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Halász, G.; Batenburg, Marinus F. van; Pérusse, Joëlle R.; Hua, Sujun; Lu, Xiang; White, Kevin P.; Bussemaker, Harmen J.

doi:10.1186/gb-2006-7-7-r59

Cited by 19 publications

(13 citation statements)

References 32 publications

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“…Negative control probes that represent non-specific background hybridization were randomly selected based on the median signal intensity (depicted as a dotted line in Fig. 2c) 20 . The microarray signals were subsequently transformed to binary signals, representing presence (probes expressed above background) and absence probes (background).…”

Section: Resultsmentioning

confidence: 99%

“…Following the normalization, we employed the ‘TranscriptionDetector’ algorithm (TD) to determine probes expressed above background level 20 . To determine the background level, we selected negative control probes that represent non-specific background hybridization to evaluate the significance of expression of individual probes ( p -value calculation).…”

Section: Methodsmentioning

confidence: 99%

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The transcription unit architecture of the Escherichia coli genome

et al. 2009

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Bacterial genomes are organized in terms of structural and functional components. These components include promoters, transcription start and termination sites, open reading frames, regulatory non-coding regions, untranslated regions and transcription units, that together comprise the functional organization of a genome. Here, we use a systems approach that iteratively integrates multiple high-throughput measurements at a genome-scale to identify the organizational structure of the Escherichia coli K-12 MG1655 genome. Integration of the organizational components provides experimentally annotated transcription unit (TU) architecture, including alternative transcription start sites, promoter structures, boundaries and open reading frames. A total of 4,661 TUs were identified, representing an increase of > 530% over current knowledge. This comprehensive TU architecture allows for the elucidation of condition-specific uses of alternative sigma factors at the genome-scale. Furthermore, the TU architecture provides a foundation on which genome-scale transcriptional and translational regulatory networks are based.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The transcription unit architecture of the Escherichia coli genome

et al. 2009

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“…We used ''Transcription Detector'' algorithm (TD) (Halasz et al 2006) to determine probes expressed above background as described before (Cho et al 2009). Genome-wide summary of piecewise constant expression segments (i.e., RNAP-guided transcript segments [RTSs]) were obtained by assembling the expressed probes between two RNAP binding regions and then assigning genomic coordinates of first/last expressed probes to start/end genomic coordinates of each assembled region, respectively.…”

Section: Determination Of Rnap-guided Transcript Segmentsmentioning

confidence: 99%

Structural and operational complexity of the Geobacter sulfurreducens genome

Qiu¹,

Cho²,

Park³

et al. 2010

Genome Res.

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Prokaryotic genomes can be annotated based on their structural, operational, and functional properties. These annotations provide the pivotal scaffold for understanding cellular functions on a genome-scale, such as metabolism and transcriptional regulation. Here, we describe a systems approach to simultaneously determine the structural and operational annotation of the Geobacter sulfurreducens genome. Integration of proteomics, transcriptomics, RNA polymerase, and sigma factor-binding information with deep-sequencing-based analysis of primary 59-end transcripts allowed for a most precise annotation. The structural annotation is comprised of numerous previously undetected genes, noncoding RNAs, prevalent leaderless mRNA transcripts, and antisense transcripts. When compared with other prokaryotes, we found that the number of antisense transcripts reversely correlated with genome size. The operational annotation consists of 1453 operons, 22% of which have multiple transcription start sites that use different RNA polymerase holoenzymes. Several operons with multiple transcription start sites encoded genes with essential functions, giving insight into the regulatory complexity of the genome. The experimentally determined structural and operational annotations can be combined with functional annotation, yielding a new three-level annotation that greatly expands our understanding of prokaryotic genomes.

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“…Labeled cDNA was generated and processed as previously described [7]. The Transcription Detector algorithm [72] determined probes expressed above background at a FDR = 0.05.…”

Section: Methodsmentioning

confidence: 99%

The Genome Organization of Thermotoga maritima Reflects Its Lifestyle

et al. 2013

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The generation of genome-scale data is becoming more routine, yet the subsequent analysis of omics data remains a significant challenge. Here, an approach that integrates multiple omics datasets with bioinformatics tools was developed that produces a detailed annotation of several microbial genomic features. This methodology was used to characterize the genome of Thermotoga maritima—a phylogenetically deep-branching, hyperthermophilic bacterium. Experimental data were generated for whole-genome resequencing, transcription start site (TSS) determination, transcriptome profiling, and proteome profiling. These datasets, analyzed in combination with bioinformatics tools, served as a basis for the improvement of gene annotation, the elucidation of transcription units (TUs), the identification of putative non-coding RNAs (ncRNAs), and the determination of promoters and ribosome binding sites. This revealed many distinctive properties of the T. maritima genome organization relative to other bacteria. This genome has a high number of genes per TU (3.3), a paucity of putative ncRNAs (12), and few TUs with multiple TSSs (3.7%). Quantitative analysis of promoters and ribosome binding sites showed increased sequence conservation relative to other bacteria. The 5′UTRs follow an atypical bimodal length distribution comprised of “Short” 5′UTRs (11–17 nt) and “Common” 5′UTRs (26–32 nt). Transcriptional regulation is limited by a lack of intergenic space for the majority of TUs. Lastly, a high fraction of annotated genes are expressed independent of growth state and a linear correlation of mRNA/protein is observed (Pearson r = 0.63, p<2.2×10−16 t-test). These distinctive properties are hypothesized to be a reflection of this organism's hyperthermophilic lifestyle and could yield novel insights into the evolutionary trajectory of microbial life on earth.

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Untitled

Cited by 19 publications

References 32 publications

The transcription unit architecture of the Escherichia coli genome

The transcription unit architecture of the Escherichia coli genome

Structural and operational complexity of the Geobacter sulfurreducens genome

The Genome Organization of Thermotoga maritima Reflects Its Lifestyle

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