scholarly journals Investigating the Modularity and Evolution of Adjacent Gene Coregulation

2021 ◽  
Author(s):  
Dmitry Pokushalov
Keyword(s):  
Adjacent Gene

scholarly journals The Alcohol Dehydrogenase Gene Is Nested in the outspread Locus of Drosophila melanogaster

Genetics ◽  
1996 ◽  
Vol 143 (2) ◽  
pp. 897-911 ◽  
Author(s):  
S McNabb ◽  
S Greig ◽  
T Davis
Keyword(s):  
Drosophila Melanogaster ◽  
Alcohol Dehydrogenase ◽  
Pcr Amplification ◽  
Transcription Unit ◽  
Adjacent Gene ◽  
Dehydrogenase Gene ◽  
Chromosomal Breakpoints ◽  
Splicing Patterns ◽  
Somatic Musculature

Abstract This report describes the structure and expression of the outspread (osp) gene of Drosophila melanogaster. Previous work showed that chromosomal breakpoints associated with mutations of the osp locus map to both sides of the alcohol dehydrogenase gene (Adh), suggesting that Adh and the adjacent gene Adh' are nested in osp. We extended a chromosomal walk and mapped additional osp mutations to define the maximum molecular limit of osp as 119 kb. We identified a 6-kb transcript that hybridizes to osp region DNA and is altered or absent in osp mutants. Accumulation of this RNA peaks during embryonic and pupal periods. The osp cDNAs comprise two distinct classes based on alternative splicing patterns. The 5′ end of the longest cDNA was extended by PCR amplification. When hybridized to the osp walk, the 5′ extension verifies that Adh and Adh' are nested in osp and shows that osp has a transcription unit of ≥74 kb. In situ hybridization shows that osp is expressed both maternally and zygotically. In the ovary, osp is transcribed in nurse cells and localized in the oocyte. In embryos, expression is most abundant in the developing visceral and somatic musculature.

scholarly journals Allosteric Modulation of theFaecalibacterium prausnitziiHepatitis Delta Virus-like Ribozyme by Glucosamine 6-Phosphate: The Substrate of the Adjacent Gene Product

Biochemistry ◽  
2017 ◽  
Vol 56 (45) ◽  
pp. 6006-6014 ◽  
Author(s):  
Luiz F. M. Passalacqua ◽  
Randi M. Jimenez ◽  
Jennifer Y. Fong ◽  
Andrej Lupták
Keyword(s):  
Gene Product ◽  
Allosteric Modulation ◽  
Adjacent Gene ◽  
Delta Virus

scholarly journals Control of yeast gene expression by transposable elements: maximum expression requires a functional Ty activator sequence and a defective Ty promoter.

1988 ◽  
Vol 8 (10) ◽  
pp. 4009-4017 ◽  
Author(s):  
L R Coney ◽  
G S Roeder
Keyword(s):  
Gene Expression ◽  
Adjacent Gene ◽  
Multiple Sequence ◽  
Sequence Element ◽  
Cis Acting ◽  
Ty Elements ◽  
The Relationship ◽  
Maximum Expression ◽  
Modest Effect

Integration of a transposable element adjacent to a gene frequently results in an alteration in expression of the nearby gene. The purpose of our experiments was to identify cis-acting sequences within a yeast transposon (Ty) that are important for expression of the adjacent gene. The role of these sequences in Ty transcription was also analyzed in order to examine the relationship between Ty and adjacent gene expression. Three naturally occurring Ty elements located at the HIS4 locus were examined. These Ty elements differed by multiple sequence changes and had different effects on HIS4 expression. To determine which sequences were important to Ty and HIS4 expression, Ty::lacZ and Ty::HIS4::lacZ fusion genes were constructed and analyzed. Results of these experiments indicated that a sequence element is present in the Ty epsilon region that is necessary for HIS4 expression but which has only a modest effect on Ty transcription. Additionally, a mutation in the Ty promoter region decreased Ty transcription and increased HIS4 expression. The opposite effects of this mutation on Ty and adjacent gene expression were probably caused by promoter competition.

Transposable element-mediated enhancement of gene expression in Saccharomyces cerevisiae involves sequence-specific binding of a trans-acting factor

1988 ◽  
Vol 8 (6) ◽  
pp. 2572-2580
Author(s):  
A Goel ◽  
R E Pearlman
Keyword(s):  
Gene Expression ◽  
Base Pair ◽  
Specific Binding ◽  
Adjacent Gene ◽  
Cis Acting ◽  
Contact Sites ◽  
Cell Extracts ◽  
Single Base Pair ◽  
Beta Galactosidase

In our studies on the regulation of adjacent-gene expression by Ty sequences, we demonstrated that a single-base-pair change (T-A----C-G) in the epsilon sequence of Ty917-derived elements is primarily responsible for enhancement of beta-galactosidase expression from lacZ fusion plasmids. Using an electrophoretic gel mobility assay, we showed that the same base pair transition is required for binding of a trans-acting factor, TyBF, from crude cell extracts in vitro. We identified the site of TyBF binding and determined the guanine nucleotide contact sites required for TyBF interaction. We propose that TyBF binding to cis-acting Ty2 sequences activates adjacent-gene transcription.

Abstract 2791: SINE retrotransposons cause epigenetic reprogramming of adjacent gene promoters

2011 ◽  
Author(s):  
Marcos R.H Estecio ◽  
Mhair Dekmezian ◽  
Juan Gallegos ◽  
Shoudan Liang ◽  
Jean-Pierre Issa
Keyword(s):  
Epigenetic Reprogramming ◽  
Gene Promoters ◽  
Adjacent Gene

scholarly journals ISEcp1-Mediated Transposition and Homologous Recombination Can Explain the Context of blaCTX-M-62 Linked to qnrB2

2010 ◽  
Vol 54 (7) ◽  
pp. 3039-3042 ◽  
Author(s):  
Zhiyong Zong ◽  
Sally R. Partridge ◽  
Jonathan R. Iredell
Keyword(s):  
Homologous Recombination ◽  
Klebsiella Pneumoniae ◽  
Conjugative Plasmid ◽  
Adjacent Gene ◽  
Class 1 Integron ◽  
Class 1

ABSTRACT bla CTX-M-62, a C508T variant of bla CTX-M-3b, was transferred from Klebsiella pneumoniae JIE137 on a conjugative plasmid together with a class 1 integron containing the dfrA12-gcuF-aadA2 cassette array, ISCR1, and qnrB2. bla CTX-M-62 lies between intact and rearranged copies of ISEcp1 in a configuration that can be explained by a combination of transposition and homologous recombination and which also illustrates the ability of ISEcp1 to mobilize an adjacent gene as part of transposition units of different sizes.

A SEARCH FOR COMPLEXITY AT THE MATING-TYPE LOCUS OF NEUROSPORA CRASSA

1973 ◽  
Vol 15 (3) ◽  
pp. 577-585 ◽  
Author(s):  
Dorothy Newmeyer ◽  
H. Branch Howe Jr. ◽  
Donna R. Galeazzi
Keyword(s):  
Neurospora Crassa ◽  
Mating Type ◽  
Adjacent Gene ◽  
Opposite Mating Type ◽  
Type Locus ◽  
Linked Gene ◽  
Heterokaryon Incompatibility ◽  
Mating Type Locus ◽  
Incompatibility Reaction ◽  
The Right

Evidence for complexity at the mating-type locus of Neurospora crassa was sought by selecting recombinants between closely linked markers on either side. All recombinants were tested for crossing ability, to test the hypothesis that the two mating-type alleles are actually closely linked self-sterile mutants; such tests should also detect subunits analogous to the α and β subunits of the A factor of Schizophyllum or Coprinus. No change in crossing ability was found among the 5,019 recombinants tested, representing 235,000 viable ascospores. The results indicate that if subunits exist, they are not more than 0.002 units apart. Twelve hundred and forty of the recombinants were tested in a way that should also have detected subunits analogous to the A and B factors of Schizophyllum and Coprinus, except that A and B would be closely linked. No such subunits were detected.N. crassa strains of opposite mating type are heterokaryon-incompatible during vegetative growth, and observations of various investigators have suggested that the heterokaryon incompatibility might be controlled by a separate closely-linked gene rather than by mating type itself. A sample of the recombinants was therefore tested for separation of the heterokaryon-incompatibility and crossing-compatibility functions. (Heterokaryon-incompatibility was scored by the presence of an incompatibility reaction in duplications heterozygous for mating type; this technique is simple and eliminates complications due to unlinked heterokaryon-incompatibility loci, several of which are known in N. crassa.) No separation was found. The results indicate that if an adjacent gene is responsible for the heterokaryon-incompatibility, it is not more than 0.0078 units from mating type, if on the left, and not more than 0.018 units from mating type, if on the right.

scholarly journals Pipeline to detect the relationship between transposable elements and adjacent genes in host genome

2021 ◽  
Author(s):  
Caroline Meguerditchian ◽  
Ayse Ergun ◽  
Veronique DECROOCQ ◽  
Marie LEFEBVRE ◽  
Quynh Trang Bui
Keyword(s):  
Gene Expression ◽  
Transposable Elements ◽  
Transcriptional Activity ◽  
Potential Role ◽  
Host Genome ◽  
Signalling Pathways ◽  
Adjacent Gene ◽  
Replication Intermediates ◽  
The Relationship ◽  
Affect Gene Expression

Understanding the relationship between transposable elements (TEs) and their associated genes in the host genome is a key point to explore their potential role in genome evolution. Transposable elements can regulate and affect gene expression not only because of their mobility within the genome but also because of its transcriptional activity. Gene expression can be suppressed, decreased or increased and cellular signalling pathways can be activated through the act of the nearby TE expression itself or subsequent TE replication intermediates. We implemented a pipeline which is capable to reveal the relationship between TEs and adjacent gene distribution in the host genome. Our tool is freely available here : https://github.com/marieBvr/TEs_genes_relationship_pipeline

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