TY - JOUR
T1 - Signaling landscape of mitochondrial non-coding RNAs
AU - Mutharasu, Gnanavel
AU - Murugesan, Akshaya
AU - Kondamani, Saravnan
AU - Thiyagarajan, Ramesh
AU - Yli-Harja, Olli
AU - Kandhavelu, Meenakshisundaram
N1 - Funding Information:
We acknowledge Center for International Mobility (CIMO) Finland, for the grant support. We thank CSC (Finnish IT Center for Science) for providing us with a computational facility to carry out the research work. We also thank Ms. Nilakhi Poddar for the computational research assistance.
Publisher Copyright:
© 2023 Informa UK Limited, trading as Taylor & Francis Group.
PY - 2023
Y1 - 2023
N2 - Human mitochondria are the vital cell organelle acting as a storehouse of energy generation and diverse regulatory functions. Mitochondrial DNA comprises 93% coding region and 7% non-coding regions, in which the non-coding region hypothesized as responsible for signaling is our specific interest. Here, we explored the unknown functions of mitochondrial non-coding RNAs by studying their respective signaling pathways. We retrieved conserved motifs of interactions from known experimental protein-RNA complexes to model unknown mitochondrial ncRNA sequences. Our results provide the ncRNAs list and show their involvement in four crucial pathways, such as (i) Processing of Capped Intron-Containing Pre-mRNA, (ii) Spliceosome, (iii) Spliceosomal assembly, and (iv) RNA Polymerase II Transcription, respectively. The interactome analysis revealed that the SRSF2 and U2AF2 proteins interact with ncRNAs. Further, we have simulated the selected ncRNA-protein complexes in cell-like environmental conditions and found them stable in terms of energetics. Through our study, we have identified an apparent interaction of mitochondrial ncRNAs with proteins and their role in critical signaling pathways, providing new insights into mitochondrial ncRNA-dependent gene regulation. Communicated by Ramaswamy H. Sarma.
AB - Human mitochondria are the vital cell organelle acting as a storehouse of energy generation and diverse regulatory functions. Mitochondrial DNA comprises 93% coding region and 7% non-coding regions, in which the non-coding region hypothesized as responsible for signaling is our specific interest. Here, we explored the unknown functions of mitochondrial non-coding RNAs by studying their respective signaling pathways. We retrieved conserved motifs of interactions from known experimental protein-RNA complexes to model unknown mitochondrial ncRNA sequences. Our results provide the ncRNAs list and show their involvement in four crucial pathways, such as (i) Processing of Capped Intron-Containing Pre-mRNA, (ii) Spliceosome, (iii) Spliceosomal assembly, and (iv) RNA Polymerase II Transcription, respectively. The interactome analysis revealed that the SRSF2 and U2AF2 proteins interact with ncRNAs. Further, we have simulated the selected ncRNA-protein complexes in cell-like environmental conditions and found them stable in terms of energetics. Through our study, we have identified an apparent interaction of mitochondrial ncRNAs with proteins and their role in critical signaling pathways, providing new insights into mitochondrial ncRNA-dependent gene regulation. Communicated by Ramaswamy H. Sarma.
KW - gene regulation
KW - interactions networks
KW - Nucleic acids
KW - pathways
KW - signaling
U2 - 10.1080/07391102.2022.2164520
DO - 10.1080/07391102.2022.2164520
M3 - Article
C2 - 36617957
AN - SCOPUS:85146709301
SN - 0739-1102
VL - 41
SP - 12016
EP - 12025
JO - JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS
JF - JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS
IS - 21
ER -