Long Noncoding RNA Expression Profiling During the Neuronal Differentiation of Glial Precursor Cells from Rat Dorsal Root Ganglia

Abstract

Long noncoding RNAs (lncRNAs) play important roles in the process of cell fate determination. However, their function and expression profiles have not yet been systematically investigated during the transdifferentiation of glial precursor cells derived from dorsal root ganglia (DRG) in the peripheral nervous system. Our results demonstrated significant differences in gene architecture and expression among the three transcript types (lncRNA, mRNA, and TUCP). Distinct differences in transcript length, exon number, and ORF length were identified between lncRNAs and mRNAs after comparative analysis of their structure and sequence conservation. We found that the upregulated lncRNAs outnumbered the downregulated lncRNAs in glial precursor cells cultured with proBDNF antiserum compared with the levels in glial precursor cells cultured without proBDNF antiserum. By a series of GO and KEGG analyses, we found that the effects of some lncRNAs on their target genes in cis were related to nerve growth factor-induced cell cycle, cell phenotype change, and neuronal differentiation. The qRT-PCR verification results of lncRNAs ENSRNOT00000091991, ENSRNOT00000087717, and LNC000429 were mostly consistent with the sequencing results. The candidate lncRNAs may be associated with the neuronal transdifferentiation of glial precursor cells. Our study provides the first evidence for a remarkably diverse pattern of lncRNA expression during neuronal differentiation of glial precursor cells from rat DRG and also provides a resource for lncRNA studies in the field of cell differentiation.

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Abbreviations

lncRNA:

long noncoding RNA

DRG:

dorsal root ganglia

lincRNA:

intergenic lncRNA

lincRNA:

long intergenic ncRNA

SP:

substance P

shRNA:

short hairpin RNA

PDL:

poly D-lysine hydrobromide

GS:

glutamine synthetase

PBS:

phosphate-buffered saline

Tuj 1:

neuron-specific class III beta-rubulin

CGRP:

calcitonin gene-related peptide

FPKM:

the fragments per kilobase of transcript per million fragments mapped

CNCI:

Coding-Noncoding Index

CPC:

Coding Potential Calculator

ORF:

open reading frame

GO:

Gene Ontology

KEGG:

Kyoto Encyclopedia of Genes and Genomes

PPI:

protein-protein interactions

qRT-PCR:

quantitative real time-polymerase chain reaction

proBDNF:

precursor brain-derived neurotrophic factor

PFAM:

Pfam-scan

TUCP:

transcript of uncertain coding potential

PI3K:

phosphatidylinositol 3-kinase

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Acknowledgements

We thank Liwen Bianji, Edanz Group China (www.liwenbianji.cn/ac), for editing the English text of a draft of this manuscript.

Funding

This work was supported by the National Natural Science Foundation of China (No. 31560295, to L.Y.L.); Yunnan Applied Basic Research Projects [No. 2018FE001(-163), to L.Y.L.; 2018FE001(-016), to W.M.]; Major Scientific and Technological Achievements Cultivation Projects of Kunming Medical University (CGPY201802, to L.Y.L.); and Research Innovation Team of Yunnan Province (2019HC022).

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L.Y.L. and J.H.G designed the study, and provided the funds and financial support for this research. Y.F.D., W.M., T.Z., J.W.Y, C.H.Z., K.P.L., X.B.W., J.W.W., Z.W., X.K.Z., C.Y.L, J.J..L., and X.P.W. carried out the experimental study and analyzed the data. Y.F.D., W.M., and T.Z. wrote the manuscript. All authors read and approved the final manuscript.

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Correspondence to Jianhui Guo or Liyan Li.

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Table S1. Glial cell culture medium

Table S2. The primer sequence information

Table S3. Gene structure and expression analysis of annotated lncRNA

Table S4. Gene structure and expression analysis of novel lncRNA

Table S5. Gene structure and expression analysis of mRNA

Table S6. The expression levels of lncRNA transcripts

Table S7. The expression levels of TUCP transcripts

Table S8. The expression levels of mRNA transcripts

Table S9. lncRNA target gene enrichment analysis in cis form

Table S10. KEGG pathways analysis of the proB12h vs. control group in cis form

Table S11. KEGG pathways analysis of the proB24h vs. control group in cis form

Table S12. KEGG pathways analysis of the proB3d vs. control group in cis form

Table S13. KEGG pathways analysis of the proB7d vs. control group in cis form

Table S14. KEGG pathways analysis of the proB12h vs. control group in trans form

Table S15. KEGG pathways analysis of the proB24h vs. control group in trans form

Table S16. KEGG pathways analysis of the proB3d vs. control group in trans form

Table S17. KEGG pathways analysis of the proB7d vs. control group in trans form

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Dai, Y., Ma, W., Zhang, T. et al. Long Noncoding RNA Expression Profiling During the Neuronal Differentiation of Glial Precursor Cells from Rat Dorsal Root Ganglia. Biotechnol Bioproc E 25, 356–373 (2020). https://doi.org/10.1007/s12257-019-0317-x

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Keywords

  • lncRNA
  • mRNA
  • expression profiling
  • glial precursor cell
  • differentiation
  • proBDNF