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Michael Heide, Wieland B. Huttner, Felipe Mora-Bermúdez
Brain organoids as models to study human neocortex development and evolution.
Curr Opin Cell Biol, 55 8-16 (2018)
PubMed Source   

Since their recent development, organoids that emulate human brain tissue have allowed in vitro neural development studies to go beyond the limits of monolayer culture systems, such as neural rosettes. We present here a review of organoid studies that focuses on cortical wall development, starting with a technical comparison between pre-patterning and self-patterning brain organoid protocols. We then follow neocortex development in space and time and list those aspects where organoids have succeeded in emulating in vivo development, as well as those aspects that continue to be pending tasks. Finally, we present a summary of medical and evolutionary insight made possible by organoid technology.
@article{Heide7174,
author={Michael Heide, Wieland B. Huttner, Felipe Mora-Bermúdez},
title={Brain organoids as models to study human neocortex development and evolution.},
journal={Current opinion in cell biology},
volume={55},
pages={8--16},
year=2018
}

Jana Královicová, Ivana Ševcíková, Eva Stejskalová, Mina Obuca, Michael Hiller, David R. Stanek, Igor Vorechovský
PUF60-activated exons uncover altered 3' splice-site selection by germline missense mutations in a single RRM.
Nucleic Acids Res, 46(12) 6166-6187 (2018)
PubMed Source   

PUF60 is a splicing factor that binds uridine (U)-rich tracts and facilitates association of the U2 small nuclear ribonucleoprotein with primary transcripts. PUF60 deficiency (PD) causes a developmental delay coupled with intellectual disability and spinal, cardiac, ocular and renal defects, but PD pathogenesis is not understood. Using RNA-Seq, we identify human PUF60-regulated exons and show that PUF60 preferentially acts as their activator. PUF60-activated internal exons are enriched for Us upstream of their 3' splice sites (3'ss), are preceded by longer AG dinucleotide exclusion zones and more distant branch sites, with a higher probability of unpaired interactions across a typical branch site location as compared to control exons. In contrast, PUF60-repressed exons show U-depletion with lower estimates of RNA single-strandedness. We also describe PUF60-regulated, alternatively spliced isoforms encoding other U-bound splicing factors, including PUF60 partners, suggesting that they are co-regulated in the cell, and identify PUF60-regulated exons derived from transposed elements. PD-associated amino-acid substitutions, even within a single RNA recognition motif (RRM), altered selection of competing 3'ss and branch points of a PUF60-dependent exon and the 3'ss choice was also influenced by alternative splicing of PUF60. Finally, we propose that differential distribution of RNA processing steps detected in cells lacking PUF60 and the PUF60-paralog RBM39 is due to the RBM39 RS domain interactions. Together, these results provide new insights into regulation of exon usage by the 3'ss organization and reveal that germline mutation heterogeneity in RRMs can enhance phenotypic variability at the level of splice-site and branch-site selection.
@article{Královicová7139,
author={Jana Královicová, Ivana Ševcíková, Eva Stejskalová, Mina Obuca, Michael Hiller, David R. Stanek, Igor Vorechovský},
title={PUF60-activated exons uncover altered 3' splice-site selection by germline missense mutations in a single RRM.},
journal={Nucleic acids research},
volume={46},
issue ={12},
pages={6166--6187},
year=2018
}

Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching.
Nucleic Acids Res, 46(W1) 25-29 (2018)
PubMed Source   

The Freiburg RNA tools webserver is a well established online resource for RNA-focused research. It provides a unified user interface and comprehensive result visualization for efficient command line tools. The webserver includes RNA-RNA interaction prediction (IntaRNA, CopraRNA, metaMIR), sRNA homology search (GLASSgo), sequence-structure alignments (LocARNA, MARNA, CARNA, ExpaRNA), CRISPR repeat classification (CRISPRmap), sequence design (antaRNA, INFO-RNA, SECISDesign), structure aberration evaluation of point mutations (RaSE), and RNA/protein-family models visualization (CMV), and other methods. Open education resources offer interactive visualizations of RNA structure and RNA-RNA interaction prediction as well as basic and advanced sequence alignment algorithms. The services are freely available at http://rna.informatik.uni-freiburg.de.
@article{Raden7140,
author={Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, Rolf Backofen},
title={Freiburg RNA tools: a central online resource for RNA-focused research and teaching.},
journal={Nucleic acids research},
volume={46},
issue ={W1},
pages={25--29},
year=2018
}

Marisa Karow, J Gray Camp, Sven Falk, Tobias Gerber, Abhijeet Pataskar, Malgorzata Gac-Santel, Jorge Kageyama, Agnieska Brazovskaja, Angela Garding, Wenqiang Fan, Therese Riedemann, Antonella Casamassa, Andrej Smiyakin, Christian Schichor, Magdalena Götz, Vijay K Tiwari, Barbara Treutlein, Benedikt Berninger
Direct pericyte-to-neuron reprogramming via unfolding of a neural stem cell-like program.
Nat Neurosci, 21(7) 932-940 (2018)
PubMed Source   

Ectopic expression of defined transcription factors can force direct cell-fate conversion from one lineage to another in the absence of cell division. Several transcription factor cocktails have enabled successful reprogramming of various somatic cell types into induced neurons (iNs) of distinct neurotransmitter phenotype. However, the nature of the intermediate states that drive the reprogramming trajectory toward distinct iN types is largely unknown. Here we show that successful direct reprogramming of adult human brain pericytes into functional iNs by Ascl1 and Sox2 encompasses transient activation of a neural stem cell-like gene expression program that precedes bifurcation into distinct neuronal lineages. During this transient state, key signaling components relevant for neural induction and neural stem cell maintenance are regulated by and functionally contribute to iN reprogramming and maturation. Thus, Ascl1- and Sox2-mediated reprogramming into a broad spectrum of iN types involves the unfolding of a developmental program via neural stem cell-like intermediates.
@article{Karow7157,
author={Marisa Karow, J Gray Camp, Sven Falk, Tobias Gerber, Abhijeet Pataskar, Malgorzata Gac-Santel, Jorge Kageyama, Agnieska Brazovskaja, Angela Garding, Wenqiang Fan, Therese Riedemann, Antonella Casamassa, Andrej Smiyakin, Christian Schichor, Magdalena Götz, Vijay K Tiwari, Barbara Treutlein, Benedikt Berninger},
title={Direct pericyte-to-neuron reprogramming via unfolding of a neural stem cell-like program.},
journal={Nature neuroscience},
volume={21},
issue ={7},
pages={932--940},
year=2018
}

Jie Wang, Jeong-Mo Choi, Alex S Holehouse, Hyun O. Lee, Xiaojie Zhang, Marcus Jahnel, Shovamayee Maharana, Regis P. Lemaitre, Andrei I. Pozniakovsky, David N. Drechsel, Ina Poser, Rohit V Pappu, Simon Alberti, Anthony Hyman
A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins.
Cell, 174 Art. No. doi: 10.1016/j.cell.2018.06.006 (2018)
PubMed Source   

Proteins such as FUS phase separate to form liquid-like condensates that can harden into less dynamic structures. However, how these properties emerge from the collective interactions of many amino acids remains largely unknown. Here, we use extensive mutagenesis to identify a sequence-encoded molecular grammar underlying the driving forces of phase separation of proteins in the FUS family and test aspects of this grammar in cells. Phase separation is primarily governed by multivalent interactions among tyrosine residues from prion-like domains and arginine residues from RNA-binding domains, which are modulated by negatively charged residues. Glycine residues enhance the fluidity, whereas glutamine and serine residues promote hardening. We develop a model to show that the measured saturation concentrations of phase separation are inversely proportional to the product of the numbers of arginine and tyrosine residues. These results suggest it is possible to predict phase-separation properties based on amino acid sequences.
@article{Wang7156,
author={Jie Wang, Jeong-Mo Choi, Alex S Holehouse, Hyun O. Lee, Xiaojie Zhang, Marcus Jahnel, Shovamayee Maharana, Regis P. Lemaitre, Andrei I. Pozniakovsky, David N. Drechsel, Ina Poser, Rohit V Pappu, Simon Alberti, Anthony Hyman},
title={A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins.},
journal={Cell},
volume={174},
pages={1--1},
year=2018
}

Rory M Power, Jan Huisken
Adaptable, illumination patterning light sheet microscopy.
Sci Rep, 8(1) Art. No. 9615 (2018)
PubMed Source   

Minimally-invasive optical imaging requires that light is delivered efficiently to limit the detrimental impact of photodamage on delicate biological systems. Light sheet microscopy represents the exemplar in tissue specific optical imaging of small and mesoscopic samples alike. However, further gains towards gentler imaging require a more selective imaging strategy to limit exposure to multiple yet discrete tissues without overexposing the sample, particularly where the information content is sparse or particularly optically sensitive tissues are present. The development of sample-adaptive imaging techniques is crucial in pursuit of the next generation of smart, autonomous microscopes. Herein, we report a microscope capable of performing 4D (x, y, z, t) light patterning to selectively illuminate multiple, rapidly reconfigurable regions of interest while maintaining the rapid imaging speed and high contrast associated with light sheet microscopy. We illustrate this utility in living zebrafish larvae and phantom samples.
@article{Power7166,
author={Rory M Power, Jan Huisken},
title={Adaptable, illumination patterning light sheet microscopy.},
journal={Scientific reports},
volume={8},
issue ={1},
pages={null--null},
year=2018
}

Simon Alberti, Shambaditya Saha, Jeffrey Woodruff, Titus Franzmann, Jie Wang, Anthony Hyman
A User's Guide for Phase Separation Assays with Purified Proteins.
J Mol Biol, Art. No. doi: 10.1016/j.jmb.2018.06.038 (2018)
PubMed Source   

The formation of membrane-less organelles and compartments by protein phase separation is an important way in which cells organize their cytoplasm and nucleoplasm. In vitro phase separation assays with purified proteins have become the standard way to investigate proteins that form membrane-less compartments. By now, various proteins have been purified and tested for their ability to phase separate and form liquid condensates in vitro. However, phase-separating proteins are often aggregation-prone and difficult to purify and handle. As a consequence, the results from phase separation assays often differ between labs and are not easily reproduced. Thus, there is an urgent need for high-quality proteins, standardized procedures, and generally agreed-upon practices for protein purification and conducting phase separation assays. This paper provides protocols for protein purification and guides the user through the practicalities of in vitro protein phase separation assays, including best-practice approaches and pitfalls to avoid. We believe that this compendium of protocols and practices will provide a useful resource for scientists studying the phase behavior of proteins.
@article{Alberti7168,
author={Simon Alberti, Shambaditya Saha, Jeffrey Woodruff, Titus Franzmann, Jie Wang, Anthony Hyman},
title={A User's Guide for Phase Separation Assays with Purified Proteins.},
journal={Journal of molecular biology},
volume={},
pages={1--1},
year=2018
}

Miroslav P Ivanov, Rene Ladurner, Ina Poser, Rebecca Beveridge, Evelyn Rampler, Otto Hudecz, Maria Novatchkova, Jean-Karim Hériché, Gordana Wutz, Petra van der Lelij, Emanuel Kreidl, James R A Hutchins, Heinz Axelsson-Ekker, Jan Ellenberg, Anthony Hyman, Karl Mechtler, Jan-Michael Peters
The replicative helicase MCM recruits cohesin acetyltransferase ESCO2 to mediate centromeric sister chromatid cohesion.
EMBO J, Art. No. e97150 (2018)
PubMed Source   

Chromosome segregation depends on sister chromatid cohesion which is established by cohesin during DNA replication. Cohesive cohesin complexes become acetylated to prevent their precocious release by WAPL before cells have reached mitosis. To obtain insight into how DNA replication, cohesion establishment and cohesin acetylation are coordinated, we analysed the interaction partners of 55 human proteins implicated in these processes by mass spectrometry. This proteomic screen revealed that on chromatin the cohesin acetyltransferase ESCO2 associates with the MCM2-7 subcomplex of the replicative Cdc45-MCM-GINS helicase. The analysis of ESCO2 mutants defective in MCM binding indicates that these interactions are required for proper recruitment of ESCO2 to chromatin, cohesin acetylation during DNA replication, and centromeric cohesion. We propose that MCM binding enables ESCO2 to travel with replisomes to acetylate cohesive cohesin complexes in the vicinity of replication forks so that these complexes can be protected from precocious release by WAPL Our results also indicate that ESCO1 and ESCO2 have distinct functions in maintaining cohesion between chromosome arms and centromeres, respectively.
@article{Ivanov7170,
author={Miroslav P Ivanov, Rene Ladurner, Ina Poser, Rebecca Beveridge, Evelyn Rampler, Otto Hudecz, Maria Novatchkova, Jean-Karim Hériché, Gordana Wutz, Petra van der Lelij, Emanuel Kreidl, James R A Hutchins, Heinz Axelsson-Ekker, Jan Ellenberg, Anthony Hyman, Karl Mechtler, Jan-Michael Peters},
title={The replicative helicase MCM recruits cohesin acetyltransferase ESCO2 to mediate centromeric sister chromatid cohesion.},
journal={The EMBO journal},
volume={},
pages={null--null},
year=2018
}

Titus Franzmann, Simon Alberti
Prion-like low-complexity sequences: Key regulators of protein solubility and phase behavior.
J Biol Chem, Art. No. doi: 10.1074/jbc.TM118.001190 (2018)
PubMed Source   

Many proteins, such as RNA-binding proteins, have complex folding landscapes. How cells maintain the solubility and folding state of such proteins, particularly under stress conditions, is largely unknown. Here, we argue that prion-like low-complexity regions (LCRs) are key regulators of protein solubility and folding. We discuss emerging evidence that prion-like LCRs are not, as commonly thought, autonomous aggregation modules that adopt amyloid-like conformations, but protein-specific sequences with chaperone-like functions. On the basis of recent findings, we propose that prion-like LCRs have evolved to regulate protein phase behavior and to protect proteins against proteotoxic damage.
@article{Franzmann7169,
author={Titus Franzmann, Simon Alberti},
title={Prion-like low-complexity sequences: Key regulators of protein solubility and phase behavior.},
journal={The Journal of biological chemistry},
volume={},
pages={1--1},
year=2018
}

Sonja Kroschwald, Matthias Munder, Shovamayee Maharana, Titus Franzmann, Doris Richter, Martine Ruer, Anthony Hyman, Simon Alberti
Different Material States of Pub1 Condensates Define Distinct Modes of Stress Adaptation and Recovery.
Cell Rep, 23(11) 3327-3339 (2018)
PubMed Source   

How cells adapt to varying environmental conditions is largely unknown. Here, we show that, in budding yeast, the RNA-binding and stress granule protein Pub1 has an intrinsic property to form condensates upon starvation or heat stress and that condensate formation is associated with cell-cycle arrest. Release from arrest coincides with condensate dissolution, which takes minutes (starvation) or hours (heat shock). In vitro reconstitution reveals that the different dissolution rates of starvation- and heat-induced condensates are due to their different material properties: starvation-induced Pub1 condensates form by liquid-liquid demixing and subsequently convert into reversible gel-like particles; heat-induced condensates are more solid-like and require chaperones for disaggregation. Our data suggest that different physiological stresses, as well as stress durations and intensities, induce condensates with distinct physical properties and thereby define different modes of stress adaptation and rates of recovery.
@article{Kroschwald7162,
author={Sonja Kroschwald, Matthias Munder, Shovamayee Maharana, Titus Franzmann, Doris Richter, Martine Ruer, Anthony Hyman, Simon Alberti},
title={Different Material States of Pub1 Condensates Define Distinct Modes of Stress Adaptation and Recovery.},
journal={Cell reports},
volume={23},
issue ={11},
pages={3327--3339},
year=2018
}