprogramming to induced pluripotent stem cells (iPSC). We also studied adult stromal cells that do not yield iPSC colonies to identify potential reprogramming barriers. ATAC‐seq analysis identified distinct cell type clustering patterns and chromatin remodeling during embryonic fibroblast reprogramming. Compared with embryonic fibroblasts, adult stromal cells had a chromatin accessibility landscape that reflects phenotypic differentiation and somatic cell‐fate stability. We ultimately identified 76 candidate genes and several transcription factor binding motifs that may be impeding somatic cell reprogramming to iPSC, and could be targeted for inhibition or activation, in order to improve the process in canines. These results provide a vast resource for better understanding of pluripotency regulators in dogs and provide an unbiased rationale for novel canine‐specific reprogramming approaches.

【 授权许可】

Unknown