Biology subjects

Schueller, A.

Publications and source records attributed to Schueller, A..

5 recordsLinked to original sources

bioRxiv2024

Locus-specific chromatin proteomics using dCas-guided proximity labelling in Aspergillus nidulans.

Proximity labelling that uses promiscuous biotin ligases (BirA) fused to a bait protein is a powerful tool to identify protein interaction partners in vivo under different metabolic or developmental conditions. BirA can also be used to determine protein composition and interaction partners at specific chromatin locations when it is fused with enzymatically-disabled Cas9 (dCas9) and then guided to the location of interest by sgRNAs. We adapted this method (called CasID) for fungal cells using the nitrate assimilation gene cluster of A. nidulans as a model locus and estrogen-inducible expression of the dCas9-BirA fusion to improve condition-specific labelling. For method establishment, we first verified the presence of dCas-BirA and a known transcription factor at the nitrate locus by chromatin immunoprecipitation (ChIP). Results show that both dCas-BirA and the AreA transcription factor are present at the locus of interest under the conditions used for biotinylation. We then optimized the CasID procedure for efficient labelling and background reduction using the CasID-sgRNA strain and two control strains, one lacking the sgRNA and another one lacking the whole CasID system. Here we provide proof-of-concept for the suitability of the method by showing that biotinylated proteins are enriched in the CasID strains in comparison to the controls. After background reduction, 32 proteins remained in two independent experiments exclusively enriched in the Cas-ID-sgRNA strain. Among these proteins was NmrA, an AreA-interacting regulator, and we also found several chromatin-associated proteins. Overall, our results demonstrate that Cas-ID is suitable for locus-specific labelling and identification of chromatin-associated proteins and transcription factors in A. nidulans. However, the high background of proteins that are biotinylated out of chromatin context or unspecifically attach to the affinity purification matrix needs to be addressed by implementing a set of rigorous controls. In summary, we herewith provide a detailed protocol for application of the method that proved to be useful for the identification of novel chromatin-associated proteins and their interaction partners at a specific genomic locus in divers metabolic and developmental conditions. Author summaryThis study demonstrates that locus-specific proteomics can be carried out by dCas-BirA guided proximity labelling in Aspergillus nidulans. For establishment, we targeted the well-described bidirectional promoter region between niaD, a nitrate reductase, and niiA, a nitrite reductase. At this locus we could test by chromatin immunoprecipitation (ChIP) in combination with qPCR if both, the dCas9-BirA fusion as well as a central transcription factor are at the locus under the conditions of our Cas-ID experiment. After this first control step, we considered that unspecific labelling by dCas-BirA during the time from translation to landing at the targeted chromatin locus may be one of the most relevant drawbacks of the method. Therefore, we developed a number of control strains that would allow us to clearly discriminate between background and sgRNA-dependent specific labelling at the locus. Our protein MS results validated these estimates and only considering the results of these controls enabled us to distinguish the set of locus-specific proteins from a very high general background. Finally, enrichment of biotinylated proteins through affinity purification with streptavidin resin and subsequent LC-MS/MS analysis showed that more than 800 proteins were detected in each sample, emphasizing the high background of the purification method. After background reduction of the control samples, we were able to identify 32 proteins which were exclusively detected in the test strain in two independent measurements, including several chromatin-associated proteins and NmrA, a negative regulator of the nitrate locus transcription factor AreA.

molecular biology↗

bioRxiv2024

No evidence of musical training influencing the cortical contribution to the speech-FFR and its modulation through selective attention

Musicians can have better abilities to understand speech in adverse conditions such as background noise than non-musicians. However, the neural mechanisms behind such enhanced behavioral performances remain largely unclear. Studies have found that the subcortical frequency-following response to the fundamental frequency of speech and its higher harmonics (speech-FFR) may be involved since it is larger in people with musical training than in those without. Recent research has shown that the speech-FFR consists of a cortical contribution in addition to the subcortical sources. Both the subcortical and the cortical contribution are modulated by selective attention to one of two competing speakers. However, it is unknown whether the strength of the cortical contribution to the speech-FFR, or its attention modulation, is influenced by musical training. Here we investigate these issues through magnetoencephalographic (MEG) recordings of 52 subjects (18 musicians, 25 non-musicians, and 9 neutral participants) listening to two competing male speakers while selectively attending one of them. The speech-in-noise comprehension abilities of the participants were not assessed. We find that musicians and non-musicians display comparable cortical speech-FFRs and additionally exhibit similar subject-to-subject variability in the response. Furthermore, we also do not observe a difference in the modulation of the neural response through selective attention between musicians and non-musicians. Moreover, when assessing whether the cortical speech-FFRs are influenced by particular aspects of musical training, no significant effects emerged. Taken together, we did not find any effect of musical training on the cortical speech-FFR. Significance statementIn previous research musicians have been found to exhibit larger subcortical responses to the pitch of a speaker than non-musicians. These larger responses may reflect enhanced pitch processing due to musical training and may explain why musicians tend to understand speech better in noisy environments than people without musical training. However, higher-level cortical responses to the pitch of a voice exist as well and are influenced by attention. We show here that, unlike the subcortical responses, the cortical activities do not differ between musicians and non-musicians. The attentional effects are not influenced by musical training. Our results suggest that, unlike the subcortical response, the cortical response to pitch is not shaped by musical training.

neuroscience↗

bioRxiv2023

Attentional modulation of the cortical contribution to the frequency-following response evoked by continuous speech

Selective attention to one of several competing speakers is required for comprehending a target speaker amongst other voices and for successful communication with them. Selective attention has been found to involve the neural tracking of low-frequency speech rhythms in the auditory cortex. Effects of selective attention have also been found in subcortical neural activities, in particular regarding the high-frequency neural response at the fundamental frequency of speech, the speech-FFR. Recent investigations have, however, shown that the speech-FFR contains cortical contributions as well. It remains unclear whether these are also modulated by selective attention. Here we employed magnetoencephalography (MEG) to assess the attentional modulation of the cortical contributions to the speech-FFR. We presented participants with two competing speech signals and analyzed the cortical responses during attentional switching between the two speakers. Our findings revealed robust attentional modulation of the cortical contribution to the speech-FFR: the neural responses were higher when the speaker was attended than when they were ignored. We also found that, regardless of attention, a voice with a lower fundamental frequency elicited a larger cortical contribution to the speech-FFR than a voice with a higher fundamental frequency. Our results show that the attentional modulation of the speech-FFR does not only occur subcortically but extends to the auditory cortex as well.

neuroscience↗

bioRxiv2023

Early subcortical response at the fundamental frequency of continuous speech measured with MEG

Most parts of speech are voiced, exhibiting a degree of periodicity with a fundamental frequency and many higher harmonics. Some neural populations respond to this temporal fine structure, in particular at the fundamental frequency. This frequency-following response to speech (speech-FFR) consists of both subcortical and cortical contributions and can be measured through electroen-cephalography (EEG) as well as through magnetoencephalography (MEG), although both differ in the aspects of neural activity that they capture: EEG is sensitive to both radial and tangential sources as well as to deep sources, while MEG is more restrained to the measurement of tangential and superficial neural activity. EEG responses to continuous speech have shown an early subcortical contribution, at a latency of around 9 ms, in agreement with MEG measurements in response to short speech tokens, whereas MEG responses to continuous speech have not yet revealed such an early component. Here we analyze MEG responses to long segments of continuous speech. We find an early subcortical response at a latency of 9 ms, followed by later right-lateralized cortical activities at delays of 20 - 57 ms as well as potential subcortical activities. Our results show that the early subcortical component of the FFR to continuous speech can be measured from MEG, and that its latency agrees with that measured with EEG. They furthermore show that the early subcortical component is temporally well separated from later cortical contributions, enabling an independent assessment of both components towards further aspects of speech processing.

neuroscience↗

bioRxiv2020

Activation of silent secondary metabolite gene clusters by nucleosome map-guided positioning of the synthetic transcription factor VPR-dCas9

Current methods for forced expression of selected target genes are based on promoter exchange or on overexpressing native or hybrid transcriptional activators in which gene-specific DNA binding domains are coupled to strong activation domains. While these approaches are very useful for promoters with known or synthetically introduced transcription factor binding sites, they are not suitable to turn on genes in biosynthetic gene clusters which often lack pathway-specific activators. To expand the discovery toolbox, we designed a Cas9-based RNA guided synthetic transcription activation system for Aspergillus nidulans based on enzymatically disabled dCas9 fused to three consecutive activation domains (VPR-dCas9). Targeting two biosynthetic gene clusters involved in the production of secondary metabolites, we demonstrate the utility of the system. Especially in silent regions facultative heterochromatin and strictly positioned nucleosomes can constitute a relevant obstacle to the transcriptional machinery. To avoid this negative impact and to facilitate optimal positioning of RNA-guided VPR-dCas9 to our targeted promoters we have created a genome-wide nucleosome map to identify the cognate nucleosome-free-regions (NFRs). Based on these maps, different single-guide RNAs (sgRNA) were designed and tested for their targeting and activation potential. Our results demonstrate that the system can be used to activate silent BGCs in A. nidulans, partially to very high expression levels and also open the opportunity to stepwise turn on individual genes within a BGC that allows to decipher the correlated biosynthetic pathway.

bioengineering↗