scholarly journals The ubiquitous potential Z-forming sequence of eucaryotes, (dT-dG)n . (dC-dA)n, is not detectable in the genomes of eubacteria, archaebacteria, or mitochondria.

1986 ◽  
Vol 6 (8) ◽  
pp. 3010-3013 ◽  
Author(s):  
D S Gross ◽  
W T Garrard
Keyword(s):  
Sequence Analysis ◽  
Nuclear Dna ◽  
Repeat Element ◽  
Phylogenetic Distribution ◽  
Base Pairs ◽  
Nuclear Genomes

The potential Z-forming sequence (dT-dG)n . (dC-dA)n is an abundant, interspersed repeat element that is ubiquitous in eucaryotic nuclear genomes. We report that in contrast to eucaryotic nuclear DNA, the genomes of eubacteria, archaebacteria, and mitochondria lack this sequence, since even a single tract of greater than or equal to 14 base pairs in length is not detectable through either hybridization or sequence analysis. Interestingly, the phylogenetic distribution of the (dT-dG)n . (dC-dA)n repeat exhibits a striking parallel to that of (dT-dC)n . (dG-dA)n, but not to other homocopolymeric sequences such as (dC-dG)n . (dC-dG)n or (dT-dA)n . (dT-dA)n.

The ubiquitous potential Z-forming sequence of eucaryotes, (dT-dG)n . (dC-dA)n, is not detectable in the genomes of eubacteria, archaebacteria, or mitochondria

1986 ◽  
Vol 6 (8) ◽  
pp. 3010-3013
Author(s):  
D S Gross ◽  
W T Garrard
Keyword(s):  
Sequence Analysis ◽  
Nuclear Dna ◽  
Repeat Element ◽  
Phylogenetic Distribution ◽  
Base Pairs ◽  
Nuclear Genomes

The potential Z-forming sequence (dT-dG)n . (dC-dA)n is an abundant, interspersed repeat element that is ubiquitous in eucaryotic nuclear genomes. We report that in contrast to eucaryotic nuclear DNA, the genomes of eubacteria, archaebacteria, and mitochondria lack this sequence, since even a single tract of greater than or equal to 14 base pairs in length is not detectable through either hybridization or sequence analysis. Interestingly, the phylogenetic distribution of the (dT-dG)n . (dC-dA)n repeat exhibits a striking parallel to that of (dT-dC)n . (dG-dA)n, but not to other homocopolymeric sequences such as (dC-dG)n . (dC-dG)n or (dT-dA)n . (dT-dA)n.

scholarly journals LENGTH MUTATIONS IN HUMAN MITOCHONDRIAL DNA

Genetics ◽  
1983 ◽  
Vol 104 (4) ◽  
pp. 699-711
Author(s):  
R L Cann ◽  
A C Wilson
Keyword(s):  
Nuclear Dna ◽  
Average Rate ◽  
Rapid Evolution ◽  
Human Species ◽  
Base Pairs ◽  
Human Mitochondrial Dna ◽  
Noncoding Sequences ◽  
Mitochondrial Dnas ◽  
D Loop ◽  
Length Mutations

ABSTRACT By high-resolution, restriction mapping of mitochondrial DNAs purified from 112 human individuals, we have identified 14 length variants caused by small additions and deletions (from about 6 to 14 base pairs in length). Three of the 14 length differences are due to mutations at two locations within the D loop, whereas the remaining 11 occur at seven sites that are probably within other noncoding sequences and at junctions between coding sequences. In five of the nine regions of length polymorphism, there is a sequence of five cytosines in a row, this sequence being comparatively rare in coding DNA. Phylogenetic analysis indicates that, in most of the polymorphic regions, a given length mutation has arisen several times independently in different human lineages. The average rate at which length mutations have been arising and surviving in the human species is estimated to be many times higher for noncoding mtDNA than for noncoding nuclear DNA. The mystery of why vertebrate mtDNA is more prone than nuclear DNA to evolve by point mutation is now compounded by the discovery of a similar bias toward rapid evolution by length mutation.

scholarly journals DNA SEQUENCES OF FRAMESHIFT AND OTHER MUTATIONS INDUCED BY ICR-170 IN YEAST

Genetics ◽  
1985 ◽  
Vol 111 (2) ◽  
pp. 233-241
Author(s):  
Joachim F Ernst ◽  
D Michael Hampsey ◽  
Fred Sherman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Sequence Analysis ◽  
Genetic Analysis ◽  
Dna Sequences ◽  
Induced Mutations ◽  
Sequence Analyses ◽  
Base Pairs ◽  
Yeast Saccharomyces Cerevisiae ◽  
Frameshift Mutations

ABSTRACT ICR-170-induced mutations in the CYC1 gene of the yeast Saccharomyces cerevisiae were investigated by genetic and DNA sequence analyses. Genetic analysis of 33 cyc1 mutations induced by ICR-170 and sequence analysis of eight representatives demonstrated that over one-third were frameshift mutations that occurred at one site corresponding to amino acid positions 29-30, whereas the remaining mutations were distributed more-or-less randomly, and a few of these were not frameshift mutations. The sequence results indicate that ICR-170 primarily induces G·C additions at sites containing monotonous runs of three G·C base pairs. However, some (see PDF) sites within the CYC1 gene were not mutated by ICR-170. Thus, ICR-170 is a relatively specific mutagen that preferentially acts on certain sites with monotonous runs of G·C base pairs.

Reconstruction of complexes of histone and superhelical nuclear DNA

1981 ◽  
Vol 50 (1) ◽  
pp. 209-224
Author(s):  
J.M. Levin ◽  
P.R. Cook
Keyword(s):  
Nuclear Dna ◽  
Micrococcal Nuclease ◽  
Base Pairs ◽  
The Core ◽  
Ionic Detergent ◽  
Nuclear Rna ◽  
Core Histones ◽  
Non Destructive ◽  
Rna And Dna ◽  
General Method

When HeLa cells are lysed in solutions containing a non-ionic detergent and 2 M-NaCl, structures are released that retain many of the morphological features of nuclei. These nucleoids contain all the nuclear RNA and DNA but few of the proteins characteristic of chromatin. Their DNA is supercoiled and so intact. Using a simple and rapid procedure we have reconstructed nucleohistone complexes from nucleoids and the ‘core’ histones without breaking the DNA. We have probed the integrity and structure of the reconstructed complexes using a non-destructive fluorometric approach, which provides a general method for detecting agents that bind to DNA and alter its supercoiling. The superhelical status of the DNA in the reconstructed complexes is indistinguishable from that found in control nucleoids containing core histones. Experiments with micrococcal nuclease confirm that the DNA in the reconstructed complexes is organized into nucleosome-like structures. These, however, are spaced 145 base-pairs apart and not 200 base-pairs apart as is found in native chromatin.

DNA polymorphism of dogs (Canis familiaris L.). I. Origin, distribution of dogs in the light of molecular biological data about their mitochondrial and nuclear genomes

Biomics ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 298-308
Author(s):  
D.A. Chemeris ◽  
Yu.R. Giniyatov ◽  
R.R. Garafutdinov ◽  
A.V. Chemeris
Keyword(s):  
Western Europe ◽  
Dna Polymorphism ◽  
Nuclear Dna ◽  
Canis Familiaris ◽  
Biological Data ◽  
Migration Routes ◽  
Points Of View ◽  
Nuclear Genomes ◽  
Biological Methods ◽  
Mtdna Polymorphism

Information is given on the size and organization of the mitochondrial and nuclear genomes of dogs, including information on polymorphisms of some loci used to clarify the phylogenetic relationships of wolves and the first dogs, including hypotheses about the places of domestication of ancient now extinct wolves and the dates of these events. It is noted that the introduction of molecular biological methods in archaeology has allowed to obtain the principally new data on ancient wolves and dogs. Based on mtDNA polymorphism and nuclear DNA polymorphism, migration routes of already domesticated dogs together with humans have been tracked. The previously existing points of view about the origin of the first dogs in Western Europe, as well as in East Asia, have been supplemented in recent years by assumptions about the appearance of the first proto-dogs in Siberia.

The heart in neuromuscular disease: primary mitochondrial diseases

ESC CardioMed ◽  
2018 ◽  
pp. 1528-1530
Author(s):  
Denis Duboc
Keyword(s):  
Neuromuscular Disease ◽  
Nuclear Dna ◽  
Single Cells ◽  
Mitochondrial Diseases ◽  
Respiratory Chain Complexes ◽  
Base Pairs ◽  
Daughter Cells ◽  
Dna Molecule ◽  
Chain Complexes ◽  
Genes Encoding

Mitochondria are responsible for energy production in most eukaryotic cells. Each cell contains at least one mitochondrion and every mitochondrion contains two to ten copies of a circular DNA molecule (mitochondrial DNA or mtDNA). Cardiomyocytes contain approximately 10,000 mtDNA copies. MtDNA is composed of around 16,500 base pairs and 37 genes encoding 13 subunits of the respiratory chain complexes I, III, IV, and V, 22 mitochondrial tRNAs and 2 rRNAs. With each cell division, mitochondria and mtDNA are randomly distributed to daughter cells. In humans, mitochondria are inherited exclusively from the mother. In healthy people mtDNA copies are usually identical at birth (homoplasmy) but with ageing, mtDNA is particularly prone to somatic mutation because, unlike nuclear DNA, it is continuously replicated, even in non-dividing tissues such as myocardium. This can lead to the propagation of somatic mutations within single cells by a process called clonal expansion. In addition, mtDNA lacks an extensive DNA repair mechanism.

scholarly journals Archaic mitochondrial DNA inserts in modern day nuclear genomes

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Robert Bücking ◽  
Murray P Cox ◽  
Georgi Hudjashov ◽  
Lauri Saag ◽  
Herawati Sudoyo ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Nuclear Dna ◽  
Modern Human ◽  
Sub Saharan Africa ◽  
Next Generation Sequencing Data ◽  
Human Populations ◽  
Sequencing Data ◽  
Modern Humans ◽  
High Coverage ◽  
Nuclear Genomes

Abstract Background Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Saharan Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs). Results We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin, present in 15 analysed genomes; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male. Conclusions Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.

scholarly journals Archaic mitochondrial DNA inserts in modern day nuclear genomes

2019 ◽  
Author(s):  
Robert Bücking ◽  
Murray P Cox ◽  
Georgi Hudjashov ◽  
Lauri Saag ◽  
Herawati Sudoyo ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Nuclear Dna ◽  
Modern Human ◽  
Next Generation Sequencing Data ◽  
Human Populations ◽  
Sequencing Data ◽  
Modern Humans ◽  
High Coverage ◽  
Nuclear Genomes ◽  
Generation Sequencing

Abstract Background: Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Sahara Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs). Results: We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male. Conclusions: Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.

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