WONGSURAWAT Thidathip

R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops

R-loopDB (http://rloop.bii.a-star.edu.sg) was originally constructed as a collection of computationally predicted R-loop forming sequences (RLFSs) in the human genic regions. The renewed R-loopDB provides updates, improvements and new options, including access to recent experimental data. It includes genome-scale prediction of RLFSs for humans, six other animals and yeast. Using the extended quantitative model of RLFSs (QmRLFS), we significantly increased the number of RLFSs predicted in the human genes and identified RLFSs in other organism genomes.

type: 
Journal Paper
journal: 
Nucleic Acids Research, 2016, 1, doi: 10.1093/nar/gkw1054
Url: 
https://academic.oup.com/nar/article/45/D1/D119/2605726/R-loopDB-a-database-for-R-loop-forming-sequences
Impact Factor: 
9.202
Date of acceptance: 
2016-10-20

QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences

The possible formation of three-stranded RNA and DNA hybrid structures (R-loops) in thousands of functionally important guanine-rich genic and inter-genic regions could suggest their involvement in transcriptional regulation and even development of diseases. Here, we introduce the first freely available R-loop prediction program called Quantitative Model of R-loop Forming Sequence (RLFS) finder (QmRLFS-finder), which predicts RLFSs in nucleic acid sequences based on experimentally supported structural models of RLFSs. QmRLFS-finder operates via a web server or a stand-alone command line tool.

type: 
Journal Paper
journal: 
Nucleic Acids Research, 2015, 1, doi: 10.1093/nar/gkv344
pubmed: 
25883153
Url: 
http://www.ncbi.nlm.nih.gov/pubmed/25883153
Date of acceptance: 
2015-04-06

R-loops in proliferating cells but not in the brain: implications for AOA2 and other autosomal recessive ataxias

Disruption of the Setx gene, defective in ataxia oculomotor apraxia type 2 (AOA2) leads to the accumulation of DNA/RNA hybrids (R-loops), failure of meiotic recombination and infertility in mice. We report here the presence of R-loops in the testes from other autosomal recessive ataxia mouse models, which correlate with fertility in these disorders. R-loops were coincident in cells showing high basal levels of DNA double strand breaks and in those cells undergoing apoptosis.

type: 
Journal Paper
journal: 
PLOS One, March 2014, Vol. 9, Issue 3, doi: 10.1371/journal.pone.0090219
pubmed: 
24637776
Url: 
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0090219
Impact Factor: 
3.73
Date of acceptance: 
2014-01-27

Quantitative model of R-loop forming structures reveals a novel level of RNA–DNA interactome complexity

R-loop is the structure co-transcriptionally formed between nascent RNA transcript and DNA template, leaving the non-transcribed DNA strand unpaired. This structure can be involved in the hyper-mutation and dsDNA breaks in mammalian immunoglobulin (Ig) genes, oncogenes and neurodegenerative disease related genes. R-loops have not been studied at the genome scale yet. To identify the R-loops, we developed a computational algorithm and mapped R-loop forming sequences (RLFS) onto 66 803 sequences defined by UCSC as ‘known’ genes.

type: 
Journal Paper
journal: 
Nucleic Acids Research 2012 January; 40(2): e16, doi: 10.1093/nar/gkr1075
pubmed: 
22121227
Impact Factor: 
8.026
Date of acceptance: 
2011-11-25
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