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Unterauer, E.M., and Jungmann, R.
Front Synaptic Neurosci, 2022, 13, 798267.
doi: 10.3389/fnsyn.2021.798267

Quantitative Imaging With DNA-PAINT for Applications in Synaptic Neuroscience

Super-resolution (SR) microscopy techniques have been advancing the understanding of neuronal protein networks and interactions. Unraveling the arrangement of proteins with molecular resolution provided novel insights into neuron cytoskeleton structure and actin polymerization dynamics in synaptic spines. Recent improvements in quantitative SR imaging have been applied to synaptic protein clusters and with improved multiplexing technology, the interplay of multiple protein partners in synaptic active zones has been elucidated. While all SR techniques come with benefits and drawbacks, true molecular quantification is a major challenge with the most complex requirements for labeling reagents and careful experimental design. In this perspective, we provide an overview of quantitative SR multiplexing and discuss in greater detail the quantification and multiplexing capabilities of the SR technique DNA-PAINT. Using predictable binding kinetics of short oligonucleotides, DNA-PAINT provides two unique approaches to address multiplexed molecular quantification: qPAINT and Exchange-PAINT. With precise and accurate quantification and spectrally unlimited multiplexing, DNA-PAINT offers an attractive route to unravel complex protein interaction networks in neurons. Finally, while the SR community has been pushing technological advances from an imaging technique perspective, the development of universally available, small, efficient, and quantitative labels remains a major challenge in the field.



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Diana Inês Lopes Amaro

Neuronal Representation of Sound Source Location in the Auditory Cortex during Active Navigation 

RG: Benedikt Grothe



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Jan Rieckmann

Immune Cell Proteomes 

RG: Felix Meißner



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Brandstetter, K., Zülske, T., Ragoczy, T., Hörl, D., Guirao-Ortiz, M., Steinek, C., Barnes, T., Stumberger, G., Schwach, J., Haugen, E., Rynes, E., Korber, P., Stamatoyannopoulos, J.A., Leonhardt, H., Wedemann, G., and Harz, H.
(IMPRS-LS students are in bold)
Biophys J., 2022, online ahead of print.
doi: 10.1016/j.bpj.2022.02.009

Differences in nanoscale organization of regulatory active and inactive human chromatin

Methodological advances in conformation capture techniques have fundamentally changed our understanding of chromatin architecture. However, the nanoscale organization of chromatin and its cell-to-cell variance are less studied. Analyzing genome-wide data from 733 human cell and tissue samples, we identified 2 prototypical regions that exhibit high or absent hypersensitivity to deoxyribonuclease I, respectively. These regulatory active or inactive regions were examined in the lymphoblast cell line K562 by using high-throughput super-resolution microscopy. In both regions, we systematically measured the physical distance of 2 fluorescence in situ hybridization spots spaced by only 5 kb of DNA. Unexpectedly, the resulting distance distributions range from very compact to almost elongated configurations of more than 200-nm length for both the active and inactive regions. Monte Carlo simulations of a coarse-grained model of these chromatin regions based on published data of nucleosome occupancy in K562 cells were performed to understand the underlying mechanisms. There was no parameter set for the simulation model that can explain the microscopically measured distance distributions. Obviously, the chromatin state given by the strength of internucleosomal interaction, nucleosome occupancy, or amount of histone H1 differs from cell to cell, which results in the observed broad distance distributions. This large variability was not expected, especially in inactive regions. The results for the mechanisms for different distance distributions on this scale are important for understanding the contacts that mediate gene regulation. Microscopic measurements show that the inactive region investigated here is expected to be embedded in a more compact chromatin environment. The simulation results of this region require an increase in the strength of internucleosomal interactions. It may be speculated that the higher density of chromatin is caused by the increased internucleosomal interaction strength.



A team from the Max Planck Institue of Biochemistry in Martinsried and the Martin Luther University Halle-Wittenberg has discovered how an essential final step in the production of mRNA precisely works.

Proteins need to interact in a complex manner for a so-called “messenger RNA” (mRNA) to be created in human cells from a precursor molecule. mRNA provides a blueprint for proteins; the first vaccines against the coronavirus are also based on mRNAs. A team from the Max Planck Institute (MPI) of Biochemistry in Martinsried and the Martin Luther University Halle-Wittenberg (MLU) has discovered how an essential final step in the production of mRNA precisely works. The study was published in Genes & Development.

Proteins are responsible for all of the body’s essential processes. In a sense, the genes in the human genome act as building instructions for them. However, an intermediate step is necessary before new proteins can be created: “First the DNA must be transcribed: A chain-like precursor RNA is produced which is an exact copy of the DNA. From this, several steps are required to create the mature mRNA. This process is essential for the cell to build new proteins,” says biochemist Professor Elmar Wahle from MLU who led the team alongside Professor Elena Conti, an expert in structural biology at the MPI of Biochemistry. 

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Matthias Scherr

The Dynamics of Eukaryotic Replication Initiation Revealed at the Single-Molecule Level 

RG: Karl Duderstadt



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Stefan Bauernfried

Humanes NLRP1 ist ein Sensor für Doppelstrang-RNA

RG: Veit Hornung



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Karl, L.A., Peritore, M., Galanti, L., and Pfander, B.
(IMPRS-LS students are in bold)
Front Genet, 2021, 12, 821543.
DOI: 10.3389/fgene.2021.821543

DNA Double Strand Break Repair and Its Control by Nucleosome Remodeling

DNA double strand breaks (DSBs) are repaired in eukaryotes by one of several cellular mechanisms. The decision-making process controlling DSB repair takes place at the step of DNA end resection, the nucleolytic processing of DNA ends, which generates single-stranded DNA overhangs. Dependent on the length of the overhang, a corresponding DSB repair mechanism is engaged. Interestingly, nucleosomes-the fundamental unit of chromatin-influence the activity of resection nucleases and nucleosome remodelers have emerged as key regulators of DSB repair. Nucleosome remodelers share a common enzymatic mechanism, but for global genome organization specific remodelers have been shown to exert distinct activities. Specifically, different remodelers have been found to slide and evict, position or edit nucleosomes. It is an open question whether the same remodelers exert the same function also in the context of DSBs. Here, we will review recent advances in our understanding of nucleosome remodelers at DSBs: to what extent nucleosome sliding, eviction, positioning and editing can be observed at DSBs and how these activities affect the DSB repair decision.



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Oz, T., Mengoli, V., Rojas, J., Jonak, K., Braun, M., Zagoriy, I., and Zachariae, W.
(IMPRS-LS students/alumni are bold)
EMBO J, 2022, e109446.
DOI: 10.15252/embj.2021109446

The Spo13/Meikin pathway confines the onset of gamete differentiation to meiosis II in yeast

Sexual reproduction requires genome haploidization by the two divisions of meiosis and a differentiation program to generate gametes. Here, we have investigated how sporulation, the yeast equivalent of gamete differentiation, is coordinated with progression through meiosis. Spore differentiation is initiated at metaphase II when a membrane-nucleating structure, called the meiotic plaque, is assembled at the centrosome. While all components of this structure accumulate already at entry into meiosis I, they cannot assemble because centrosomes are occupied by Spc72, the receptor of the γ-tubulin complex. Spc72 is removed from centrosomes by a pathway that depends on the polo-like kinase Cdc5 and the meiosis-specific kinase Ime2, which is unleashed by the degradation of Spo13/Meikin upon activation of the anaphase-promoting complex at anaphase I. Meiotic plaques are finally assembled upon reactivation of Cdk1 at entry into metaphase II. This unblocking-activation mechanism ensures that only single-copy genomes are packaged into spores and might serve as a paradigm for the regulation of other meiosis II-specific processes.



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Isa-Maria Gross

Combined Behavioral and Neural Investigations of Pup Retrieval - A neural code for pup call representations in the mouse auditory cortex

RG: Tobias Bonhoeffer