Gene Expression Analysis Using Oligonucleotide Arrays Produced by Maskless Photolithography

Nuwaysir, Emile F.; Huang, Wei; Albert, Thomas; Singh, Jaz; Nuwaysir, Kate; Pitas, Alan; Richmond, Todd; Gorski, T.; Berg, James P.; Ballin, Jeff D.; McCormick, Mark R.; Norton, Jason E.; Pollock, T. J.; Sumwalt, Terry; Butcher, Lawrence; Porter, DeAnn; Molla, Michael; Hall, Christine; Blattner, Fred R.; Sussman, Michael R.; Wallace, Rodney L.; Cerrina, F.; Green, Roland D.

doi:10.1101/gr.362402

Cited by 320 publications

(241 citation statements)

References 12 publications

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“…Nearly 400,000 36-mer oligonucleotide probes, tiling the entire yeast genome including the mitochondrial chromosome with an average gap of 10 bases between two consecutive probes, were synthesized on glass slides by using a maskless array synthesizer (20) (Fig. 1a).…”

Section: Resultsmentioning

confidence: 99%

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Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway

Samanta

Tongprasit

Sethi

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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Noncoding RNAs (ncRNAs) perform essential cellular tasks and play key regulatory roles in all organisms. Although several new ncRNAs in yeast were recently discovered by individual studies, to our knowledge no comprehensive empirical search has been conducted. We demonstrate a powerful and versatile method for global identification of previously undescribed ncRNAs by modulating an essential RNA processing pathway through the depletion of a key ribonucleoprotein enzyme component, and monitoring differential transcriptional activities with genome tiling arrays during the time course of the ribonucleoprotein depletion. The entire Saccharomyces cerevisiae genome was scanned during cell growth decay regulated by promoter-mediated depletion of Rpp1, an essential and functionally conserved protein component of the RNase P enzyme. In addition to most verified genes and ncRNAs, expression was detected in 98 antisense and intergenic regions, 74 that were further confirmed to contain previously undescribed RNAs. A class of ncRNAs, located antisense to coding regions of verified protein-coding genes, is discussed in this article. One member, HRA1, is likely involved in 18S rRNA maturation.HRA1 ͉ microarray ͉ RNase P ͉ yeast

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Section: Resultsmentioning

confidence: 99%

“…Eight identical glass-based high-density arrays were constructed by using a maskless array synthesizer (20). Each array contained 388,562 36-mer oligonucleotide probes.…”

Section: Methodsmentioning

confidence: 99%

Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway

Samanta

Tongprasit

Sethi

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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show abstract

“…Maskless array synthesis and hybridization were carried out with 100 ng of amplified 5C libraries at NimbleGen Systems Inc. as previously described (Singh-Gasson et al 1999;Nuwaysir et al 2002;Kim et al 2005;Selzer et al 2005). Each array featured the sense strand of predicted 5C ligation products.…”

Section: C Library Microarray Analysismentioning

confidence: 99%

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

Dostie¹,

et al. 2006

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Physical interactions between genetic elements located throughout the genome play important roles in gene regulation and can be identified with the Chromosome Conformation Capture (3C) methodology. 3C converts physical chromatin interactions into specific ligation products, which are quantified individually by PCR. Here we present a high-throughput 3C approach, 3C-Carbon Copy (5C), that employs microarrays or quantitative DNA sequencing using 454-technology as detection methods. We applied 5C to analyze a 400-kb region containing the human ␤-globin locus and a 100-kb conserved gene desert region. We validated 5C by detection of several previously identified looping interactions in the ␤-globin locus. We also identified a new looping interaction in K562 cells between the ␤-globin Locus Control Region and the ␥-␦-globin intergenic region. Interestingly, this region has been implicated in the control of developmental globin gene switching. 5C should be widely applicable for large-scale mapping of cis-and trans-interaction networks of genomic elements and for the study of higher-order chromosome structure.

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“…This technology has been used successfully on different organisms (5)(6)(7)(8)(9)(10)(11)(12). A recent study on A. thaliana reported measuring transcriptional activities of four different cell lines by using 25-mer-based tiling arrays that were developed with a chromium masking-based photolithography technique (11).…”

mentioning

confidence: 99%

Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays

Štolc

Samanta

Tongprasit

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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142

116

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Using a maskless photolithography method, we produced DNA oligonucleotide microarrays with probe sequences tiled throughout the genome of the plant Arabidopsis thaliana. RNA expression was determined for the complete nuclear, mitochondrial, and chloroplast genomes by tiling 5 million 36-mer probes. These probes were hybridized to labeled mRNA isolated from liquid grown T87 cells, an undifferentiated Arabidopsis cell culture line. Transcripts were detected from at least 60% of the nearly 26,330 annotated genes, which included 151 predicted genes that were not identified previously by a similar genome-wide hybridization study on four different cell lines. In comparison with previously published results with 25-mer tiling arrays produced by chromium masking-based photolithography technique, 36-mer oligonucleotide probes were found to be more useful in identifying intronexon boundaries. Using two-dimensional HPLC tandem mass spectrometry, a small-scale proteomic analysis was performed with the same cells. A large amount of strongly hybridizing RNA was found in regions ''antisense'' to known genes. Similarity of antisense activities between the 25-mer and 36-mer data sets suggests that it is a reproducible and inherent property of the experiments. Transcription activities were also detected for many of the intergenic regions and the small RNAs, including tRNA, small nuclear RNA, small nucleolar RNA, and microRNA. Expression of tRNAs correlates with genome-wide amino acid usage.higher plant ͉ transcriptome ͉ maskless array synthesizer

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Gene Expression Analysis Using Oligonucleotide Arrays Produced by Maskless Photolithography

Cited by 320 publications

References 12 publications

Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway

Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays

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