Biology subjects

Koch, B.

Publications and source records attributed to Koch, B..

6 recordsLinked to original sources

bioRxiv2018

The anaphase-promoting complex regulates the degradation of the inner nuclear membrane protein Mps3 in budding yeast

The nucleus is enclosed by the inner nuclear membrane (INM) and the outer nuclear membrane (ONM). While the ONM is continuous with the endoplasmic reticulum (ER), the INM is independent and separates the nucleoplasm from the ER lumen. To maintain INM homeostasis, proteins mislocalized to the INM are degraded by the ER-associated protein degradation (ERAD) pathway. However, the mechanism for turnover of resident INM proteins is less clear. Here we show that the anaphase-promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase, regulates the degradation of Mps3, a conserved integral protein of the INM. Turnover of Mps3 requires the ubiquitin-conjugating enzymes Ubc7 and Ubc6, but not the three known ERAD ubiquitin ligases, Doa10, Hrd1, and the Asi1-Asi3 complex. Using a genetic approach, we have found that Cdh1, a coactivator of APC/C, modulates Mps3 stability. APC/C controls Mps3 degradation through Mps3s N-terminus, which resides in the nucleoplasm and possesses two putative APC/C-dependent destruction motifs. Accumulation of Mps3 at the INM impairs nuclear morphological changes and cell division. Our findings therefore reveal an unexpected mechanism of APC/C-mediated protein quality control at the INM that coordinates nuclear morphogenesis and cell-cycle progression.

cell biology↗

bioRxiv2018

A quantitative map of human Condensins provides new insights into mitotic chromosome architecture

The two Condensin complexes in human cells are essential for mitotic chromosome structure. We used homozygous genome editing to fluorescently tag Condensin I and II subunits and mapped their absolute abundance, spacing and dynamic localization during mitosis by fluorescence correlation spectroscopy-calibrated live cell imaging and super-resolution microscopy. While [~]35,000 Condensin II complexes are stably bound to chromosomes throughout mitosis, [~]195,000 Condensin I complexes dynamically bind in two steps, in prometaphase and early anaphase. The two Condensins rarely co-localize at the chromatid axis, where Condensin II is centrally confined but Condensin I reaches [~]50% of the chromatid diameter from its center. Based on our comprehensive quantitative data, we propose a three-step hierarchical loop model of mitotic chromosome compaction: Condensin II initially fixes loops of a maximum size of [~]450 kb at the chromatid axis whose size is then reduced by Condensin I binding to [~]90 kb in prometaphase and [~]70 kb in anaphase, achieving maximum chromosome compaction upon sister chromatid segregation.

cell biology↗

bioRxiv2017

An experimental and computational framework to build a dynamic protein atlas of human cell division

Essential biological functions, such as mitosis, require tight coordination of hundreds of proteins in space and time. Localization, timing of interactions and changes in cellular structure are all crucial to ensure correct assembly, function and regulation of protein complexes1-4. Live cell imaging can reveal protein distributions and dynamics but experimental and theoretical challenges prevented its use to produce quantitative data and a model of mitosis that comprehensively integrates information and enables analysis of the dynamic interactions between the molecular parts of the mitotic machinery within changing cellular boundaries.\n\nTo address this, we generated a 4D image data-driven, canonical model of the morphological changes during mitotic progression of human cells. We used this model to integrate dynamic 3D concentration data of many fluorescently knocked-in mitotic proteins, imaged by fluorescence correlation spectroscopy-calibrated microscopy5. The approach taken here in the context of the MitoSys consortium to generate a dynamic protein atlas of human cell division is generic. It can be applied to systematically map and mine dynamic protein localization networks that drive cell division in different cell types and can be conceptually transferred to other cellular functions.

systems biology↗

bioRxiv2017

Generation and validation of homozygous fluorescent knock-in cells using genome editing

Gene tagging with fluorescent proteins is essential to investigate the dynamic properties of cellular proteins. CRISPR/Cas9 technology is a powerful tool for inserting fluorescent markers into all alleles of the gene of interest (GOI) and permits functionality and physiological expression of the fusion protein. It is essential to evaluate such genome-edited cell lines carefully in order to preclude off-target effects caused by either (i) incorrect insertion of the fluorescent protein, (ii) perturbation of the fusion protein by the fluorescent proteins or (iii) non-specific genomic DNA damage by CRISPR/Cas9. In this protocol1, we provide a step-by-step description of our systematic pipeline to generate and validate homozygous fluorescent knock-in cell lines.\n\nWe have used the paired Cas9D10A nickase approach to efficiently insert tags into specific genomic loci via homology-directed repair with minimal off-target effects. It is time- and cost-consuming to perform whole genome sequencing of each cell clone. Therefore, we have developed an efficient validation pipeline of the generated cell lines consisting of junction PCR, Southern Blot analysis, Sanger sequencing, microscopy, Western blot analysis and live cell imaging for cell cycle dynamics. This protocol takes between 6-9 weeks. Using this protocol, up to 70% of the targeted genes can be tagged homozygously with fluorescent proteins and result in physiological levels and phenotypically functional expression of the fusion proteins.\n\nEditorial SummaryThis protocol provides a detailed workflow describing how to insert fluorescent markers into all alleles of a gene of interest using CRISPR/Cas 9 technology and how to generate and validate homozygous fluorescent knock-in cell lines.

molecular biology↗

bioRxiv2017

Quantitative mapping of fluorescently tagged cellular proteins using FCS-calibrated four dimensional imaging

EDITORIAL SUMMARYThis protocol describes how to estimate and spatially resolve the concentration and copy number of fluorescently tagged proteins in live cells using fluorescence imaging and fluorescence correlation spectroscopy (FCS).\n\nTWEETDetermining protein concentrations and copy numbers in live cells using fluorescence correlation spectroscopy (FCS)-calibrated imaging.\n\nCOVER TEASER Map protein concentrations with FCS-calibrated imagingUp to four primary research articles where the protocol has been used and/or developed:\n\nO_LIWalther, N., Hossain, M. J., Politi, A. Z., Koch, B., Kueblbeck, M., Oedegaard-Fougner, O., Lampe, M. and J. Ellenberg (2018). A quantitative map of human Condensins provides new insights into mitotic chromosome architecture. bioRxiv, 237834. https://doi.org/10.1101/2378342.\nC_LIO_LICai, Y., Hossain, M. J., Heriche, J.-K., Politi, A. Z., Walther, N., Koch, B., Wachsmuth, M., Nijmeijer, B., Kueblbeck, M., Martinic, M., Ladurner, R., Peters, J.M. and J. Ellenberg (2017). An experimental and computational framework to build a dynamic protein atlas of human cell division. bioRxiv, 227751 https://doi.org/10.1101/227751\nC_LIO_LIGermier, T., Kocanova, S., Walther, N., Bancaud, A., Shaban, H.A., Sellou, H., Politi, A.Z., Ellenberg, J., Gallardo, F. and K. Bystricky (2017). Real-Time Imaging of a Single Gene Reveals Transcription-Initiated Local Confinement. Biophysical Journal, 113(7), 1383-1394, https://doi.org/10.1016/j.bpj.2017.08.014.\nC_LIO_LICuylen, S., Blaukopf, C., Politi, A. Z., Muller-Reichert, T., Neumann, B., Poser, I., Ellenberg, J., Hyman, A.A., and D.W. Gerlich (2016). Ki-67 acts as a biological surfactant to disperse mitotic chromosomes. Nature, 535(7611), 308-312. http://doi.org/10.1038/nature18610.\nC_LI\n\nAbstractThe ability to tag a protein at its endogenous locus with a fluorescent protein (FP) enables the quantitative understanding of protein dynamics at the physiological level. Genome editing technology has now made this powerful approach routinely applicable to mammalian cells and many other model systems, opening up the possibility to systematically and quantitatively map the cellular proteome in four dimensions. 3D time-lapse confocal microscopy (4D imaging) is an essential tool to investigate spatial and temporal protein dynamics, however it lacks the required quantitative power to make absolute and comparable measurements required for systems analysis. Fluorescence correlation spectroscopy (FCS) on the other hand provides quantitative proteomic and biophysical parameters such as protein concentration, hydrodynamic radius and oligomerization but lacks the ability for high-throughput application in 4D spatial and temporal imaging. Here, we present an automated experimental and computational workflow that integrates both methods and delivers quantitative 4D imaging data in high-throughput. These data is processed to yield a calibration curve relating the fluorescence intensities of image voxels to absolute protein abundance. The calibration curve allows the conversion of the arbitrary fluorescence intensities to protein amounts for all voxels of 4D imaging stacks. With our workflow the users can acquire and analyze hundreds of FCS-calibrated image series to map their proteins of interest in four dimensions. Compared to other protocols, the current protocol does not require additional calibration standards and provides an automated acquisition pipeline for FCS and imaging data. The protocol can be completed in 1 day.

molecular biology↗

bioRxiv2017

CTCF, WAPL and PDS5 proteins control the formation of TADs and loops by cohesin

Mammalian genomes are organized into compartments, topologically-associating domains (TADs) and loops to facilitate gene regulation and other chromosomal functions. Compartments are formed by nucleosomal interactions, but how TADs and loops are generated is unknown. It has been proposed that cohesin forms these structures by extruding loops until it encounters CTCF, but direct evidence for this hypothesis is missing. Here we show that cohesin suppresses compartments but is essential for TADs and loops, that CTCF defines their boundaries, and that WAPL and its PDS5 binding partners control the length of chromatin loops. In the absence of WAPL and PDS5 proteins, cohesin passes CTCF sites with increased frequency, forms extended chromatin loops, accumulates in axial chromosomal positions (vermicelli) and condenses chromosomes to an extent normally only seen in mitosis. These results show that cohesin has an essential genome-wide function in mediating long-range chromatin interactions and support the hypothesis that cohesin creates these by loop extrusion, until it is delayed by CTCF in a manner dependent on PDS5 proteins, or until it is released from DNA by WAPL.

genomics↗