scholarly journals MitoVisualize: A resource for analysis of variants in human mitochondrial RNAs and DNA

2021 ◽  
Author(s):  
Nicole J Lake ◽  
Lily Zhou ◽  
Jenny Xu ◽  
Monkol Lek
Keyword(s):  
Mitochondrial Dna ◽  
Ribosomal Rna ◽  
Source Code ◽  
Large Deletion ◽  
Transfer Rna ◽  
Variant Interpretation ◽  
Rna Structures ◽  
Human Mitochondrial Dna ◽  
Mtdna Variation ◽  
Mitochondrial Transfer

We present MitoVisualize, a new tool for analysis of the human mitochondrial DNA (mtDNA). MitoVisualize enables visualization of: (1) the position and effect of variants in mitochondrial transfer RNA (tRNA) and ribosomal RNA (rRNA) secondary structures alongside curated variant annotations, (2) data across RNA structures, such as to show all positions with disease-associated variants or with post-transcriptional modifications, and (3) the position of a base, gene or region in the circular mtDNA map, such as to show the location of a large deletion. All visualizations can be easily downloaded as figures for reuse. MitoVisualize can be useful for anyone interested in exploring mtDNA variation, though is designed to facilitate mtDNA variant interpretation in particular. MitoVisualize can be accessed via https://www.mitovisualize.org/. The source code is available at https://github.com/leklab/mito_visualize/.

Nucleotide sequences of small ribosomal RNA and adjacent transfer RNA genes in rat mitochondrial DNA

Gene ◽  
1981 ◽  
Vol 16 (1-3) ◽  
pp. 297-307 ◽  
Author(s):  
Kobayashi Midori ◽  
Seki Tetsunori ◽  
Yaginuma Katsuyuki ◽  
Koike Katsuro
Keyword(s):  
Mitochondrial Dna ◽  
Ribosomal Rna ◽  
Transfer Rna ◽  
Nucleotide Sequences ◽  
Rna Genes

Hybridization of mitochondrial transfer RNA and mitochondrial DNA in petite mutants of yeast

1972 ◽  
Vol 63 (3) ◽  
pp. 441-451 ◽  
Author(s):  
M. Cohen ◽  
J. Casey ◽  
M. Rabinowitz ◽  
G.S. Getz
Keyword(s):  
Mitochondrial Dna ◽  
Transfer Rna ◽  
Petite Mutants ◽  
Mitochondrial Transfer

scholarly journals Transcripts and processing patterns for the ribosomal RNA and transfer RNA region of Neurospora crassa mitochondrial DNA.

1981 ◽  
Vol 256 (4) ◽  
pp. 2027-2034
Author(s):  
M.R. Green ◽  
M.F. Grimm ◽  
R.R. Goewert ◽  
R.A. Collins ◽  
M.D. Cole ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Neurospora Crassa ◽  
Ribosomal Rna ◽  
Transfer Rna

scholarly journals Geographic variation in human mitochondrial DNA from Papua New Guinea.

Genetics ◽  
1990 ◽  
Vol 124 (3) ◽  
pp. 717-733 ◽  
Author(s):  
M Stoneking ◽  
L B Jorde ◽  
K Bhatia ◽  
A C Wilson
Keyword(s):  
Mitochondrial Dna ◽  
High Resolution ◽  
Papua New Guinea ◽  
Statistical Significance ◽  
New Guinea ◽  
Human Populations ◽  
Restriction Maps ◽  
Population Movements ◽  
Human Mitochondrial Dna ◽  
Mtdna Variation

Abstract High resolution mitochondrial DNA (mtDNA) restriction maps, consisting of an average of 370 sites per mtDNA map, were constructed for 119 people from 25 localities in Papua New Guinea (PNG). Comparison of these PNG restriction maps to published maps from Australian, Caucasian, Asian and African mtDNAs reveals that PNG has the lowest amount of mtDNA variation, and that PNG mtDNA lineages originated from Southeast Asia. The statistical significance of geographic structuring of populations with respect to mtDNA was assessed by comparing observed GST values to a distribution of GST values generated by random resampling of the data. These analyses show that there is significant structuring of mtDNA variation among worldwide populations, between highland and coastal PNG populations, and even between two highland PNG populations located approximately 200 km apart. However, coastal PNG populations are essentially panmictic, despite being spread over several hundred kilometers. Highland PNG populations also have more mtDNA variability and more mtDNA types represented per founding lineage than coastal PNG populations. All of these observations are consistent with a more ancient, restricted origin of highland PNG populations, internal isolation of highland PNG populations from one another and from coastal populations, and more recent and extensive population movements through coastal PNG. An apparent linguistic effect on PNG mtDNA variation disappeared when geography was taken into account. The high resolution technique for examining mtDNA variation, coupled with extensive geographic sampling within a single defined area, leads to an enhanced understanding of the influence of geography on mtDNA variation in human populations.

Complete mitogenome of Parum colligata (Lepidoptera: Sphingidae) and its phylogenetic position within the Sphingidae

Zootaxa ◽  
2019 ◽  
Vol 4652 (1) ◽  
pp. 126-134 ◽  
Author(s):  
JUN LI ◽  
KUNJIE HU ◽  
YAQI ZHAO ◽  
RUIRUI LIN ◽  
YAOYAO ZHANG ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Transfer Rna ◽  
Phylogenetic Position ◽  
Rich Region ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Complete Mitogenome ◽  
Rna Genes

In this study, the complete mitochondrial DNA sequence of Parum colligata (Lepidoptera: Sphingidae: Smerinthinae) was sequenced firstly. The mitogenome is 15,288 bp in size, containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and an A+T-rich region. In the mitogenome, Ile, Leu2, and Phe are the most frequently used codon families, while codons GCG, TGC, GGC, CTG, AGG, and ACG are absent. The A+T-rich region is 358 bp in length including a motif ‘ATAGA’, an 18 bp poly-T stretch, three copies of a 12 bp ‘TATATATATATA’, and a short poly-A element. The nucleotides sequence of A+T-rich region is closer to Sphinginae than Macroglossinae. Phylogenetic analyses, based on the PCGs by using Maximum Likelihood (ML) and Bayesian Inference (BI) methods, generated consistent results that Smerinthinae was clustered together with Sphinginae to be the sister groups rather than Macroglossinae. 

scholarly journals Stable transplantation of human mitochondrial DNA by high-throughput, pressurized isolated mitochondrial delivery

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Alexander J Sercel ◽  
Alexander N Patananan ◽  
Tianxing Man ◽  
Ting-Hsiang Wu ◽  
Amy K Yu ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Oxidative Phosphorylation ◽  
Mammalian Cells ◽  
Nuclear Dna ◽  
Cell Fates ◽  
Human Mitochondrial Dna ◽  
Isolated Mitochondria ◽  
Mitochondrial Transfer ◽  
Communication And Coordination ◽  
Transfer Device

Generating mammalian cells with specific mitochondrial DNA (mtDNA)–nuclear DNA (nDNA) combinations is desirable but difficult to achieve and would be enabling for studies of mitochondrial-nuclear communication and coordination in controlling cell fates and functions. We developed ‘MitoPunch’, a pressure-driven mitochondrial transfer device, to deliver isolated mitochondria into numerous target mammalian cells simultaneously. MitoPunch and MitoCeption, a previously described force-based mitochondrial transfer approach, both yield stable isolated mitochondrial recipient (SIMR) cells that permanently retain exogenous mtDNA, whereas coincubation of mitochondria with cells does not yield SIMR cells. Although a typical MitoPunch or MitoCeption delivery results in dozens of immortalized SIMR clones with restored oxidative phosphorylation, only MitoPunch can produce replication-limited, non-immortal human SIMR clones. The MitoPunch device is versatile, inexpensive to assemble, and easy to use for engineering mtDNA–nDNA combinations to enable fundamental studies and potential translational applications.

Sign in / Sign up

Export Citation Format

Share Document