Two novel lncRNAs discovered in human mitochondrial DNA using PacBio full-length transcriptome data

Gao, Shan; Tian, Xiaoxuan; Chang, Hong; Sun, Yu; Wu, Zhenfeng; Cheng, Zhi; Dong, Pin; Zhao, Qiang; Ruan, Jishou; Bu, Wenjun

doi:10.1016/j.mito.2017.08.002

Cited by 75 publications

(94 citation statements)

References 14 publications

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“…Whether these lncRNAs act in the mitochondria themselves or are exported from the mitochondria to other cellular compartments (Cesana et al., ; Landerer et al., ) using and/or contributing to the mitochondrial–nuclear communication pathway (Butow & Avadhani, ), and what their roles are, is still to be determined. Recently, two new lncRNAs encoded by the human mitogenome, MDL1 and MDL1AS , were discovered in the MCF‐7 breast cancer cell line (Gao et al., ). These lncRNAs might be involved in positive and negative feedback systems that increase or stabilize the expression of mitochondrial transcripts (Gao et al., ).…”

Section: Long Non‐coding Rnas In the Mitochondriamentioning

confidence: 99%

“…Recently, two new lncRNAs encoded by the human mitogenome, MDL1 and MDL1AS, were discovered in the MCF-7 breast cancer cell line (Gao et al, 2018). These lncRNAs might be involved in positive and negative feedback systems that increase or stabilize the expression of mitochondrial transcripts (Gao et al, 2018). A set of chimeric lncRNAs also exists in mouse and human mitochondria (Dong, Yoshitomi, Hu, & Cui, 2017), but with no evidence of expression in muscle tissue in either case.…”

Section: Long Non-coding Rnas In the Mitochondriamentioning

confidence: 99%

“…RNA sequencing performed on mouse testis, mouse small intestine and human small intestine tissue later confirmed that the human and murine mitogenomes potentially encode thousands of small ncRNAs (Ro et al., ). In addition, we now know that lncRNAs can also be encoded by the mitochondrial genome (Gao et al., ; Landerer et al., ; Rackham et al., ) and selectively localize in different cell compartments, including the nucleus, the cytoplasm (Djebali et al., ) and the mitochondria.…”

Section: Introductionmentioning

confidence: 99%

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Mitochondrial regulation in skeletal muscle: A role for non‐coding RNAs?

Silver

Wadley

Lamon

2018

Experimental Physiology

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Skeletal muscle is a highly metabolic tissue characterized by high mitochondrial abundance. As such, skeletal muscle homeostasis relies on the tight control of mitochondrial gene expression to ensure efficient mitochondrial function. Mitochondria retain a conserved genome from prokaryotic ancestors, and mitochondrial gene regulation relies on communication between mitochondrial- and nuclear-encoded transcripts. Small and long non-coding RNAs (ncRNAs) have regulatory roles in the modulation of gene expression. Emerging evidence demonstrates that regulatory ncRNAs, particularly microRNAs (miRNAs) and long ncRNAs (lncRNAs), localize within the mitochondria in diverse physiological and pathological states. These molecules present intriguing possibilities for the regulation of mitochondrial gene expression. Current research suggests that all known miRNAs are encoded by the nuclear genome but can target mitochondrial genes. Initial investigations demonstrate direct interactions between the muscle-enriched miR-1 and miR-181c and mitochondrial transcripts, suggesting advanced roles of miRNAs in mitochondrial gene regulation. This review draws evidence from the current literature to discuss the hypothesis that a level of ncRNA-mediated gene regulation, in particular miRNA-mediated gene regulation, takes place in the mitochondria. Although ncRNA-mediated regulation of the mitochondrial genome is a relatively unexplored field, it presents exciting possibilities to further our understanding of mitochondrial metabolism and human muscle physiology.

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Section: Long Non‐coding Rnas In the Mitochondriamentioning

confidence: 99%

Section: Long Non-coding Rnas In the Mitochondriamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Mitochondrial regulation in skeletal muscle: A role for non‐coding RNAs?

Silver

Wadley

Lamon

2018

Experimental Physiology

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“…Gao et al 87 constructed the first quantitative transcription map of animal mitochondrial genomes by sequencing the full-88 length transcriptome of the insect Erthesina fullo Thunberg [1] on the PacBio platform [2]. New findings 89 included the 3′ polyadenylation and possible 5′ m 7 G caps of rRNAs [1], the polycistronic transcripts [1], the 90 antisense transcripts of all mitochondrial genes [1], and novel long non-coding RNAs (lncRNAs) [3]. Based 91 on these findings, we proposed the mitochondrial cleavage model [3] and the mitochondrial tRNA 92 processing model [4].…”

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confidence: 99%

Precise annotation of tick mitochondrial genomes reveals multiple STR variation and one transposon-like element

Chen

Xu²,

Yang

et al. 2019

Preprint

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48In this study, we used long-PCR amplification combined with Next-Generation Sequencing (NGS) to 49 obtain complete mitochondrial genomes of individual ticks and performed precise annotation of these 50 genomes. These annotations were confirmed by the PacBio full-length transcriptome data to cover both 51 entire strands of the mitochondrial genomes without any gaps or overlaps. Based on these annotations, most 52 of our findings were consistent with those from previous studies. Moreover, two important findings were 53 reported for the first time, contributing fundamental knowledge to mitochondrial biology. The first was the 54 discovery of a transposon-like element that may reveal the mechanisms of mitochondrial gene order 55 rearrangement and genomic structural variation. Another finding was that Short Tandem Repeat (STRs) are 56 the dominant variation type causing mitochondrial sequence diversity within an individual tick, insect, 57 mouse and human. Comparisons between interindividual and intraindividual variation showed that 58 polynucleotides and STRs with longer repeat units had the same variation pattern. Particularly, mitochondria 59 containing deleterious mutations can accumulate in cells and deleterious STR mutations irreversibly change 60 the proteins made from their mRNAs. Therefore, we proposed that deleterious STR mutations in 61 mitochondria cause aging and diseases. This finding helped to ultimately reveal the mechanisms of 62 mitochondrial DNA variation and its consequences (e.g., aging and diseases) in animals. Our study will give 63 rise to the reconsideration of the importance of STRs and a unified study of STR variation with longer and 64 shorter repeat units (particularly polynucleotides) in both nuclear and mitochondrial genomes. The complete 65 mitochondrial genome sequence of Dermacentor silvarum is available at the NCBI GenBank database under 66 the accession number MN347015 and the raw data is available at the NCBI SRA database under the 67 accession number SRP178347 . 68 69 70 71 72 73 74 75 76 77 78 79 80

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“…143 The RNA extraction of D. nuttalli and cDNA synthesis were performed using the protocol published in 144 our previous study [14]. The DNA extraction of D. nuttalli, D. silvarum, sheep and bovine was performed 145 using the protocol published in our previous study [15].…”

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confidence: 99%

DNA segment of African Swine Fever Virus first detected in hard ticks from sheep and bovine

Chen

Yang

et al. 2018

Preprint

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23In this study, we aimed to detect viruses in hard ticks using the small RNA sequencing based method. 24 A 235-bp DNA segment was detected in Dermacentor nuttalli (hard ticks) and D. silvarum (hard ticks) from 25 sheep and bovine, respectively. The detected 235-bp segment had an identity of 99% to a 235-bp DNA 26 segment of African Swine Fever Virus (ASFV) and contained three single nucleotide mutations (C38T, 27 C76T and A108C). C38T, resulting in an single amino acid mutation G66D, suggests the existence of a new 28 ASFV strain, which is different from all reported ASFV strains in NCBI GenBank database. These results 29 also suggest that ASFV could have a wide range of hosts or vectors, beyond the well known Suidae family 30 and soft ticks. Our findings pave the way toward further studies of ASFV transmission and development of 31 prevention and control measures.

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Two novel lncRNAs discovered in human mitochondrial DNA using PacBio full-length transcriptome data

Cited by 75 publications

References 14 publications

Mitochondrial regulation in skeletal muscle: A role for non‐coding RNAs?

Mitochondrial regulation in skeletal muscle: A role for non‐coding RNAs?

Precise annotation of tick mitochondrial genomes reveals multiple STR variation and one transposon-like element

DNA segment of African Swine Fever Virus first detected in hard ticks from sheep and bovine

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