scholarly journals Positional Conservation of Clusters of Overlapping Promoter-Like Sequences in Enterobacterial Genomes

2006 ◽  
Vol 23 (5) ◽  
pp. 997-1010 ◽  
Author(s):  
Araceli M. Huerta ◽  
Julio Collado-Vides ◽  
M. Pilar Francino
Keyword(s):  
Positional Conservation

scholarly journals Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Paulo P. Amaral ◽  
Tommaso Leonardi ◽  
Namshik Han ◽  
Emmanuelle Viré ◽  
Dennis K. Gascoigne ◽  
...  
Keyword(s):  
Anchor Point ◽  
Positional Conservation

scholarly journals Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations

2009 ◽  
Vol 19 (9) ◽  
pp. 1562-1569 ◽  
Author(s):  
S. Kumar ◽  
M. P. Suleski ◽  
G. J. Markov ◽  
S. Lawrence ◽  
A. Marco ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Correct Diagnosis ◽  
Positional Conservation ◽  
Amino Acid Mutations

Rescue and regulation of proboscipedia: a homeotic gene of the Antennapedia Complex

Development ◽  
1991 ◽  
Vol 113 (1) ◽  
pp. 257-271 ◽  
Author(s):  
F.M. Randazzo ◽  
D.L. Cribbs ◽  
T.C. Kaufman
Keyword(s):  
Biological Significance ◽  
Regulatory Elements ◽  
P Element ◽  
Homeotic Gene ◽  
Its Sequence ◽  
Drosophila Genome ◽  
Homeotic Genes ◽  
Cis Acting ◽  
Positional Conservation ◽  
Hox Clusters

The extraordinary positional conservation of the homeotic genes within the Antennapedia and the Bithorax Complexes (ANT-C and BX-C) in Drosophila melanogaster and the murine Hox and human HOX clusters of genes can be interpreted as a reflection of functional necessity. The homeotic gene proboscipedia (pb) resides within the ANT-C, and its sequence is related to that of Hox-1.5. We show that two independent pb minigene P-element insertion lines completely rescue the labial palp-to-first leg homeotic transformation caused by pb null mutations; thus, a homeotic gene of the ANT-C can properly carry out its homeotic function outside of the complex. Despite the complete rescue of the null, the minigene expresses pb protein in only a subset of pb's normal domains of expression. Therefore, the biological significance of the excluded expression pattern elements remains unclear except to note they appear unnecessary for specifying normal labial identity. Additionally, by using reporter gene constructs inserted into the Drosophila genome and by comparing pb-associated genomic sequences from two divergent species, we have located cis-acting regulatory elements required for pb expression in embryos and larvae.

scholarly journals Novel MicroRNAs (miRNAs) Encoded by Herpesvirus of Turkeys: Evidence of miRNA Evolution by Duplication

2009 ◽  
Vol 83 (13) ◽  
pp. 6969-6973 ◽  
Author(s):  
Yongxiu Yao ◽  
Yuguang Zhao ◽  
Lorraine P. Smith ◽  
Michael Watson ◽  
Venugopal Nair
Keyword(s):  
Disease Virus ◽  
Virus Type ◽  
Phylogenetic Relationships ◽  
Viral Genome ◽  
Herpesvirus Of Turkeys ◽  
Positional Conservation ◽  
Disease Virus Type ◽  
Mirna Evolution ◽  
Close Sequence

ABSTRACT Herpesviruses account for 134 out of the 140 virus-encoded microRNAs (miRNAs) known today. Here we report the identification of 11 novel miRNAs encoded by herpesvirus of turkey (HVT), a virus used as a live vaccine in poultry against the highly oncogenic Marek's disease virus type 1. Ten of these miRNAs were clustered together within the repeat long region of the viral genome, demonstrating some degree of positional conservation with other mardiviruses. Close sequence and phylogenetic relationships of some miRNAs in this cluster indicate evolution by duplication. HVT miRNAs represent the first example of virus-encoded miRNAs that show evolution by duplication.

scholarly journals Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci

2016 ◽  
Author(s):  
Paulo P. Amaral ◽  
Tommaso Leonardi ◽  
Namshik Han ◽  
Emmanuelle Viré ◽  
Dennis K. Gascoigne ◽  
...  
Keyword(s):  
Noncoding Rnas ◽  
Conserved Sequence ◽  
Positional Conservation ◽  
Large Numbers ◽  
Human Genomes ◽  
Mammalian Genomes ◽  
Recognition Motifs ◽  
Definition Of

The mammalian genome is transcribed into large numbers of long noncoding RNAs (lncRNAs), but the definition of functional lncRNA groups has proven difficult, partly due to their low sequence conservation and lack of identified shared properties. Here we consider positional conservation across mammalian genomes as an indicator of functional commonality. We identify 665 conserved lncRNA promoters in mouse and human genomes that are preserved in genomic position relative to orthologous coding genes. The identified ‘positionally conserved’ lncRNA genes are primarily associated with developmental transcription factor loci with which they are co-expressed in a tissue-specific manner. Strikingly, over half of all positionally conserved RNAs in this set are linked to distinct chromatin organization structures, overlapping the binding sites for the CTCF chromatin organizer and located at chromatin loop anchor points and borders of topologically associating domains (TADs). These topological anchor point (tap)RNAs possess conserved sequence domains that are enriched in potential recognition motifs for Zinc Finger proteins. Characterization of these noncoding RNAs and their associated coding genes shows that they are functionally connected: they regulate each other’s expression and influence the metastatic phenotype of cancer cells in vitro in a similar fashion. Thus, interrogation of positionally conserved lncRNAs identifies a new subset of tapRNAs with shared functional properties. These results provide a large dataset of lncRNAs that conform to the “extended gene” model, in which conserved developmental genes are genomically and functionally linked to regulatory lncRNA loci across mammalian evolution.

scholarly journals Identification of introns harboring functional sequence elements through positional conservation

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Michal Chorev ◽  
Alan Joseph Bekker ◽  
Jacob Goldberger ◽  
Liran Carmel
Keyword(s):  
Functional Sequence ◽  
Positional Conservation ◽  
Sequence Elements
Sign in / Sign up

Export Citation Format

Share Document