scholarly journals The peach latent mosaic viroid replication initiation site is located at a universal position that appears to be defined by a conserved sequence

Virology ◽  
2008 ◽  
Vol 373 (2) ◽  
pp. 362-375 ◽  
Author(s):  
Julie Motard ◽  
François Bolduc ◽  
Dan Thompson ◽  
Jean-Pierre Perreault
Keyword(s):  
Initiation Site ◽  
Replication Initiation ◽  
Conserved Sequence ◽  
Viroid Replication

scholarly journals The human mitochondrial transcription factor A is a versatile G-quadruplex binding protein

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Sébastien Lyonnais ◽  
Aleix Tarrés-Solé ◽  
Anna Rubio-Cosials ◽  
Anna Cuppari ◽  
Reicy Brito ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Binding Protein ◽  
Critical Role ◽  
Replication Initiation ◽  
Mitochondrial Transcription ◽  
Hmg Box ◽  
Conserved Sequence ◽  
Mitochondrial Transcription Factor ◽  
G Quadruplex ◽  
Mitochondrial Transcription Factor A

Abstract The ability of the guanine-rich strand of the human mitochondrial DNA (mtDNA) to form G-quadruplex structures (G4s) has been recently highlighted, suggesting potential functions in mtDNA replication initiation and mtDNA stability. G4 structures in mtDNA raise the question of their recognition by factors associated with the mitochondrial nucleoid. The mitochondrial transcription factor A (TFAM), a high-mobility group (HMG)-box protein, is the major binding protein of human mtDNA and plays a critical role in its expression and maintenance. HMG-box proteins are pleiotropic sensors of DNA structural alterations. Thus, we investigated and uncovered a surprising ability of TFAM to bind to DNA or RNA G4 with great versatility, showing an affinity similar than to double-stranded DNA. The recognition of G4s by endogenous TFAM was detected in mitochondrial extracts by pull-down experiments using a G4-DNA from the mtDNA conserved sequence block II (CSBII). Biochemical characterization shows that TFAM binding to G4 depends on both the G-quartets core and flanking single-stranded overhangs. Additionally, it shows a structure-specific binding mode that differs from B-DNA, including G4-dependent TFAM multimerization. These TFAM-G4 interactions suggest functional recognition of G4s in the mitochondria.

Ectoderm nuclei from sea urchin embryos contain a Spec-DNA binding protein similar to the vertebrate transcription factor USF

Development ◽  
1990 ◽  
Vol 110 (1) ◽  
pp. 259-272 ◽  
Author(s):  
C.R. Tomlinson ◽  
M.T. Kozlowski ◽  
W.H. Klein
Keyword(s):  
Transcription Factor ◽  
Sea Urchin ◽  
Sea Urchins ◽  
Dna Interaction ◽  
Initiation Site ◽  
Upstream Stimulatory Factor ◽  
Transcriptional Initiation ◽  
Lytechinus Pictus ◽  
Conserved Sequence ◽  
A Cell

The Spec gene family of Stronglyocentrotus purpuratus is expressed exclusively in aboral ectoderm cells during embryogenesis. To investigate the regulation of Spec gene activity, the region around the Spec1 transcriptional initiation site was analyzed for sites of protein-DNA interaction. One high-affinity site bound a factor termed SpF1 within the Spec1 5′ untranslated leader region at position +39 to +60. The core sequence recognized by SpF1, CACGTG, is the same as that of the upstream stimulatory factor (USF), a widely occurring vertebrate transcription factor containing a myc-HLH motif. A comparison of USF- and SpF1-binding activities suggested that SpF1 was a sea urchin version of USF. SpF1 activity was detectable only in ectoderm cells of the embryo, implying that it has a role as a cell type-specific transcription factor. SpF1-binding sites were also found upstream of the Spec2a and Spec2c genes in the same conserved sequence block as Spec1. Extracts from Lytechinus pictus embryos showed an SpF1-like activity, suggesting that SpF1 is conserved in sea urchins. Surprisingly, changes in the Spec1, Spec2a, or Spec2c genes that removed or modified the SpF1-binding site had no effect on expression when reporter gene fusions containing these mutations were injected into sea urchin eggs and analyzed for expression during embryogenesis. We propose that, while SpF1 may not be essential for expression of the exogenously introduced reporter genes, it may be required for proper regulation of the endogenous Spec genes.

scholarly journals Determination of human DNA replication origin position and efficiency reveals principles of initiation zone organisation

2021 ◽  
Author(s):  
Guillaume Guilbaud ◽  
Pierre Murat ◽  
Helen S Wilkes ◽  
Leticia Koch Lerner ◽  
Julian Sale ◽  
...  
Keyword(s):  
Dna Replication ◽  
Replication Origin ◽  
Gradient Centrifugation ◽  
Initiation Site ◽  
Efficiency Score ◽  
Replication Initiation ◽  
Equilibrium Density ◽  
Replication Origins ◽  
Origin Firing ◽  
Dna Replication Origin

Replication of the human genome initiates within broad zones of ~ 150 kb. The extent to which firing of individual DNA replication origins within initiation zones is spatially stochastic or localised at defined sites remains a matter of debate. A thorough characterisation of the dynamic activation of origins within initiation zones is hampered by the lack of a high-resolution map of both their position and efficiency. To address this shortcoming, we describe a modification of initiation site sequencing (ini-seq) based on density substitution. Newly-replicated DNA is rendered heavy-light (HL) by incorporation of BrdUTP, unreplicated DNA remaining light-light (LL). Replicated HL-DNA is separated from unreplicated LL-DNA by equilibrium density gradient centrifugation, then both fractions are subjected to massive parallel sequencing. This allows precise mapping of 23,905 replication origins simultaneously with an assignment of a replication initiation efficiency score to each. We show that origin firing within initiation zones is not randomly distributed. Rather, origins are arranged hierarchically with a set of very highly efficient origins marking zone boundaries. We propose that these origins explain much of the early firing activity arising within initiation zones, helping to unify the concept of replication initiation zones with the identification of discrete replication origin sites.

scholarly journals A conserved sequence element is present around the transcription initiation site for RNA polymerase A inSaccharomycetoideae

1984 ◽  
Vol 12 (2) ◽  
pp. 1137-1148 ◽  
Author(s):  
Martin Ph. Verbeet ◽  
Jacobus Klootwijk ◽  
Harm van Heerikhuizen ◽  
Ruud D. Fontijn ◽  
Erno Vreugdenhil ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Transcription Initiation ◽  
Initiation Site ◽  
Transcription Initiation Site ◽  
Sequence Element ◽  
Conserved Sequence

scholarly journals Mapping of replication initiation site inMycoplasma capricolumgenome by two-dimensional gel-electrophoretic analysis

1993 ◽  
Vol 21 (20) ◽  
pp. 4816-4823 ◽  
Author(s):  
Makoto Miyata ◽  
Ken-lchi Sano ◽  
Ryosuke Okada ◽  
Takashi Fukumura
Keyword(s):  
Electrophoretic Analysis ◽  
Initiation Site ◽  
Replication Initiation ◽  
Two Dimensional

scholarly journals Nature of a paramyxovirus replication promoter influences a nearby transcription signal

2005 ◽  
Vol 86 (1) ◽  
pp. 171-180 ◽  
Author(s):  
Diane Vulliémoz ◽  
Samuel Cordey ◽  
Geneviève Mottet-Osman ◽  
Laurent Roux
Keyword(s):  
Transcription Initiation ◽  
Sendai Virus ◽  
Initiation Site ◽  
Essential Elements ◽  
Replication Initiation ◽  
Start Site ◽  
Mrna Synthesis ◽  
Gene Start ◽  
Or Gene ◽  
Transcription And Replication

The genomic and antigenomic 3′ ends of the Sendai virus replication promoters are bi-partite in nature. They are symmetrically composed of leader or trailer sequences, a gene start (gs) or gene end (ge) site, respectively, and a simple hexameric repeat. Studies of how mRNA synthesis initiates from the first gene start site (gs1) have been hampered by the fact that gs1 is located between two essential elements of the replication promoter. Transcription initiation, then, is separated from the replication initiation site by only 56 nt on the genome, so that transcription and replication may sterically interfere with each other. In order to study the initiation of Sendai virus mRNAs without this possible interference, Sendai virus mini-genomes were prepared having tandem promoters in which replication takes place from the external one, whereas mRNA synthesis occurs from the internal one. Transcription now initiates at position 146 rather than position 56 relative to the genome 3′ end. Under these conditions, it was found that the frequency with which mRNA synthesis initiates depends, in an inverse fashion, on the strength of the external replication promoter. It was also found that the sequences essential for replication are not required for basic mRNA synthesis as long as there is an external replication promoter at which viral RNA polymerase can enter the nucleocapsid template. The manner in which transcription and replication initiations influence each other is discussed.

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