The Mapping of Predicted Triplex DNA:RNA in the Drosophila Genome Reveals a Prominent Location in Development- and Morphogenesis-Related Genes

G3 : Genes - Genomes - Genetics
Claude PasquierAlain Robichon

Abstract

Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand. A nucleic acid triplex occurs according to Hoogsteen rules that predict the stability and affinity of the third strand bound to the Watson-Crick duplex. The "triplex-forming oligonucleotide" (TFO) can be a short sequence of RNA that binds to the major groove of the targeted duplex only when this duplex presents a sequence of purine or pyrimidine bases in one of the DNA strands. Many nuclear proteins are known to bind triplex DNA or DNA:RNA, but their biological functions are unexplored. We identified sequences that are capable of engaging as the "triplex-forming oligonucleotide" in both the pre-lncRNA and pre-mRNA collections of Drosophila melanogaster These motifs were matched against the Drosophila genome in order to identify putative sequences of triplex formation in intergenic regions, promoters, and introns/exons. Most of the identified TFOs appear to be located in the intronic region of the analyzed genes. Computational prediction of the most targeted genes by TFOs originating from pre-lncRNAs and pre-mRNAs revealed that they are restrictively associated with development- and morphogenesis-related gene networks. The r...Continue Reading

References

Jan 1, 1992·Progress in Biophysics and Molecular Biology·Y K Cheng, B M Pettitt
Jan 1, 1995·Annual Review of Biochemistry·M D Frank-Kamenetskii, S M Mirkin
Mar 1, 1995·Current Biology : CB·H GranokS C Elgin
Apr 30, 1996·Proceedings of the National Academy of Sciences of the United States of America·R W Roberts, D M Crothers
Jun 1, 1996·Current Opinion in Structural Biology·J S SunC Hélène
Sep 12, 1998·The Journal of Biological Chemistry·E Jiménez-GarcíaF Azorín
Nov 1, 2000·Nucleic Acids Research·M MussoM W Van Dyke
Oct 24, 2001·Human Molecular Genetics·M P Knauert, P M Glazer
Dec 31, 2003·Trends in Genetics : TIG·Michael Lehmann
May 16, 2006·Chembiochem : a European Journal of Chemical Biology·Anton Granzhan, Heiko Ihmels
Jul 4, 2006·Genetics·Kara JuneauRonald W Davis
Jul 11, 2006·Nature Reviews. Molecular Cell Biology·Jonathan HouseleyDavid Tollervey
Mar 29, 2008·Methods in Molecular Biology·Erica B SchleifmanPeter M Glazer
Jul 18, 2008·Current Topics in Microbiology and Immunology·A B Rose
Feb 4, 2009·Nature Reviews. Genetics·Tim R MercerJohn S Mattick
Jul 3, 2009·Genes & Development·Jeremy E WiluszDavid L Spector
Mar 25, 2010·Biochemistry·Irit LubitzAlexander Kotlyar
Apr 3, 2010·Molecular Biology and Evolution·Svetlana A ShabalinaEugene V Koonin
Jul 10, 2010·Science·Miao-Chih TsaiHoward Y Chang
Apr 29, 2011·RNA Biology·Fabian A BuskeTimothy L Bailey
Apr 21, 2012·Frontiers in Genetics·Michal Chorev, Liran Carmel
May 3, 2012·Genome Research·Fabian A BuskeTimothy L Bailey
Jun 6, 2012·Annual Review of Biochemistry·John L Rinn, Howard Y Chang
Sep 25, 2012·Molecular Cell·Rajani Kanth GudipatiDomenico Libri
Oct 10, 2013·Nature Reviews. Molecular Cell Biology·Sarah Geisler, Jeff Coller
May 9, 2014·Nature Reviews. Genetics·Marjori A Matzke, Rebecca A Mosher
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Jianxin WangYi Pan
Oct 3, 2015·Genome Research·Loyal A Goff, John L Rinn
Dec 17, 2015·Nature Reviews. Genetics·Jeffrey J Quinn, Howard Y Chang
May 20, 2016·International Journal of Molecular Sciences·Rui LiYunbo Luo
Aug 9, 2016·Trends in Biochemical Sciences·Ling-Ling Chen

❮ Previous
Next ❯

Methods Mentioned

BETA
pull-down
PCR

Software Mentioned

modENCODE
ClusterViz
Triplexator

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.