LASAGNA-Search 2.0: integrated transcription factor binding site search and visualization in a browser

Lee, Chih; Huang, Chun-Hsi

doi:10.1093/bioinformatics/btu115

Cited by 59 publications

(56 citation statements)

References 12 publications

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“…LASAGNA-Search 2.0 [19, 20] identified a total of 1655 transcription factor binding sites (TFBSs) in intron 1 of chicken NRG3 . The distribution of TFBSs was not biased in the highly conserved 5′ region of intron 1 using a 50-bp window (Additional file 2: Figure S2).…”

Section: Resultsmentioning

confidence: 99%

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Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion

Abe

Aoya²,

Takeuchi

et al. 2017

BMC Genet

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BackgroundNeuregulin 3 (NRG3) plays a key role in central nervous system development and is a strong candidate for human mental disorders. Thus, genetic variation in NRG3 may have some impact on a variety of phenotypes in non-mammalian vertebrates. Recently, genome-wide screening for short insertions and deletions in chicken (Gallus gallus) genomes has provided useful information about structural variation in functionally important genes. NRG3 is one such gene that has a putative frameshift deletion in exon 2, resulting in premature termination of translation. Our aims were to characterize the structure of chicken NRG3 and to compare expression patterns between NRG3 isoforms.ResultsDepending on the presence or absence of the 2-bp deletion in chicken NRG3, 3 breeds (red junglefowl [RJF], Boris Brown [BB], and Hinai-jidori [HJ]) were genotyped using flanking primers. In the commercial breeds (BB and HJ), approximately 45% of individuals had at least one exon 2 allele with the 2-bp deletion, whereas there was no deletion allele in RJF. The lack of a homozygous mutant indicated the existence of duplicated NRG3 segments in the chicken genome. Indeed, highly conserved elements consisting of exon 1, intron 1, exon 2, and part of intron 2 were found in the reference RJF genome, and quantitative PCR detected copy number variation (CNV) between breeds as well as between individuals. The copy number of conserved elements was significantly higher in chicks harboring the 2-bp deletion in exon 2. We identified 7 novel transcript variants using total mRNA isolated from the amygdala. Novel isoforms were found to lack the exon 2 cassette, which probably harbored the premature termination codon. The relative transcription levels of the newly identified isoforms were almost the same between chick groups with and without the 2-bp deletion, while chicks with the deletion showed significant suppression of the expression of previously reported isoforms.ConclusionsA putative frameshift deletion and CNV in chicken NRG3 are structural mutations that occurred before the establishment of commercial chicken lines. Our results further suggest that the putative frameshift deletion in exon 2 may potentially affect the expression level of particular isoforms of chicken NRG3.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-017-0537-z) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

“…We used LASAGNA-Search 2.0 [19, 20] to identify TFBSs in intron 1 of chicken NRG3 . The JASPER core database was selected for searching matrices (cutoff p -value <0.01).…”

Section: Methodsmentioning

confidence: 99%

Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion

Abe

Aoya²,

Takeuchi

et al. 2017

BMC Genet

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“…4A). We queried −950 to +50 bp relative to the human transcriptional start site using the LASAGNA algorithm [53] and identified two novel RBP-Jκ binding motifs with potential high affinity located at positions −81 bp (S3) and −10 bp (S4) (Fig. 4A).…”

Section: Resultsmentioning

confidence: 99%

Sox9 mediates Notch1-induced mesenchymal features in lung adenocarcinoma

Capaccione

Hong²,

Morgan

et al. 2014

Oncotarget

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Sox9 has gained increasing importance both functionally and as a prognostic factor in cancer. We demonstrate a functional role for Sox9 in inducing a mesenchymal phenotype in lung ADC. We show that Sox9 mRNA and protein are overexpressed in lung ADC, particularly those with KRAS mutations. Sox9 expression correlated with the Notch target gene Hes1, and numerous other Notch pathway components. We observed that Sox9 is a potent inducer of lung cancer cell motility and invasion, and a negative regulator of E-cadherin, a key protein that is lost during epithelial-mesenchymal transition (EMT). Moreover, we show that Notch1 signaling directly regulates Sox9 expression through a SOX9 promoter binding site, independently of the TGF-β pathway, and that Sox9 participates in Notch-1 induced cell motility, cell invasion, and loss of E-cadherin expression. Together, the results identify a new functional role for a Notch1-Sox9 signaling axis in lung ADC that may explain the correlation of Sox9 with tumor progression, higher tumor grade, and poor lung cancer survival. In addition to Notch and TGF-β, Sox9 also acts downstream of NF-κB and Wnt/β-catenin signaling. Thus, Sox9 could potentially act as a hub to mediate cross-talk among key oncogenic pathways in lung ADC. Targeting Sox9 expression or transcriptional activity could potentially reduce resistance to targeted therapy for lung ADC caused by pathway redundancy.

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“…With the purpose of uncovering the main potential TF involved in controlling glucose transport and lactose synthesis, we have performed our analysis of the promoter region of main genes involved in those functions in bovine using the LASA-GNA software (118) (Fig. 6).…”

Section: Potential Tf Involved In the Regulation Of The Lactose Synthmentioning

confidence: 99%

Biosynthesis of milk fat, protein, and lactose: roles of transcriptional and posttranscriptional regulation

Osorio

Lohakare

Bionaz

2016

Physiological Genomics

190

182

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LASAGNA-Search 2.0: integrated transcription factor binding site search and visualization in a browser

Abstract: LASAGNA-Search 2.0 is freely available without registration at http://biogrid.engr.uconn.edu/lasagna_search/.

Cited by 59 publications

References 12 publications

Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion

Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion

Sox9 mediates Notch1-induced mesenchymal features in lung adenocarcinoma

Biosynthesis of milk fat, protein, and lactose: roles of transcriptional and posttranscriptional regulation

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