Description
In the past decade, the development of new methods has enabled the global analysis of transcriptomes and proteomes. Together with the establishment of quantitative strategies, this enables global studies to analyze gene expression at different molecular levels. We use these techniques to investigate various genomic, virologic and cell-biological questions.
Proteotranscriptomics annotation
We employ next-generation RNA-Seq and mass spectrometry-based proteomics to obtain information about expressed RNA transcripts and translated proteins to perform systematic annotation of protein-coding genes combining sequence information from both levels. This allows to identify genes previously missed or wrongly annotated by genome annotation projects. We have demonstrated the power of this approach for a dozen of nematodes including species without a genome annotation and discovered two new genes in the well-annotated model species C. elegans. In the future, we want to extend this approach to a more diverse set of species including understudied farm animals.
Literature:
- Ceron-Noriega A, Almeida MV, Levin M, Butter F. Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis. Genome Res. 2023
- Levin M, Butter F. Proteotranscriptomics - A facilitator in omics research. Comput Struct Biotechnol J. 2022
- Levin M, Scheibe M, Butter F. Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line. BMC Genomics. 2020
Gene regulation in animal parasites
African trypanosomes (T. brucei), the causative agent of Nagana in cattle, are early branching eukaryotes with particular gene regulatory features, but are also used for the study of fundamental biological questions. We have previously shown that gene expression levels between transcriptome and proteome are different likely due to polycistronic expression units and trans-splicing of a leader sequence determining a strong influence of post-transcriptional regulation on gene expression. In collaboration, we sed this animal pathogen as a model to determine the nuclear proteome by spatial proteomics, for the investigation of epigenetic regulation and the crosstalk between differentiation and metabolism. In the future, we will extend these studies to other kinetoplast pathogens posing threads to animal and human health.
Literature:
- Trindade S, De Niz M, Costa-Sequeira M, Bizarra-Rebelo T, Bento F, Dejung M, Narciso MV, López-Escobar L, Ferreira J, Butter F, Bringaud F, Gjini E, Figueiredo LM. Slow growing behavior in African trypanosomes during adipose tissue colonization. Nat Commun. 2022
- Vellmer T, Hartleb L, Fradera Sola A, Kramer S, Meyer-Natus E, Butter F, Janzen CJ.A novel SNF2 ATPase complex in Trypanosoma brucei with a role in H2A.Z-mediated chromatin remodelling. PLoS Pathog. 2022
- Eisenhuth N, Vellmer T, Rauh ET, Butter F, Janzen CJ. A DOT1B/Ribonuclease H2 Protein Complex Is Involved in R-Loop Processing, Genomic Integrity, and Antigenic Variation in Trypanosoma brucei. mBio 2021
- Doleželová E, Kunzová M, Dejung M, Levin M, Panicucci B, Regnault C, Janzen CJ, Barrett MP, Butter F, Zíková A. Cell-based and multi-omics profiling reveals dynamic metabolic repurposing of mitochondria to drive developmental progression of Trypanosoma brucei. PLoS Biol. 2020
- Goos C, Dejung M, Janzen CJ, Butter F, Kramer S. The nuclear proteome of Trypanosoma brucei. PLoS One 2017
- Dejung M, Subota I, Bucerius F, Dindar G, Freiwald A, Engstler M, Boshart M, Butter F, Janzen CJ. Quantitative Proteomics Uncovers Novel Factors Involved in Developmental Differentiation of Trypanosoma brucei. PLoS Pathog. 2016
- Ericson M, Janes MA, Butter F, Mann M, Ullu E, Tschudi C. On the extent and role of the small proteome in the parasitic eukaryote Trypanosoma brucei. BMC Biol. 2014
- Butter F, Bucerius F, Michel M, Cicova Z, Mann M, Janzen CJ. Comparative proteomics of two life cycle stages of stable isotope-labeled Trypanosoma brucei reveals novel components of the parasite's host adaptation machinery. Mol Cell Proteomics. 2013
Developmental systems biology
Working on the interface between transcriptomics and proteomics, we currently explore global gene regulation patterns. We have thus far studied developmental differentiation in trypanosomes, outlining that transcriptomics in this parasite has no strong correlation to proteome levels probably due to polycistronic transcription units. Furthermore, we generated a large-scale developmental proteome of Drosophila melanogaster showing that for a subset of the proteome, proteins can be stable long after transcription. Matching the embryonic time-course proteome dataset of this study, with a paired transcriptome, we applied ordinary differential equations (ODE) as a mathematical framework to correlate transcriptome and proteome during embryogenesis and successfully predicted translational regulators.
Literature:
- Becker K, Bluhm A, Casas-Vila N, Dinges N, Dejung M, Sayols S, Kreutz C, Roignant JY, Butter F, Legewie S. Quantifying post-transcriptional regulation in the development of Drosophila melanogaster. Nat Commun. 2018
- Casas-Vila N, Bluhm A, Sayols S, Dinges N, Dejung M, Altenhein T, Kappei D, Altenhein B, Roignant JY, Butter F. The developmental proteome of Drosophila melanogaster. Genome Res. 2017
- Dejung M, Subota I, Bucerius F, Dindar G, Freiwald A, Engstler M, Boshart M, Butter F, Janzen CJ. Quantitative Proteomics Uncovers Novel Factors Involved in Developmental Differentiation of Trypanosoma brucei. PLoS Pathog. 2016
Telomere stability and regulation in animals
Telomeres are an important feature of eukaryotic genome integrity and are involved in ageing and cancer progression in animals. We previously employed a phylointeractomics screen to unveil putative telomere-associated proteins from ray-boned fish to mammals and already validated several candidates, such as HOT1, ZBTB10, ZBTB48 and ZNF524 as new telomeric proteins. Additionally, we also investigate telomeric binding proteins in other animal species such as C. elegans and T. brucei to understand basic principles of telomere regulation and stability.
Literature:
- Braun H, Xu Z, Chang F, Viceconte N, Rane G, Levin M, Lototska L, Roth F, Hillairet A, Fradera-Sola A, Khanchandani V, Dreesen O, Yang Y, Shi Y, Li F, Butter F, Kappei D. ZNF524 directly interacts with telomeric DNA and supports telomere integrity. Biorxiv 2022
- Dietz S, Almeida MV, Nischwitz E, Schreier J, Viceconte N, Fradera-Sola A, Renz C, Ceron-Noriega A, Ulrich HD, Kappei D, Ketting RF, Butter F. The double-stranded DNA-binding proteins TEBP-1 and TEBP-2 form a telomeric complex with POT-1. Nat Commun. 2021
- Bluhm A, Viceconte N, Li F, Rane G, Ritz S, Wang S, Levin M, Shi Y, Kappei D, Butter F. ZBTB10 binds the telomeric variant repeat TTGGGG and interacts with TRF2. Nucleic Acids Res. 2019
- Reis H, Schwebs M, Dietz S, Janzen CJ, Butter F. TelAP1 links telomere complexes with developmental expression site silencing in African trypanosomes. Nucleic Acids Res. 2018
- Jahn A, Rane G, Paszkowski-Rogacz M, Sayols S, Bluhm A, Han CT, Draškovič I, Londoño-Vallejo JA, Kumar AP, Buchholz F, Butter F, Kappei D. ZBTB48 is both a vertebrate telomere-binding protein and a transcriptional activator. EMBO Rep. 2017
- Kappei D, Scheibe M, Paszkowski-Rogacz M, Bluhm A, Gossmann TI, Dietz S, Dejung M, Herlyn H, Buchholz F, Mann M, Butter F. Phylointeractomics reconstructs functional evolution of protein binding. Nat Commun. 2017
- Kappei D, Butter F, Benda C, Scheibe M, Draškovič I, Stevense M, Novo CL, Basquin C, Araki M, Araki K, Krastev DB, Kittler R, Jessberger R, Londoño-Vallejo JA, Mann M, Buchholz F. HOT1 is a mammalian direct telomere repeat-binding protein contributing to telomerase recruitment. EMBO J. 2013