Examplepictures of DNA-Structures
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June 01 - June 30

4 entries found

CANCELLED: ..
Start date: June 03
10:00 am 11:30 am

Spatial Gen..
Start date: June 04
05:00 pm 06:00 pm

Description: 

Link to the conference -  Meeting ID: 961 6566 0841, Password: 0X=V&s

Abstract:

Imaging the transcriptome in situ with high accuracy has been a major challenge in single cell biology, particularly hindered by the limits of optical resolution and the density of transcripts in single cells. We developed seqFISH+, that can image the mRNAs for 10,000 genes in single cells with high accuracy and sub-diffraction-limit resolution, in the mouse brain cortex, subventricular zone, and the olfactory bulb, using a standard confocal microscope. The transcriptome level profiling of seqFISH+ allows unbiased identification of cell classes and their spatial organization in tissues. In addition, seqFISH+ reveals subcellular mRNA localization patterns in cells and ligand-receptor pairs across neighboring cells. This technology demonstrates the ability to generate spatial cell atlases and to perform discovery-driven studies of biological processes in situ.

5 most important publications:

1. Eng, Chee-Huat Linus, Michael Lawson, Qian Zhu, Ruben Dries, GC Yuan, and Long Cai. “Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+"  Nature. 2019 (7751):235-239. 
2. Sheel Shah, Yodai Takei, Wen Zhou, Eric Lubeck, Jina Yun, Mina Amin, Long Cai.  Dynamics of global transcriptional activity in single stem cells by intron seqFISH.  Cell.  2018.  174, 1-14, July 12, 2018.  Published online June 7, 2018. 
3. Kirsten L. Frieda, James M. Linton, Sahand Hormoz, Joonhyuk Choi, Ke-Huan K. Chow, Zakary S. Singer, Mark W. Budde, Michael B. Elowitz*, Long Cai*. Synthetic recording and in situ readout of lineage information in single cells.  Nature. 2017. 541(7635):107-111. doi: 10.1038/nature20777.
4. Sheel Shah, Eric Lubeck, Wen Zhou, and Long Cai.  In situ transcription profiling of single cells in brain slices reveals spatial organization of the hippocampus.  Neuron. 2016. 92: 342-357. 
5. Lubeck E, Coskun AF, Zhiyentayev T, Ahmad M, Long Cai. Single-cell in situ RNA profiling by sequential hybridization. Nat Methods. 2014 Apr;11(4):360-1. PMCID: PMC4085791

Finding you..
Start date: June 18
01:00 pm 02:00 pm

Description: 

Link to the conference -  Zoom Meeting ID:  972 3820 1359, Password: 647556

Abstract:

Transcription factors only bind a minority of their motifs in large mammalian genomes. One potential explanation is that many motifs are not accessible for binding due to the action of chromatin and DNA methylation. We are using mammalian stem cell models to understand this important interplay between gene regulation, chromatin structure and DNA methylation. We study the dynamics of the epigenome and test regulatory models in cellular models by genetic perturbation and genome editing approaches.

I will discuss our recent efforts in understanding how the sensitivity to DNA methylation can limit transcription factor binding in the context of the cell and how TFs rely on specific chromatin remodelers for access to their binding sites.

5 most important publications:

Darko Barisic*, Michael Stadler*, Mario Iurlaro* and Dirk Schübeler. (2019) Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors, Nature 569(7754):136-140   

Domcke, S.*, Bardet, A. F.*, Ginno, P., Hartl, D., Burger, L., and Schübeler, D. (2015) Competition between DNA methylation and transcription factors determines binding of NRF1. (*joint 1st), Nature, 528 (7583); 575-579.   

Tuncay Baubec, Robert Ivanek, Florian Lienert and Dirk Schübeler. (2013) Methylation-dependent and -independent genomic targeting principles of the MBD protein family, Cell 153, 480–492   

Michael B. Stadler*, Rabih Murr*, Lukas Burger*, Robert Ivanek, Florian Lienert, Anne Schöler, Christiane Wirbelauer, Erik van Nimwegen, Edward J. Oakeley, Dimos Gaidatzis, Vijay K. Tiwari and Dirk Schübeler. (2011) DNA binding factors shape the mouse methylome at distal regulatory regions, Nature, 480, 490-495

Weber, M., Hellmann, I., Stadler, M., Ramos, L., Pääbo, S., Rebhan, M. and Schübeler, D. (2007). Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome, Nature Genetics, 39, 457-466

Everybody is very welcome!

Visualising..
Start date: June 25
01:00 pm 02:00 pm

Description: 

Link to the conference -  Zoom Meeting ID: 873 3947 3679, Password: 245197

Abstract:

DNA repair and mutagenesis define the balance between genome stability and plasticity. To understand the molecular mechanisms and their regulation, our group develops microscopy methods to visualise DNA repair proteins at a single-molecule level and to detect mutations in real-time within living bacterial cells. These tools provide an unprecedented direct view into the molecular processes that guard DNA stability or promote mutagenesis when bacteria experience stress conditions.

5 most important publications:

Lawarée E, Jankevicius G, Cooper C, Ahel I, Uphoff S, Tang C., DNA ADP-Ribosylation Stalls Replication and Is Reversed by RecF-Mediated Homologous Recombination and Nucleotide Excision Repair, Cell Reports 30, 1373-1384 (2020)

Uphoff S, Real-time dynamics of mutagenesis reveal the chronology of DNA repair and damage tolerance responses in single cells, PNAS 115, E6516-E6525 (2018)

Stracy M, Jaciuk M, Uphoff S, Kapanidis AN, Nowotny M, Sherratt DJ, Zawadzki P., Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli, Nature Communications, 7, 12568 (2016)

Uphoff S, Lord ND, Potvin-Trottier L, Okumus B, Sherratt DJ, Paulsson J., Stochastic activation of a DNA damage response causes cell-to-cell mutation rate variation, Science, 27290, 1094-1097 (2016)

Uphoff S, Reyes-Lamothe R, Garza de Leon F, Sherratt DJ, Kapanidis AN, Single-molecule DNA repair in live bacteria, PNAS , 110(20), 8063-8068 (2013)

Everybody is very welcome!

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