JENJAROENPUN Piroon

Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons

Published date : 13 Oct 2017

The stochastic dynamics and regulatory mechanisms that govern differentiation of individual human neural precursor cells (NPC) into mature neurons are currently not fully understood. Here, we used single-cell RNA-sequencing (scRNA-seq) of developing neurons to dissect/identify NPC subtypes and critical developmental stages of alternative lineage specifications.

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Journal Paper
journal
Genome Research 2017, 27, Pg 1783-1794, doi: 10.1101/gr.223313.117
Impact Factor
11.922

Transposon insertional mutagenesis in mice identifies human breast cancer susceptibility genes and signatures for stratification

Published date : 01 Mar 2017

Robust prognostic gene signatures and therapeutic targets are difficult to derive from expression profiling because of the significant heterogeneity within breast cancer (BC) subtypes. Here, we performed forward genetic screening in mice using Sleeping Beauty transposon mutagenesis to identify candidate BC driver genes in an unbiased manner, using a stabilized N-terminal truncated β-catenin gene as a sensitizer. We identified 134 mouse susceptibility genes from 129 common insertion sites within 34 mammary tumors.

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Journal Paper
journal
Proceedings of the National Academy of Sciences of the Unites States of America, PNAS, Vol. 114, No. 11, E2215–E2224, doi: 10.1073/pnas.1701512114
Impact Factor
9.661

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

Published date : 28 Nov 2016

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
Impact Factor
9.202

Abstract 1990: The key role of MECOM complex locus and its products in high-grade ovarian carcinoma pathogenesis and clinical outcomes

Published date : 01 Aug 2015

The ecotropic virus integration site 1(Evi1) transcription factor, encoded in the MECOM complex locus, is implicated in several cancers, including ovarian cancer(OC). High-grade serous OC(HG-SOC) represents its most common and aggressive form. The pathobiological and clinical roles of MECOM and its products in HG-SOC are poorly understood.

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Journal Paper
journal
Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA: Cancer Research Aug 1, 2015 75,1990, doi: 10.1158/1538-7445.AM2015-1990

Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress

Published date : 29 May 2015

Oxidative stress (OS) is caused by an imbalance between pro- and anti-oxidant reactions leading to accumulation of reactive oxygen species within cells. We here investigate the effect of OS on the transcriptome of human fibroblasts. OS causes a rapid and transient global induction of transcription characterized by pausing of RNA polymerase II (PolII) in both directions, at specific promoters, within 30 minutes of the OS response.

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Journal Paper
journal
Scientific Reports 5,Article no: 9737, 2015, doi: 10.1038/srep09737

Duplex stem-loop-containing quadruplex motifs in the human genome: a combined genomic and structural study

Published date : 09 May 2015

Duplex stem-loops and four-stranded G-quadruplexes have been implicated in (patho)biological processes. Overlap of stem-loop- and quadruplex-forming sequences could give rise to quadruplex-duplex hybrids (QDH), which combine features of both structural forms and could exhibit unique properties. Here, we present a combined genomic and structural study of stem-loop-containing quadruplex sequences (SLQS) in the human genome. Based on a maximum loop length of 20 nt, our survey identified 80 307 SLQS, embedded within 60 172 unique clusters.

type
Journal Paper
journal
Nuclei Acids Research 2015, Vol. 43, No. 11, Pg 5630-5646, doi: 10.1093/nar/gkv355
Impact Factor
9.112

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

Published date : 16 Apr 2015

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.

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Journal Paper
journal
Nucleic Acids Research, 2015, 1, doi: 10.1093/nar/gkv344

The TTSMI database: a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome

Published date : 16 Oct 2014

A triplex target DNA site (TTS), a stretch of DNA that is composed of polypurines, is able to form a triple-helix (triplex) structure with triplex-forming oligonucleotides (TFOs) and is able to influence the site-specific modulation of gene expression and/or the modification of genomic DNA. The co-localization of a genomic TTS with gene regulatory signals and functional genome structures suggests that TFOs could potentially be exploited in antigene strategies for the therapy of cancers and other genetic diseases.

type
Journal Paper
journal
Nucleic Acids Research, 2014, doi: 10.1093/nar/gku970

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

Published date : 17 Mar 2014

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.

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Journal Paper
journal
PLOS One, March 2014, Vol. 9, Issue 3, doi: 10.1371/journal.pone.0090219
Impact Factor
3.73

Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencing

Published date : 05 Nov 2013

Exosomes are nanosized (30-100 nm) membrane vesicles secreted by most cell types. Exosomes have been found to contain various RNA species including miRNA, mRNA and long non-protein coding RNAs. A number of cancer cells produce elevated levels of exosomes. Because exosomes have been isolated from most body fluids they may provide a source for non-invasive cancer diagnostics.

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Journal Paper
journal
PeerJ. 2013 Nov 5, http://dx.doi.org/10.7717/peerj.201