E-Mail: julia.micheel@uni-jena.de
Room: FLI 2.060
Phone: +493641-65-6842
Publications
2024
Micheel, Julia; Safrastyan, Aram; Aron, Franziska; Wollny, Damian
Exploring the impact of primer length on efficient gene detection via high-throughput sequencing Journal Article
In: Nature Communications, vol. 15, iss. 1, 2024.
@article{nokey_64,
title = {Exploring the impact of primer length on efficient gene detection via high-throughput sequencing},
author = {Julia Micheel and Aram Safrastyan and Franziska Aron and Damian Wollny},
doi = {10.1038/s41467-024-49685-0},
year = {2024},
date = {2024-07-12},
journal = {Nature Communications},
volume = {15},
issue = {1},
abstract = {Reverse transcription (RT) is a crucial step in most RNA analysis methods. Optimizing protocols for this initial stage is critical for effective target detection, particularly when working with limited input RNA. Several factors, such as the input material quality and reaction conditions, influence RT efficiency. However, the effect of RT primer length on gene detection efficiency remains largely unknown. Thus, we investigate its impact by generating RNA-seq libraries with random RT primers of 6, 12, 18, or 24 nucleotides. To our surprise, the 18mer primer shows superior efficiency in overall transcript detection compared to the commonly used 6mer primer, especially in detecting longer RNA transcripts in complex human tissue samples. This study highlights the critical role of primer length in RT efficiency, which has significant potential to benefit various transcriptomic assays, from basic research to clinical diagnostics, given the central role of RT in RNA-related analyses.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Reverse transcription (RT) is a crucial step in most RNA analysis methods. Optimizing protocols for this initial stage is critical for effective target detection, particularly when working with limited input RNA. Several factors, such as the input material quality and reaction conditions, influence RT efficiency. However, the effect of RT primer length on gene detection efficiency remains largely unknown. Thus, we investigate its impact by generating RNA-seq libraries with random RT primers of 6, 12, 18, or 24 nucleotides. To our surprise, the 18mer primer shows superior efficiency in overall transcript detection compared to the commonly used 6mer primer, especially in detecting longer RNA transcripts in complex human tissue samples. This study highlights the critical role of primer length in RT efficiency, which has significant potential to benefit various transcriptomic assays, from basic research to clinical diagnostics, given the central role of RT in RNA-related analyses.
2023
Micheel, Julia; Aron, Franziska; Kelani, Abdulrahman A.; Girbardt, Christian; Blango, Matthew G.; Walther, Grit; Wollny, Damian
RNA-based sensitive fungal pathogen detection Journal Article
In: bioRxiv, 2023.
@article{nokey_46,
title = {RNA-based sensitive fungal pathogen detection},
author = {Julia Micheel and Franziska Aron and Abdulrahman A. Kelani and Christian Girbardt and Matthew G. Blango and Grit Walther and Damian Wollny},
doi = {10.1101/2023.09.26.559494},
year = {2023},
date = {2023-09-26},
urldate = {2023-09-26},
journal = {bioRxiv},
abstract = {Detecting fungal pathogens, a major cause of severe systemic infections, remains challenging due to the difficulty and time-consuming nature of diagnostic methods. This delay in identification hinders targeted treatment decisions and may lead to unnecessary use of broad-spectrum antibiotics. To expedite treatment initiation, one promising approach is to directly detect pathogen nucleic acids such as DNA, which is often preferred to RNA because of its inherent stability. However, a higher number of RNA molecules per cell makes RNA a more promising diagnostic target which is particularly prominent for highly expressed genes such as rRNA. Here, we investigated the utility of a minimal input-specialized reverse transcription protocol to increase diagnostic sensitivity. This proof-of-concept study demonstrates that fungal rRNA detection by the minimal input protocol is drastically more sensitive compared to detection of genomic DNA even with high levels of human RNA background. This approach can detect several of the most relevant human pathogenic fungal genera, such as Aspergillus, Candida, and Fusarium and thus represents a powerful, cheap, and easily adaptable addition to currently available diagnostic assays.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Detecting fungal pathogens, a major cause of severe systemic infections, remains challenging due to the difficulty and time-consuming nature of diagnostic methods. This delay in identification hinders targeted treatment decisions and may lead to unnecessary use of broad-spectrum antibiotics. To expedite treatment initiation, one promising approach is to directly detect pathogen nucleic acids such as DNA, which is often preferred to RNA because of its inherent stability. However, a higher number of RNA molecules per cell makes RNA a more promising diagnostic target which is particularly prominent for highly expressed genes such as rRNA. Here, we investigated the utility of a minimal input-specialized reverse transcription protocol to increase diagnostic sensitivity. This proof-of-concept study demonstrates that fungal rRNA detection by the minimal input protocol is drastically more sensitive compared to detection of genomic DNA even with high levels of human RNA background. This approach can detect several of the most relevant human pathogenic fungal genera, such as Aspergillus, Candida, and Fusarium and thus represents a powerful, cheap, and easily adaptable addition to currently available diagnostic assays.
2022
Wollny, Damian; Vernot, Benjamin; Wang, Jie; Hondele, Maria; Safrastyan, Aram; Aron, Franziska; Micheel, Julia; He, Zhisong; Hyman, Anthony; Weis, Karsten; Camp, J. Gray; Tang, T-Y Dora; Treutlein, Barbara
Characterization of RNA content in individual phase-separated coacervate microdroplets Journal Article
In: Nat Commun, vol. 13, iss. 1, pp. 2626, 2022.
@article{nokey,
title = {Characterization of RNA content in individual phase-separated coacervate microdroplets},
author = {Damian Wollny and Benjamin Vernot and Jie Wang and Maria Hondele and Aram Safrastyan and Franziska Aron and Julia Micheel and Zhisong He and Anthony Hyman and Karsten Weis and J. Gray Camp and T-Y Dora Tang and Barbara Treutlein},
url = {10.1038/s41467-022-30158-1},
year = {2022},
date = {2022-05-12},
urldate = {2022-05-12},
journal = {Nat Commun},
volume = {13},
issue = {1},
pages = {2626},
abstract = {Condensates formed by complex coacervation are hypothesized to have played a crucial part during the origin-of-life. In living cells, condensation organizes biomolecules into a wide range of membraneless compartments. Although RNA is a key component of biological condensates and the central component of the RNA world hypothesis, little is known about what determines RNA accumulation in condensates and to which extend single condensates differ in their RNA composition. To address this, we developed an approach to read the RNA content from single synthetic and protein-based condensates using high-throughput sequencing. We find that certain RNAs efficiently accumulate in condensates. These RNAs are strongly enriched in sequence motifs which show high sequence similarity to short interspersed elements (SINEs). We observe similar results for protein-derived condensates, demonstrating applicability across different in vitro reconstituted membraneless organelles. Thus, our results provide a new inroad to explore the RNA content of phase-separated droplets at single condensate resolution.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Condensates formed by complex coacervation are hypothesized to have played a crucial part during the origin-of-life. In living cells, condensation organizes biomolecules into a wide range of membraneless compartments. Although RNA is a key component of biological condensates and the central component of the RNA world hypothesis, little is known about what determines RNA accumulation in condensates and to which extend single condensates differ in their RNA composition. To address this, we developed an approach to read the RNA content from single synthetic and protein-based condensates using high-throughput sequencing. We find that certain RNAs efficiently accumulate in condensates. These RNAs are strongly enriched in sequence motifs which show high sequence similarity to short interspersed elements (SINEs). We observe similar results for protein-derived condensates, demonstrating applicability across different in vitro reconstituted membraneless organelles. Thus, our results provide a new inroad to explore the RNA content of phase-separated droplets at single condensate resolution.
2021
Micheel, Julia; Safrastyan, Aram; Wollny, Damian
Advances in Non-Coding RNA Sequencing Journal Article
In: Noncoding RNA, vol. 7, no. 4, pp. 70, 2021.
@article{nokey,
title = {Advances in Non-Coding RNA Sequencing},
author = {Julia Micheel and Aram Safrastyan and Damian Wollny
},
doi = {10.3390/ncrna7040070},
year = {2021},
date = {2021-10-30},
journal = {Noncoding RNA},
volume = {7},
number = {4},
pages = {70},
abstract = {Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules. Since the discovery of the first ncRNA in the 1960s, ncRNAs have been shown to be involved in nearly all steps of the central dogma of molecular biology. In recent years, the pace of discovery of novel ncRNAs and their cellular roles has been greatly accelerated by high-throughput sequencing. Advances in sequencing technology, library preparation protocols as well as computational biology helped to greatly expand our knowledge of which ncRNAs exist throughout the kingdoms of life. Moreover, RNA sequencing revealed crucial roles of many ncRNAs in human health and disease. In this review, we discuss the most recent methodological advancements in the rapidly evolving field of high-throughput sequencing and how it has greatly expanded our understanding of ncRNA biology across a large number of different organisms.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules. Since the discovery of the first ncRNA in the 1960s, ncRNAs have been shown to be involved in nearly all steps of the central dogma of molecular biology. In recent years, the pace of discovery of novel ncRNAs and their cellular roles has been greatly accelerated by high-throughput sequencing. Advances in sequencing technology, library preparation protocols as well as computational biology helped to greatly expand our knowledge of which ncRNAs exist throughout the kingdoms of life. Moreover, RNA sequencing revealed crucial roles of many ncRNAs in human health and disease. In this review, we discuss the most recent methodological advancements in the rapidly evolving field of high-throughput sequencing and how it has greatly expanded our understanding of ncRNA biology across a large number of different organisms.