Involvement of a citrus meiotic recombination TTC-repeat motif in the formation of gross deletions generated by ionizing radiation and MULE activation

BMC Genomics
Javier TerolManuel Talon

Abstract

Transposable-element mediated chromosomal rearrangements require the involvement of two transposons and two double-strand breaks (DSB) located in close proximity. In radiobiology, DSB proximity is also a major factor contributing to rearrangements. However, the whole issue of DSB proximity remains virtually unexplored. Based on DNA sequencing analysis we show that the genomes of 2 derived mutations, Arrufatina (sport) and Nero (irradiation), share a similar 2 Mb deletion of chromosome 3. A 7 kb Mutator-like element found in Clemenules was present in Arrufatina in inverted orientation flanking the 5' end of the deletion. The Arrufatina Mule displayed "dissimilar" 9-bp target site duplications separated by 2 Mb. Fine-scale single nucleotide variant analyses of the deleted fragments identified a TTC-repeat sequence motif located in the center of the deletion responsible of a meiotic crossover detected in the citrus reference genome. Taken together, this information is compatible with the proposal that in both mutants, the TTC-repeat motif formed a triplex DNA structure generating a loop that brought in close proximity the originally distinct reactive ends. In Arrufatina, the loop brought the Mule ends nearby the 2 distinct inserti...Continue Reading

References

Dec 3, 1987·Nature·S M MirkinM D Frank-Kamenetskii
Jan 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·A WeinrebB K Birshtein
Jan 1, 1995·Annual Review of Biochemistry·M D Frank-Kamenetskii, S M Mirkin
Jan 1, 1994·International Journal of Radiation Biology·D T Goodhead
Jan 1, 1997·International Journal of Radiation Biology·R K SachsD J Brenner
Jul 17, 1998·Current Opinion in Structural Biology·C B Burge, S Karlin
Oct 12, 2002·Plant Physiology·François RoudierPhilip N Benfey
Nov 6, 2002·Trends in Plant Science·Damon Lisch
Feb 13, 2003·Current Opinion in Structural Biology·Anita ChangelaAlfonso Mondragón
Nov 20, 2003·The Journal of Biological Chemistry·Marek NapieralaRobert D Wells
Jun 1, 1996·Annual Review of Plant Physiology and Plant Molecular Biology·Eugene J. Szymkowiak, Ian M. Sussex
Jul 12, 2005·Nucleic Acids Research·Robert D WellsLeslie S Son
Jun 28, 2006·Yi chuan xue bao = Acta genetica Sinica·Xian-Min Diao, Damon Lisch
Jun 30, 2006·DNA Repair·Albino BacollaRobert D Wells
Oct 3, 2006·Nucleic Acids Research·Sarah BurgeStephen Neidle
Dec 14, 2007·Annual Review of Genetics·Cédric Feschotte, Ellen J Pritham
Jan 24, 2008·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Robert D Wells
Feb 7, 2008·American Journal of Human Genetics·Menno C van ZelmMirjam van der Burg
Mar 10, 2009·BMC Bioinformatics·Chao Xie, Martti T Tammi
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Aug 12, 2009·The Journal of Heredity·Ellen J Pritham
Dec 10, 2009·Nature Biotechnology·Ruiqiang LiJian Wang
Dec 28, 2010·Mutation Research·Evelyne Sage, Lynn Harrison
Apr 19, 2011·Nucleic Acids Research·Mridula Nambiar, Sathees C Raghavan
Aug 19, 2011·Nature Reviews. Genetics·Henry L Levin, John V Moran
Oct 4, 2011·Nucleic Acids Research·Yuan Hu XuanChang-deok Han
Jan 26, 2012·Molecular Genetics and Genomics : MGG·Dongying Gao
Nov 14, 2012·Annual Review of Genetics·Cheng Ran Lisa HuangJef D Boeke
Jan 19, 2013·Nature Reviews. Genetics·Joachim WeischenfeldtJan O Korbel
Mar 5, 2013·Nature Structural & Molecular Biology·Cindy FollonierMassimo Lopes

❮ Previous
Next ❯

Citations

Aug 12, 2015·Plant Biotechnology Journal·Javier TerolManuel Talon
Dec 1, 2017·Proceedings of the National Academy of Sciences of the United States of America·Joiselle Blanche FernandesRaphael Mercier
Apr 4, 2019·Nucleic Acids Research·Rajeev KumarRaphael Mercier
Jun 13, 2017·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Lars S de HaasGeo Velikkakam James
Jul 19, 2021·The Plant Genome·Daniel Gonzalez-IbeasManuel Talon
Sep 1, 2021·The Plant Genome·Daniel Gonzalez-IbeasManuel Talon

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRX371962
PRJEB5808

Methods Mentioned

BETA
PCR
RNA-seq
transgenic
fast
electrophoresis

Software Mentioned

GATK
Genscan
InterProScan
BLAST2GO
Weblogo
Samtools
CitMule
Burrows Aligner ( BWA )
BLASTX
MEGABLASTN

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.