A highly sensitive in vivo footprinting technique for condition-dependent identification of cis elements

Gorsche, Rita; Jovanović, Birgit; Gudynaite‐Savitch, Loreta; Mach, Robert L.; Mach-Aigner, Astrid R.

doi:10.1093/nar/gkt883

Cited by 13 publications

(23 citation statements)

References 50 publications

(72 reference statements)

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“…Numbers indicate the position of the base upstream from ATG. Analysis of data and visualization was performed using ivFAST [27]. Colour codes are the same as in Figure 2.…”

Section: Resultsmentioning

confidence: 99%

A truncated form of the Carbon catabolite repressor 1 increases cellulase production in Trichoderma reesei

Mello-de-Sousa

Gorsche

Rassinger

et al. 2014

Biotechnol Biofuels

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BackgroundRut-C30 is a cellulase-hyperproducing Trichoderma reesei strain and, consequently, became the ancestor of most industry strains used in the production of plant cell wall-degrading enzymes, in particular cellulases. Due to three rounds of undirected mutagenesis its genetic background differs from the wild-type QM6a in many ways, of which two are the lack of a 83 kb large sequence in scaffold 15 and the partial lack of the gene encoding the Carbon catabolite repressor 1 (CREI). However, it is still unclear, what exactly enhances cellulase production in Rut-C30.ResultsThe investigation of the expression of two genes encoding cellulases (cbh1 and cbh2) and the gene encoding their main transactivator (xyr1) revealed that the presence of the truncated form of CREI (CREI-96) contributes more to the Rut-C30 phenotype than a general loss of CREI-mediated carbon catabolite repression (cre1 deletion strain) or the deletion of 29 genes encoded in the scaffold 15 (83 kb deletion strain). We found that the remaining cre1 in Rut-C30 (cre1-96) is transcribed into mRNA, that its putative gene product (Cre1-96) is still able to bind DNA, and that the CREI-binding sites in the upstream regulatory regions of the chosen CREI-target genes are still protected in Rut-C30. As it was previously reported that CREI acts on the nucleosome positioning, we also analyzed chromatin accessibility of the core promoters of CREI-target genes and found them open even on D-glucose in the presence of CREI-96.ConclusionsThe lack of the full version of CREI in Rut-C30 corresponds with a partial release from carbon catabolite repression but is not completely explained by the lack of CREI. In contrast, the truncated CREI-96 of Rut-C30 exerts a positive regulatory influence on the expression of target genes. Mechanistically this might be explained at least partially by a CREI-96-mediated opening of chromatin.

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“…Numbers indicate the position of the base upstream from ATG. Analysis of data and visualization was performed using ivFAST [27]. Colour codes are the same as in Figure 2.…”

Section: Resultsmentioning

confidence: 99%

A truncated form of the Carbon catabolite repressor 1 increases cellulase production in Trichoderma reesei

Mello-de-Sousa

Gorsche

Rassinger

et al. 2014

Biotechnol Biofuels

Self Cite

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“…Thus, Gorsche et al [79] modified the traditional in vivo footprinting approach to obtain a highly sensitive technique for identifying the cis elements involved in condition-dependent gene regulation. With their technique, data produced using the process of dimethyl sulphate methylation, HCl DNA cleavage, and ligationmediated PCR-CGE were analyzed with their newly developed in vivo footprinting analysis software tool (ivFAST) (Figure 7).…”

Section: Detecting and Diagnosing Fungimentioning

confidence: 99%

“…Thus, Nagel et al [87] developed RT-PCR-CGE to sensitively analyze the SVV transcriptome in SVV-infected monkey cells. They found transcripts corresponding to all 69 predicted SVV Figure 7: Schematic representation of the workflow and generation of data using a software-based, high throughput, in vivo footprinting method [79].…”

Section: Detecting and Diagnosing Virusesmentioning

confidence: 99%

Capillary electrophoresis based on nucleic acid detection for diagnosing human infectious disease

Lian

Zhao

2016

Clinical Chemistry and Laboratory Medicine (CCLM)

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Rapid transmission, high morbidity, and mortality are the features of human infectious diseases caused by microorganisms, such as bacteria, fungi, and viruses. These diseases may lead within a short period of time to great personal and property losses, especially in regions where sanitation is poor. Thus, rapid diagnoses are vital for the prevention and therapeutic intervention of human infectious diseases. Several conventional methods are often used to diagnose infectious diseases, e.g. methods based on cultures or morphology, or biochemical tests based on metabonomics. Although traditional methods are considered gold standards and are used most frequently, they are laborious, time consuming, and tedious and cannot meet the demand for rapid diagnoses. Disease diagnosis using capillary electrophoresis methods has the advantages of high efficiency, high throughput, and high speed, and coupled with the different nucleic acid detection strategies overcomes the drawbacks of traditional identification methods, precluding many types of false positive and negative results. Therefore, this review focuses on the application of capillary electrophoresis based on nucleic detection to the diagnosis of human infectious diseases, and offers an introduction to the limitations, advantages, and future developments of this approach.

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“…Numbers indicate the position of the base upstream from ATG. Analysis of data and visualization was performed using ivFAST [27]. Colour codes are the same as in Figure 2.…”

Section: Crei-96 Upregulates the Expression Of A Helicase-like Transcmentioning

confidence: 99%

“…In vivo methylation using DMS followed by ligationmediated PCR was performed as described previously [27]. FAM (fluorescein amidite)-labelled fragments were analyzed by capillary gel electrophoresis (Microsynth) and results were analyzed using ivFAST [27].…”

Section: In Vivo Footprintingmentioning

confidence: 99%

A truncated form of the Carbon catabolite repressor 1 increases cellulase production in Trichoderma reesei

Mello-de-Sousa

Gorsche

Rassinger

et al. 2014

Biotechnol Biofuels

Self Cite

View full text Add to dashboard Cite

Background: Rut-C30 is a cellulase-hyperproducing Trichoderma reesei strain and, consequently, became the ancestor of most industry strains used in the production of plant cell wall-degrading enzymes, in particular cellulases. Due to three rounds of undirected mutagenesis its genetic background differs from the wild-type QM6a in many ways, of which two are the lack of a 83 kb large sequence in scaffold 15 and the partial lack of the gene encoding the Carbon catabolite repressor 1 (CREI). However, it is still unclear, what exactly enhances cellulase production in Rut-C30. Results: The investigation of the expression of two genes encoding cellulases (cbh1 and cbh2) and the gene encoding their main transactivator (xyr1) revealed that the presence of the truncated form of CREI (CREI-96) contributes more to the Rut-C30 phenotype than a general loss of CREI-mediated carbon catabolite repression (cre1 deletion strain) or the deletion of 29 genes encoded in the scaffold 15 (83 kb deletion strain). We found that the remaining cre1 in Rut-C30 (cre1-96) is transcribed into mRNA, that its putative gene product (Cre1-96) is still able to bind DNA, and that the CREI-binding sites in the upstream regulatory regions of the chosen CREI-target genes are still protected in Rut-C30. As it was previously reported that CREI acts on the nucleosome positioning, we also analyzed chromatin accessibility of the core promoters of CREI-target genes and found them open even on D-glucose in the presence of CREI-96.

show abstract

A highly sensitive in vivo footprinting technique for condition-dependent identification of cis elements

Cited by 13 publications

References 50 publications

A truncated form of the Carbon catabolite repressor 1 increases cellulase production in Trichoderma reesei

A truncated form of the Carbon catabolite repressor 1 increases cellulase production in Trichoderma reesei

Capillary electrophoresis based on nucleic acid detection for diagnosing human infectious disease

A truncated form of the Carbon catabolite repressor 1 increases cellulase production in Trichoderma reesei

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