E-Mail: franziska.aron@uni-jena.de
Room: FLI 2.060
Phone: +49 3641 65-6842
Publications
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},
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.},
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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.
Aron, Franziska; Wollny, Damian
Single coacervate sequencing Technical Manual
2022.
@manual{nokey,
title = {Single coacervate sequencing},
author = {Franziska Aron and Damian Wollny},
doi = {10.17504/protocols.io.bux5nxq6},
year = {2022},
date = {2022-03-07},
abstract = {Here, we present a protocol which enables the comprehensive characterization of the RNA content of single phase-separated coacervates. We adapted single-cell RNA sequencing technology in combination with fluorescence activated cell sorting (FACS) to answer the question of how one condensate differs from the other in terms of RNA composition and how it relates to condensate features such as droplet size. This approach represents a powerful addition to labor intensive and low throughput microscopy approaches which have been the state of the art approach for coacervate RNA characterization. This protocol includes droplet production, as well as a Smart-seq2 protocol adaption for lysis, reverse transcription and cDNA amplification and sequencing library preparation. This protocol ends with the library preparation. Afterwards it got sequenced on an Illumina NextSeq500 (paired end for 300 cycles).
The Smart-seq2 protocol was originally published in Picelli, S., Faridani, O., Björklund, Å. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc9, 171–181 (2014). https://doi.org/10.1038/nprot.2014.006},
keywords = {},
pubstate = {published},
tppubtype = {manual}
}
Here, we present a protocol which enables the comprehensive characterization of the RNA content of single phase-separated coacervates. We adapted single-cell RNA sequencing technology in combination with fluorescence activated cell sorting (FACS) to answer the question of how one condensate differs from the other in terms of RNA composition and how it relates to condensate features such as droplet size. This approach represents a powerful addition to labor intensive and low throughput microscopy approaches which have been the state of the art approach for coacervate RNA characterization. This protocol includes droplet production, as well as a Smart-seq2 protocol adaption for lysis, reverse transcription and cDNA amplification and sequencing library preparation. This protocol ends with the library preparation. Afterwards it got sequenced on an Illumina NextSeq500 (paired end for 300 cycles).
The Smart-seq2 protocol was originally published in Picelli, S., Faridani, O., Björklund, Å. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc9, 171–181 (2014). https://doi.org/10.1038/nprot.2014.006
The Smart-seq2 protocol was originally published in Picelli, S., Faridani, O., Björklund, Å. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc9, 171–181 (2014). https://doi.org/10.1038/nprot.2014.006
2021
Yates, James A. Fellows; Velsko, Irina M.; Aron, Franziska; Posth, Cosimo; Hofman, Courtney A.; Austin, Rita M.; Parker, Cody E.; Mann, Allison E.; Nägele, Kathrin; Arthur, Kathryn Weedman; Arthur, John W.; Bauer, Catherine C.; Crevecoeur, Isabelle; Cupillard, Christophe; Curtis, Matthew C.; Dalén, Love; Bonilla, Marta Díaz-Zorita; Fernández-Lomana, J. Carlos Díez; Drucker, Dorothée G.; Escrivá, Elena Escribano; Francken, Michael; Gibbon, Victoria E.; Morales, Manuel R. González; Mateu, Ana Grande; Harvati, Katerina; Henry, Amanda G.; Humphrey, Louise; Menéndez, Mario; Mihailović, Dušan; Peresani, Marco; Moroder, Sofía Rodríguez; Roksandic, Mirjana; Rougier, Hélène; Sázelová, Sandra; Stock, Jay T.; Straus, Lawrence Guy; Svoboda, Jiří; Teßmann, Barbara; Walker, Michael J.; Power, Robert C.; Lewis, Cecil M.; Sankaranarayanan, Krithivasan; Guschanski, Katerina; Wrangham, Richard W.; Dewhirst, Floyd E.; Salazar-García, Domingo C.; Krause, Johannes; Herbig, Alexander; Warinner, Christina
The evolution and changing ecology of the African hominid oral microbiome Journal Article
In: Proc Natl Acad Sci, vol. 118, no. 20, pp. e2021655118, 2021.
@article{Yates:21,
title = {The evolution and changing ecology of the African hominid oral microbiome},
author = {James A. Fellows Yates and Irina M. Velsko and Franziska Aron and Cosimo Posth and Courtney A. Hofman and Rita M. Austin and Cody E. Parker and Allison E. Mann and Kathrin Nägele and Kathryn Weedman Arthur and John W. Arthur and Catherine C. Bauer and Isabelle Crevecoeur and Christophe Cupillard and Matthew C. Curtis and Love Dalén and Marta Díaz-Zorita Bonilla and J. Carlos Díez Fernández-Lomana and Dorothée G. Drucker and Elena Escribano Escrivá and Michael Francken and Victoria E. Gibbon and Manuel R. González Morales and Ana Grande Mateu and Katerina Harvati and Amanda G. Henry and Louise Humphrey and Mario Menéndez and Dušan Mihailović and Marco Peresani and Sofía Rodríguez Moroder and Mirjana Roksandic and Hélène Rougier and Sandra Sázelová and Jay T. Stock and Lawrence Guy Straus and Jiří Svoboda and Barbara Teßmann and Michael J. Walker and Robert C. Power and Cecil M. Lewis and Krithivasan Sankaranarayanan and Katerina Guschanski and Richard W. Wrangham and Floyd E. Dewhirst and Domingo C. Salazar-García and Johannes Krause and Alexander Herbig and Christina Warinner},
doi = {10.1073/pnas.2021655118},
year = {2021},
date = {2021-05-18},
urldate = {2021-05-18},
journal = {Proc Natl Acad Sci},
volume = {118},
number = {20},
pages = {e2021655118},
publisher = {Proceedings of the National Academy of Sciences},
abstract = {The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine–platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine–platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.