News | IMPRS for Molecules of Life

Publication of IMPRS-LS student Sebastian Pünzeler

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Pünzeler S, Link S, Wagner G, Keilhauer EC, Kronbeck N, Spitzer RM, Leidescher S, Markaki Y, Mentele E, Regnard C, Schneider K, Takahashi D, Kusakabe M, Vardabasso C, Zink LM, Straub T, Bernstein E, Harata M, Leonhardt H, Mann M, Rupp RA, Hake SB.
EMBO J, 2017, doi: 10.15252/embj.201695757. [Epub ahead of print]

Multivalent binding of PWWP2A to H2A.Z regulates mitosis and neural crest differentiation.

Replacement of canonical histones with specialized histone variants promotes altering of chromatin structure and function. The essential histone variant H2A.Z affects various DNA-based processes via poorly understood mechanisms. Here, we determine the comprehensive interactome of H2A.Z and identify PWWP2A as a novel H2A.Z-nucleosome binder. PWWP2A is a functionally uncharacterized, vertebrate-specific protein that binds very tightly to chromatin through a concerted multivalent binding mode. Two internal protein regions mediate H2A.Z-specificity and nucleosome interaction, whereas the PWWP domain exhibits direct DNA binding. Genome-wide mapping reveals that PWWP2A binds selectively to H2A.Z-containing nucleosomes with strong preference for promoters of highly transcribed genes. In human cells, its depletion affects gene expression and impairs proliferation via a mitotic delay. While PWWP2A does not influence H2A.Z occupancy, the C-terminal tail of H2A.Z is one important mediator to recruit PWWP2A to chromatin. Knockdown of PWWP2A in Xenopus results in severe cranial facial defects, arising from neural crest cell differentiation and migration problems. Thus, PWWP2A is a novel H2A.Z-specific multivalent chromatin binder providing a surprising link between H2A.Z, chromosome segregation, and organ development.

Multicoloured microcosm: 124 colours thanks to RGB technology

Red, green and blue: normally, no more than three different colours can be detected simultaneously in fluorescence microscopy. Thanks to recent RGB nanotechnology, similar to that used in computer monitors, it is now possible to generate 124 virtual colours under the microscope. The three primary colours are arranged in various mixing ratios on a special DNA lattice. This creates individual colour pixels under the microscope. The new method was developed by scientists at the Max Planck Institute of Biochemistry, Ludwig Maximilian University of Munich, Germany, and the Wyss Institute for Biologically Inspired Engineering at Harvard University in the US. The team’s work was published in the journal Science Advances

Biomedical research has made tremendous strides in recent decades. Using the latest microscopes, scientists are analyzing the function and interactions of molecules in cells with ever greater detail. Now, researchers are looking for methods to image multiple molecules simultaneously.

RGB nanotechnology
A team of scientists from Germany and the US headed by Ralf Jungmann and Peng Yin has now developed substances known as metafluorophors. “The technology can be compared to that of an RGB monitor,” explains Jungmann, Leader of the Molecular Imaging and Bionanotechnology Research Group. To display a wide range of colours on a screen, each colour is mixed from the three primary colours: red, green and blue. “We’ve transferred this approach to the nanometre scale. Instead of a single fluorescence dye molecule, multiple fluorescent molecules are applied to a carrier material, which serves as a kind of experimental board. Depending on the proportion of the three primary colours, they appear in different colours under the microscope, comparable to nanometre-scale colour pixels on a computer screen.“

Publication of IMPRS-LS student Katarzyna Jonak

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Jonak K, Zagoriy I, Oz T, Graf P, Rojas J, Mengoli V, Zachariae W.
Cell Cycle, 2017, [Epub ahead of print].

APC/C-Cdc20 mediates deprotection of centromeric cohesin at meiosis II in yeast.

Cells undergoing meiosis produce haploid gametes through one round of DNA replication followed by 2 rounds of chromosome segregation. This requires that cohesin complexes, which establish sister chromatid cohesion during S phase, are removed in a stepwise manner. At meiosis I, the separase protease triggers the segregation of homologous chromosomes by cleaving cohesin's Rec8 subunit on chromosome arms. Cohesin persists at centromeres because the PP2A phosphatase, recruited by the shugoshin protein, dephosphorylates Rec8 and thereby protects it from cleavage. While chromatids disjoin upon cleavage of centromeric Rec8 at meiosis II, it was unclear how and when centromeric Rec8 is liberated from its protector PP2A. One proposal is that bipolar spindle forces separate PP2A from Rec8 as cells enter metaphase II. We show here that sister centromere biorientation is not sufficient to "deprotect" Rec8 at meiosis II in yeast. Instead, our data suggest that the ubiquitin-ligase APC/CCdc20 removes PP2A from centromeres by targeting for degradation the shugoshin Sgo1 and the kinase Mps1. This implies that Rec8 remains protected until entry into anaphase II when it is phosphorylated concurrently with the activation of separase. Here, we provide further support for this model and speculate on its relevance to mammalian oocytes.

Publication of IMPRS-LS student Claudio Lademann

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Lademann CA, Renkawitz J, Pfander B, Jentsch S.
Cell Rep, 2017, 19, 1294-1303.

The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination.

The INO80 complex (INO80-C) is an evolutionarily conserved nucleosome remodeler that acts in transcription, replication, and genome stability. It is required for resistance against genotoxic agents and is involved in the repair of DNA double-strand breaks (DSBs) by homologous recombination (HR). However, the causes of the HR defect in INO80-C mutant cells are controversial. Here, we unite previous findings using a system to study HR with high spatial resolution in budding yeast. We find that INO80-C has at least two distinct functions during HR-DNA end resection and presynaptic filament formation. Importantly, the second function is linked to the histone variant H2A.Z. In the absence of H2A.Z, presynaptic filament formation and HR are restored in INO80-C-deficient mutants, suggesting that presynaptic filament formation is the crucial INO80-C function during HR.

Remote control of behaviour by optically activating single neurons

Scientists from the Max Planck Institute of Neurobiology in Martinsried have developed a method that allows them to identify nerve cells involved in a specific motor command. For the first time, it is now possible to evoke behaviour of a small fish by artificially activating just a handful of neurons. Understanding the core components of a neural circuit is a key step for deciphering the complex code underlying even elementary brain functions.

Recent years have seen much progress in understanding of the brain’s structure and function. Advances in microscopy and functional imaging enable researchers to monitor the activity of neuronal populations, while an animal perceives sensory stimuli or generates specific behaviours. However, these studies often cannot distinguish cause from consequence of the observed changes in activity. Using the method of optogenetics, scientists can find out which neurons are essential for the chain of events that ultimately lead to behaviour, and which neurons may serve other tasks or are merely by-standers. A particular challenge for this field of research is the staggering degree of "interconnectedness" of neuronal networks. Activating even a single neuron may send ripples through a large part of the nervous system. The new study from Herwig Baier and his team at the Max Planck Institute of Neurobiology has removed both obstacles in one sweep: it is now possible to pinpoint cause and effect to the cellular components of neural circuitry while simultaneously watching how activity propagates through the entire brain network and evokes behaviour.

The Martinsried scientists developed a workflow allowing the 3D photo-stimulation of multiple targeted neurons while, at the same time, imaging network activity in the brain of a zebrafish larva. “The zebrafish with its small, translucent brain is ideal for our new method”, explains Marco dal Maschio, one of the two lead authors of the publication describing the technique.

Publication of IMPRS-LS student Tobias Ruff

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Del Toro D*, Ruff T*, Cederfjäll E, Villalba A, Seyit-Bremer G, Borrell V, Klein R.
* co-first-author
Cell, 2017, 169, 621-635.

Regulation of Cerebral Cortex Folding by Controlling Neuronal Migration via FLRT Adhesion Molecules.

The folding of the mammalian cerebral cortex into sulci and gyri is thought to be favored by the amplification of basal progenitor cells and their tangential migration. Here, we provide a molecular mechanism for the role of migration in this process by showing that changes in intercellular adhesion of migrating cortical neurons result in cortical folding. Mice with deletions of FLRT1 and FLRT3 adhesion molecules develop macroscopic sulci with preserved layered organization and radial glial morphology. Cortex folding in these mutants does not require progenitor cell amplification but is dependent on changes in neuron migration. Analyses and simulations suggest that sulcus formation in the absence of FLRT1/3 results from reduced intercellular adhesion, increased neuron migration, and clustering in the cortical plate. Notably, FLRT1/3 expression is low in the human cortex and in future sulcus areas of ferrets, suggesting that intercellular adhesion is a key regulator of cortical folding across species.

The formation of folds on the surface of the brain

Folds in the human brain enlarge the surface of this important processing organ and in this way create more space for higher functions including thought and action. However, certain species of mammals exist whose brains have smooth surfaces, for example mice. Scientists from the Max Planck Institute of Neurobiology in Martinsried have discovered a previously unknown mechanism for brain folding. Young neurons, which migrate to the cortex during the development of a smooth-surfaced brain, have so-called FLRT receptors on their cell surface. These ensure a certain degree of adhesion between the cells and regular migratory behaviour which favours the formation of a smooth brain surface. Compared to the mouse brain, in the human brain FLRTs are much less abundant. If the expression of FLRTs in the mouse brain is reduced experimentally, folds similar to those found in the human brain form. These findings provide new insights into the evolution of smooth and folded mammalian brains.

The human brain has many grooves and furrows which enlarge the brain surface considerably compared to that of a smooth brain. Homo sapiens is not the only species to form folds in the brain, however. It is likely that the ancestral mammal, which lived around 200 million years ago, also had a folded brain. Over the course of evolution, various mammalian species lost their brain folds again. Hence mice and rats, for example, have brains with smooth surfaces.

“The evolutionary success of these and other animal species with smooth brains shows that having a brain without folds is not necessarily disadvantageous and works well for these species,” explains Rüdiger Klein, a Director at the Max Planck Institute of Neurobiology. “We were interested in how brain folds actually arise.”

Publication of IMPRS-LS student Roman Prytuliak

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Prytuliak R, Volkmer M, Meier M, Habermann BH.
Nucleic Acids Res, 2017, [Epub ahead of print].

HH-MOTiF: de novo detection of short linear motifs in proteins by Hidden Markov Model comparisons.

Short linear motifs (SLiMs) in proteins are self-sufficient functional sequences that specify interaction sites for other molecules and thus mediate a multitude of functions. Computational, as well as experimental biological research would significantly benefit, if SLiMs in proteins could be correctly predicted de novo with high sensitivity. However, de novo SLiM prediction is a difficult computational task. When considering recall and precision, the performances of published methods indicate remaining challenges in SLiM discovery. We have developed HH-MOTiF, a web-based method for SLiM discovery in sets of mainly unrelated proteins. HH-MOTiF makes use of evolutionary information by creating Hidden Markov Models (HMMs) for each input sequence and its closely related orthologs. HMMs are compared against each other to retrieve short stretches of homology that represent potential SLiMs. These are transformed to hierarchical structures, which we refer to as motif trees, for further processing and evaluation. Our approach allows us to identify degenerate SLiMs, while still maintaining a reasonably high precision. When considering a balanced measure for recall and precision, HH-MOTiF performs better on test data compared to other SLiM discovery methods. HH-MOTiF is freely available as a web-server at http://hh-motif.biochem.mpg.de.

Live from the cerebellum, the center for sensory-motor integration

The cerebellum

In order to successfully survive in a changing environment, animals must be able to combine sensory inputs with information about their own movement. Complex motor behaviors, like walking or riding a bike, would be difficult to perform without feedback signals such as the sense of the feet touching the ground or the perception of movement with respect to the world. Scientists from the Max Planck Institute of Neurobiology in Martinsried use zebrafish as a simple vertebrate model to study how different kinds of sensory and motor information map onto the cerebellum. Their recent study shows that scientists need to rethink about how this large and important part of the brain of all vertebrates, including humans, works.

In a recent study published in the journal Current Biology, Laura Knogler and her colleagues from the Portugues group at the Max Planck Institute of Neurobiology used small translucent larval zebrafish to record cerebellar activity. For the first time, scientists were thus able to record from all the granule cells in the cerebellum of an awake, behaving vertebrate. As Laura explained: “This is possible because the brains of these fish are small, less than 1 mm cubed, and because we can express fluorescent proteins in their brains that light up when neurons are active.” When asked to summarize the main findings, Laura continues: “We were surprised to see that a large fraction of the cerebellar granule cells, nearly 50%, were active when we presented simple sensory stimuli such as light flashes or moving scenes. Some neurons were only active when the fish swam.”

Researchers unravel the social network of immune cells

the social network of immune cells

Facebook, Instagram, Twitter – nowadays, good social networking and communication is more important than ever. The immune system also resembles a large social network, as shown by Felix Meissner and his team in the Experimental System Immunology Research Group at the Max Planck Institute of Biochemistry in Martinsried. With the help of proteomics they deciphered the messages exchanged between immune cells responsible for protecting us against diseases. In doing so, they have discovered complex cellular communication structures and previously unknown connections between various cell types. Their research findings were published in the journal Nature Immunology.

Social networks such as Facebook now connect people around the globe, for the exchange of countless messages and pieces of information every day. Some people prefer to use social networks passively, only reading messages, while others have a strong need to communicate with others and tend to send out a large volume of information. The cells of our immune system work in a similar manner. When cells wish to communicate with each other, they emit messengers, unique signal molecules, which are detected by other cells via cell surface receptors. These messengers disseminate information throughout the body to control immune reactions against pathogens. Some cell types are more communicative than others. “Innate immune cells such as macrophages are real chatterboxes,” Meissner says.