scholarly journals Conserved sequence block clustering and flanking inter-cluster flexibility delineate enhancers that regulate nerfin-1 expression during Drosophila CNS development

2009 ◽  
Vol 9 (2) ◽  
pp. 65-72 ◽  
Author(s):  
Alexander Kuzin ◽  
Mukta Kundu ◽  
Antonios Ekatomatis ◽  
Thomas Brody ◽  
Ward F. Odenwald
Keyword(s):  
Cns Development ◽  
Conserved Sequence ◽  
Sequence Block ◽  
Block Clustering

scholarly journals Efficient site-specific cleavage by RNase MRP requires interaction with two evolutionarily conserved mitochondrial RNA sequences.

1990 ◽  
Vol 10 (5) ◽  
pp. 2191-2201 ◽  
Author(s):  
J L Bennett ◽  
D A Clayton
Keyword(s):  
Sequence Homology ◽  
Mammalian Species ◽  
Saturation Mutagenesis ◽  
Mitochondrial Rna ◽  
Rna Sequences ◽  
Site Specific ◽  
Conserved Sequence ◽  
Sequence Block ◽  
Rnase Mrp

RNase MRP is a site-specific endonuclease that processes primer mitochondrial RNA from the leading-strand origin of mitochondrial DNA replication. Using deletional analysis and saturation mutagenesis, we have determined the substrate requirements for cleavage by mouse mitochondrial RNase MRP. Two regions of sequence homology among vertebrate mitochondrial RNA primers, conserved sequence blocks II and III, were found to be critical for both efficient and accurate cleavage; a third region of sequence homology, conserved sequence block I, was dispensable. Analysis of insertion and deletion mutations within conserved sequence block II demonstrated that the specificity of RNase MRP accommodates the natural sequence heterogeneity of conserved sequence block II in vivo. Heterologous assays with human RNase MRP and mutated mouse mitochondrial RNA substrates indicated that sequences essential for substrate recognition are conserved between mammalian species.

scholarly journals Length heterogeneity at conserved sequence block 2 in human mitochondrial DNA acts as a rheostat for RNA polymerase POLRMT activity

2016 ◽  
Vol 44 (16) ◽  
pp. 7817-7829 ◽  
Author(s):  
Benedict G. Tan ◽  
Frederick C. Wellesley ◽  
Nigel J. Savery ◽  
Mark D. Szczelkun
Keyword(s):  
Mitochondrial Dna ◽  
Rna Polymerase ◽  
Human Mitochondrial Dna ◽  
Conserved Sequence ◽  
Sequence Block

Efficient site-specific cleavage by RNase MRP requires interaction with two evolutionarily conserved mitochondrial RNA sequences

1990 ◽  
Vol 10 (5) ◽  
pp. 2191-2201
Author(s):  
J L Bennett ◽  
D A Clayton
Keyword(s):  
Sequence Homology ◽  
Mammalian Species ◽  
Saturation Mutagenesis ◽  
Mitochondrial Rna ◽  
Rna Sequences ◽  
Site Specific ◽  
Conserved Sequence ◽  
Sequence Block ◽  
Rnase Mrp

RNase MRP is a site-specific endonuclease that processes primer mitochondrial RNA from the leading-strand origin of mitochondrial DNA replication. Using deletional analysis and saturation mutagenesis, we have determined the substrate requirements for cleavage by mouse mitochondrial RNase MRP. Two regions of sequence homology among vertebrate mitochondrial RNA primers, conserved sequence blocks II and III, were found to be critical for both efficient and accurate cleavage; a third region of sequence homology, conserved sequence block I, was dispensable. Analysis of insertion and deletion mutations within conserved sequence block II demonstrated that the specificity of RNase MRP accommodates the natural sequence heterogeneity of conserved sequence block II in vivo. Heterologous assays with human RNase MRP and mutated mouse mitochondrial RNA substrates indicated that sequences essential for substrate recognition are conserved between mammalian species.

Three different macronuclear DNAs in Oxytricha fallax share a common sequence block

1984 ◽  
Vol 4 (5) ◽  
pp. 931-938
Author(s):  
S W Cartinhour ◽  
G A Herrick
Keyword(s):  
High Frequency ◽  
Base Pairs ◽  
Conserved Sequence ◽  
Sequence Block ◽  
The Family ◽  
The Common ◽  
Common Block ◽  
Common Sequence

The three members of a cross-hybridizing family of macronuclear DNAs (4,890, 2,780, and 1,640 base pairs) from the protozoan Oxytricha fallax have in common a conserved sequence block 1,300 to 1,550 base pairs long. Adjacent to the common block in the two larger DNAs are sequences which are unique to them, whereas the smallest DNA contains few if any additional sequences. The family reappears when the macronucleus is replaced after conjugation and can be detected in another O. fallax subspecies. In a random collection of cloned macronuclear DNAs, 6 of 15 hybridize to macronuclear DNA families. This high frequency suggests that families sharing common sequence blocks have an important role in macronuclear function.

A very compact mt-DNA control region in the widely distributed goby Pomatoschistus minutus (Teleostei: Gobiidae)

2002 ◽  
Vol 82 (6) ◽  
pp. 1001-1003 ◽  
Author(s):  
S. STEFANNI ◽  
I.-S. CHEN ◽  
P.J. MILLER
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Sequence Divergence ◽  
Mt Dna ◽  
Conserved Sequence ◽  
Sequence Block ◽  
Pomatoschistus Minutus ◽  
Region Length ◽  
D Loop

The control region of the mitochondrial genome was amplified and sequenced for six individuals of the gobioid fish Pomatoschistus minutus, from several European localities, and one specimen of the related Deltentosteus quadrimaculatus. The length of this region for the former species was found to be 773 bp, 7·1% shorter than that previously described as the most compact D-loop known among teleosts. Sequences from other fish have been compared and the largest gap falls in the section between the conserved sequence block and the pyrimidine tract. Alignment of P. minutus sequences was done with D. quadrimaculatus, whose control region length was 853 bp, and this gap was found to be of 61 bp. For the P. minutus sample, the intraspecific sequence divergence is 0·07%.

scholarly journals Intraspecific Genetic Distance and Phylogenetic Evolution of Schizothorax Plagiostomus Inferred from Mitochondrial D-Loop Sequences

2021 ◽  
Author(s):  
Tasleem Akhtar ◽  
Muneeb M. Musthafa ◽  
Noor Us Sehar ◽  
Ghazanfar Ali
Keyword(s):  
Phylogenetic Relationships ◽  
Nucleotide Diversity ◽  
Nucleotide Composition ◽  
Pairwise Distance ◽  
Conserved Sequence ◽  
Sequence Block ◽  
Loop Region ◽  
D Loop ◽  
Phylogenetic Evolution ◽  
Specific Nucleotide

Abstract The fish in the genus Schizothorax from the Cyprinidae family live in high-altitude Rivers andstreams, are threatened by various anthropogenic stressors. This study aims to characterize S. plagiostomus across Pakistan and throughout the world available on NCBI using the mitochondrial D-loop region, and in particular, to assess the degree of intra-specific pairwise distance among these sequences, as well as to establish their phylogenetic relationships. The percent overall nucleotide composition was 32.6% (A), 33.6% (T), 19.8% (C), and 14.0% (G), which infers that S. plagiostomus control regions is AT-rich (66.2%) and poor in G contents. The mean pair-wise intra-specific nucleotide diversity (Pi)of all the S. plagiostomus was 0.022. While, the inter-specific nucleotide diversity of all the Schizothorax species was 0.049. D-loop sequences for intra-specific variations revealed 765 sites were invariable and 10 were variable, 8 parsimony informative sites and only 2 were singletons. The overall transition/transversion ratio is R = 7.135. Three domains in S. plagiostomus were observed, namely, the termination associated sequence (TAS) domain, the central conserved sequence block (CSB) domain, and the conserved sequence block (CSB) domain. No substitution saturation was detected as an Iss value was significantly (𝑃< 0.001) lower than the Iss.c in all cases indicating the suitability of the data for phylogenetic analysis. This study signifies the importance of the control region for the genetic analysis of S. plagiostomus and also provides a hypothesis of their phylogenetic relationships.

scholarly journals The preference of the mitochondrial endonuclease for a conserved sequence block in mitochondrial DNA is highly conserved during mammalian evolution

1988 ◽  
Vol 16 (14) ◽  
pp. 6427-6445 ◽  
Author(s):  
Robert L. Low ◽  
Jenny M. Buzan ◽  
Christopher L. Couper
Keyword(s):  
Mitochondrial Dna ◽  
Mammalian Evolution ◽  
Conserved Sequence ◽  
Sequence Block

scholarly journals Precise annotation of human, chimpanzee, rhesus macaque and mouse mitochondrial genomes using 5’ and 3’ end small RNAs

2019 ◽  
Author(s):  
Zhi Cheng ◽  
Haishuo Ji ◽  
Xiufeng Jin ◽  
Bo Wang ◽  
Tungon Yau ◽  
...  
Keyword(s):  
Rhesus Macaque ◽  
Small Rnas ◽  
Molecular Phylogenetics ◽  
Feedback Mechanism ◽  
Mitochondrial Genomes ◽  
Conserved Sequence ◽  
Negative Feedback Mechanism ◽  
Sequence Block ◽  
D Loop ◽  
Loop Regions

AbstractUsing 5’ and 3’ end small RNAs, we annotated human, chimpanzee, rhesus macaque and mouse mitochondrial genomes at 1 base-pair (bp) resolution to cover both strands of the mammalian mitochondrial genome entirely without leaving any gaps or overlaps. The precise annotation of all coding and non-coding genes (e.g. ncMT1, MDL2 and MDL1AS) led to the discovery of novel functions and mechanisms of mitochondrion. In this study, we defined the conserved sequence block (CSB) region to span five CSBs (CSB1, CSB2, CSB3, LSP and HSP) and identified the motifs of five CSBs in the mitochondrial displacement loop (D-loop) regions of 52 mammals. The conserved arrangement of these five CSBs in 17 primates inspired us to investigate the function of the mtDNA D-loop, which has been puzzling scientists for more than 50 years. We found that 5’ sRNAs of MDL1AS control the expression levels of mitochondrial genes as a whole by a negative feedback mechanism. Thus, the precise annotations of three CSBs (CSB2, LSP and HSP) in more species will help to understand the function of the mtDNA D-loop. The precision annotation of animal mitochondrial genomes also provides abundant information for studying the molecular phylogenetics and evolution of animals.

Sequence variations in the mitochondrial DNA control region and their implications for the phylogeny of the Cypriniformes

2002 ◽  
Vol 80 (3) ◽  
pp. 569-581 ◽  
Author(s):  
Huanzhang Liu ◽  
Chyng-Shyan Tzeng ◽  
Hui-Yu Teng
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Control Region ◽  
Monophyletic Group ◽  
Mitochondrial Dna Control Region ◽  
Central Domain ◽  
Conserved Sequence ◽  
Sequence Block ◽  
Sequence Variations

The mitochondrial DNA control region of six cobitids and two catostomids was sequenced and compared with sequences of other cypriniforms to study their sequence variations. The extended termination associated sequence (ETAS) domain, central domain, and conserved sequence block (CSB) domain were partitioned and the ETAS sequence, CSB-D, CSB-E, ECSB-F, CSB1, CSB2, and CSB3 were identified. It is suggested that the "hairpin" TACAT-ATGTA is the key sequence of ETAS and GACATA is the symbol of CSB1. Phylogenetic analysis based on the CSB domain showed that all cyprinids evolved as one monophyletic group, while the non-cyprinid Cypriniformes could be another monophyly that is in accordance with the hypothesis proposed by Siebert. Further analysis of the phylogeny of the Cobitoidei was also conducted and it is tentatively suggested that their relationships are Catostomidae + (Gyrinocheilidae + (Botiinae + (Homalopteridae + (Cobitinae + Nemacheilinae)))).

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