Publications by Aleksandr Benke

Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation

Suliana Manley, Beat Fierz, David Michael Suter, Christian Sieben, Aleksandr Benke, Andrea Callegari

Transcription factors (TFs) regulate gene expression in both prokaryotes and eukaryotes by recognizing and binding to specific DNA promoter sequences. In higher eukaryotes, it remains unclear how the duration of TF binding to DNA relates to downstream tran ...

2019

Nanoscale Spatial Organization of Chromatin in its Cellular Context, from Telomeres to Hox

Denis Duboule, Joachim Lingner, Suliana Manley, Kyle Michael Douglass, Aleksandr Benke, Verena Pfeiffer, Pierre Raymond Fabre, Aleksandra Vancevska

Cell Press2016

In Situ Characterization of Bak Clusters Responsible for Cell Death Using Single Molecule Localization Microscopy

Suliana Manley, Aleksandr Benke

Apoptosis plays a pivotal role in development and tissue homeostasis in multicellular organisms. Clustering of Bak proteins on the mitochondrial outer membrane is responsible for the induction of apoptosis by evoking a release of pro-apoptotic proteins fro ...

Nature Research2016

A role for mitotic bookmarking of SOX2 in pluripotency and differentiation

Suliana Manley, Aleksandr Benke, David Michael Suter, Marion Leleu, Andrea Callegari, Cédric Deluz, Torgil Elias Friman, Mahé Cécile Raccaud, Daniel Strebinger

Mitotic bookmarking transcription factors remain bound to chromosomes during mitosis and were proposed to regulate phenotypic maintenance of stem and progenitor cells at the mitosis-to-G1 (M-G1) transition. However, mitotic bookmarking remains largely unex ...

Cold Spring Harbor Laboratory2016

Influence of DNA Binding Dyes on Bare DNA Structure Studied with Atomic Force Microscopy

Giovanni Dietler, Aleksandre Japaridze, Aleksandr Benke, Sylvain Renevey

Fluorescent dyes are widely used for staining and visualization of DNA in optical microscopy based methods. Even though for some dyes the mechanism of binding is known, how this binding affects DNA remains poorly understood. Here we present a novel experim ...

American Chemical Society2015

Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states

Denis Duboule, Suliana Manley, Aleksandr Benke, Pierre Raymond Fabre

Chromatin condensation plays an important role in the regulation of gene expression. Recently, it was shown that the transcriptional activation of Hoxd genes during vertebrate digit development involves modifications in 3D interactions within and around th ...

2015

Visualizing the HoxD Gene Cluster at the Nanoscale Level

Denis Duboule, Suliana Manley, Aleksandr Benke, Pierre Raymond Fabre

Transcription of HoxD cluster genes in limbs is coordinated by two topologically associating domains (TADs), neighboring the cluster and containing various enhancers. Here, we use a combination of microscopy approaches and chromosome conformation capture t ...

2015

Chromatin organization, transcription factor dynamics and gene expression in higher eukaryotes with superresolution imaging and single molecule tracking

Aleksandr Benke

Gene expression is dynamic and heterogeneous across all cell types. It serves several fundamental functions such as adaptation for changing environment and developing tissue specific phenotype and functionality during development and in adult organism. Con ...

EPFL2015

Reduced Dyes Enhance Single-Molecule Localization Density for Live Superresolution Imaging

Suliana Manley, Luc Reymond, Aleksandr Benke, Grazvydas Lukinavicius, Lina Carlini

Cell-permeable rhodamine dyes are reductively quenched by NaBH4 into a non-fluorescent leuco-rhodamine form. Quenching is reversible, and their fluorescence is recovered when the dyes are oxidized. In living cells, oxidation occurs spontaneously, and can r ...

Wiley-V C H Verlag Gmbh2014

Multicolor Single Molecule Tracking of Stochastically Active Synthetic Dyes

Suliana Manley, Aleksandr Benke, Julia Gunzenhäuser

Single particle tracking can reveal dynamic information at the scale of single molecules in living cells but thus far has been limited either in the range of potential protein targets or in the quality and number of tracks attainable. We demonstrate a new ...

American Chemical Society2012