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Systematic analysis of small RNAs associated with human mitochondria by deep sequencing: detailed analysis of mitochondrial associated miRNA

Sripada, Lakshmi ; Tomar, Dhanendra ; Prajapati, Paresh ; Singh, Rochika ; Singh, Arun Kumar ; Singh, Rajesh Pfeffer, Sebastien

PloS one, 2012-09, Vol.7 (9), p.e44873-e44873 [Periódico revisado por pares]

United States: Public Library of Science

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Título:
Systematic analysis of small RNAs associated with human mitochondria by deep sequencing: detailed analysis of mitochondrial associated miRNA
Autor: Sripada, Lakshmi ; Tomar, Dhanendra ; Prajapati, Paresh ; Singh, Rochika ; Singh, Arun Kumar ; Singh, Rajesh
Pfeffer, Sebastien
Assuntos: Analysis ; Apoptosis ; Biology ; Biotechnology ; Cell cycle ; Conserved Sequence - genetics ; Crosstalk ; Deoxyribonucleic acid ; DNA ; DNA, Mitochondrial - metabolism ; Energy metabolism ; Fractionation ; Gene expression ; Gene sequencing ; Genome ; Genomes ; Genomics ; HEK293 Cells ; HeLa Cells ; High-Throughput Nucleotide Sequencing - methods ; Humans ; Messenger RNA ; Metabolism ; MicroRNA ; MicroRNAs - metabolism ; miRNA ; Mitochondria ; Mitochondria - metabolism ; Mitochondrial DNA ; mRNA ; mRNA turnover ; Physiological aspects ; Proteins ; Regulators ; Ribonuclease, Pancreatic - metabolism ; Ribonucleic acid ; RNA ; RNA, Messenger - metabolism ; Sequence Analysis, RNA - methods ; Stem cells ; Subcellular Fractions - metabolism ; Target recognition ; Translocation
É parte de: PloS one, 2012-09, Vol.7 (9), p.e44873-e44873
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
Conceived and designed the experiments: LS Rochika Singh. Performed the experiments: LS DT. Analyzed the data: LS DT Rochika Singh Rajesh Singh. Contributed reagents/materials/analysis tools: PP AKS Rochika Singh. Wrote the paper: LS DT Rajesh Singh.
Competing Interests: The authors have declared that no competing interests exist.
Descrição: Mitochondria are one of the central regulators of many cellular processes beyond its well established role in energy metabolism. The inter-organellar crosstalk is critical for the optimal function of mitochondria. Many nuclear encoded proteins and RNA are imported to mitochondria. The translocation of small RNA (sRNA) including miRNA to mitochondria and other sub-cellular organelle is still not clear. We characterized here sRNA including miRNA associated with human mitochondria by cellular fractionation and deep sequencing approach. Mitochondria were purified from HEK293 and HeLa cells for RNA isolation. The sRNA library was generated and sequenced using Illumina system. The analysis showed the presence of unique population of sRNA associated with mitochondria including miRNA. Putative novel miRNAs were characterized from unannotated sRNA sequences. The study showed the association of 428 known, 196 putative novel miRNAs to mitochondria of HEK293 and 327 known, 13 putative novel miRNAs to mitochondria of HeLa cells. The alignment of sRNA to mitochondrial genome was also studied. The targets were analyzed using DAVID to classify them in unique networks using GO and KEGG tools. Analysis of identified targets showed that miRNA associated with mitochondria regulates critical cellular processes like RNA turnover, apoptosis, cell cycle and nucleotide metabolism. The six miRNAs (counts >1000) associated with mitochondria of both HEK293 and HeLa were validated by RT-qPCR. To our knowledge, this is the first systematic study demonstrating the associations of sRNA including miRNA with mitochondria that may regulate site-specific turnover of target mRNA important for mitochondrial related functions.
Editor: United States: Public Library of Science
Idioma: Inglês

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Systematic analysis of small RNAs associated with human mitochondria by deep sequencing: detailed analysis of mitochondrial associated miRNA

Sripada, Lakshmi ; Tomar, Dhanendra ; Prajapati, Paresh ; Singh, Rochika ; Singh, Arun Kumar ; Singh, Rajesh Pfeffer, Sebastien

United States: Public Library of Science

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