Small RNAome sequencing delineates the small RNA landscape of pluripotent adult stem cells in the planarian Schmidtea mediterranea
Yue Li,
An Zeng,
Xiao-Shuan Han,
Ge Li,
Yong-Qin Li,
Bairong Shen,
Qing Jing
Affiliations
Yue Li
Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institute for Biological Science, Shanghai Jiao-Tong University School of Medicine and Chinese Academy of Sciences, Shanghai 200031, China
An Zeng
Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institute for Biological Science, Shanghai Jiao-Tong University School of Medicine and Chinese Academy of Sciences, Shanghai 200031, China
Xiao-Shuan Han
Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institute for Biological Science, Shanghai Jiao-Tong University School of Medicine and Chinese Academy of Sciences, Shanghai 200031, China
Ge Li
Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institute for Biological Science, Shanghai Jiao-Tong University School of Medicine and Chinese Academy of Sciences, Shanghai 200031, China
Yong-Qin Li
Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institute for Biological Science, Shanghai Jiao-Tong University School of Medicine and Chinese Academy of Sciences, Shanghai 200031, China
Bairong Shen
Center for Systems Biology, Soochow University, Suzhou 215006, China
Qing Jing
Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institute for Biological Science, Shanghai Jiao-Tong University School of Medicine and Chinese Academy of Sciences, Shanghai 200031, China
Small noncoding RNAs play a pivotal role in the regulation of gene expression, and are key regulators of animal development. Freshwater planarian exhibits an extraordinary ability to regenerate any missing body parts, representing an emerging model for studying mechanism underlying stem cell regulation and tissue regeneration. Here, we utilized next-generation sequencing (NGS) to identify small RNAs that are expressed in planarian adult stem cells, and are implicated in tissue regeneration. We profiled microRNAs (miRNAs), piwi-interacting RNA (piRNAs), small rDNA-derived RNAs (srRNAs) and endogenous interfering RNAs (endo-siRNAs) population from size 18–30 nt, measured the expression of 244 conserved miRNAs, and identified 41 novel miRNAs and 64 novel endo-siRNAs. Expression profiling analyses revealed that most piRNAs and srRNAs are up-regulated during regeneration, and that the most abundantly expressed srRNAs are from 5.8s and 28s rRNA. Furthermore, a target prediction method was adopted to investigate the anti-correlation of small RNAs and mRNA expression. We built up a gene regulatory network based on the genes that are targeted by dynamically changed small RNAs. These results expand the known small RNA repertoire in planarian, and provide valuable insights and a rich resource for understanding the small RNAs landscape in stem cell-mediated regeneration.
