Results 31 to 40 of about 408,119 (206)

NicE-seq: high resolution open chromatin profiling

Genome Biology, 2017
Open chromatin profiling integrates information across diverse regulatory elements to reveal the transcriptionally active genome. Tn5 transposase and DNase I sequencing-based methods prefer native or high cell numbers. Here, we describe NicE-seq (nicking
V. K. Chaithanya Ponnaluri, Guoqiang Zhang, Pierre-Olivier Estève, George Spracklin, Stephanie Sian, Shuang-yong Xu, Touati Benoukraf, Sriharsa Pradhan   +7 more
doaj   +1 more source

HiCoP, a simple and robust method for detecting interactions of regulatory regions

Epigenetics & Chromatin, 2020
Background Chromatin physical interactions provide essential information for understanding the regulation of cis-elements like enhancers, promoters, and insulators in cell development and differentiation. The Hi-C assay is a technique detecting chromatin
Yan Zhang, Zhaoqiang Li, Shasha Bian, Hao Zhao, Delong Feng, Yanhong Chen, Yuhe Hou, Qifa Liu, Bingtao Hao   +8 more
doaj   +1 more source

Multi-omics integration identifies NK cell-mediated cytotoxicity as a therapeutic target in systemic lupus erythematosus

Frontiers in Immunology
BackgroundSystemic lupus erythematosus (SLE) is an autoimmune condition that impacts various organs. Given the intricate clinical progression of SLE, it is imperative to explore novel avenues for precise diagnosis and treatment.MethodsPeripheral blood ...
Jingjing Zhang, Ling Ma, Hanyin Deng, Wenqian Yi, Alim Tohtihan, Xiaojun Tang, Xiudi Wu, Xuebing Feng   +7 more
doaj   +1 more source

Subclone-specific microenvironmental impact and drug response in refractory multiple myeloma revealed by single‐cell transcriptomics

Nature Communications, 2021
Virtually all patients with multiple myeloma become unresponsive to treatment over time. Relapsed/refractory multiple myeloma (RRMM) is accompanied by the clonal evolution of myeloma cells with heterogeneous genomic aberrations and profound changes of ...
Stephan M. Tirier, Jan-Philipp Mallm, Simon Steiger, Alexandra M. Poos, Mohamed H. S. Awwad, Nicola Giesen, Nicola Casiraghi, Hana Susak, Katharina Bauer, Anja Baumann, Lukas John, Anja Seckinger, Dirk Hose, Carsten Müller-Tidow, Hartmut Goldschmidt, Oliver Stegle, Michael Hundemer, Niels Weinhold, Marc S. Raab, Karsten Rippe   +19 more
doaj   +1 more source

Tethering of CHROMATOR and dCTCF proteins results in decompaction of condensed bands in the Drosophila melanogaster polytene chromosomes but does not affect their transcription and replication timing. [PDF]

PLoS ONE, 2018
Instulator proteins are central to domain organization and gene regulation in the genome. We used ectopic tethering of CHROMATOR (CHRIZ/CHRO) and dCTCF to pre-defined regions of the genome to dissect the influence of these proteins on local chromatin ...
Galina V Pokholkova, Sergei A Demakov, Oleg V Andreenkov, Natalia G Andreenkova, Elena I Volkova, Elena S Belyaeva, Igor F Zhimulev   +6 more
doaj   +1 more source

Comparison of spatial transcriptomics technologies using tumor cryosections

Genome Biology
Background Spatial transcriptomics technologies are revolutionizing our understanding of intra-tumor heterogeneity and the tumor microenvironment by revealing single-cell molecular profiles within their spatial tissue context.
Anne Rademacher, Alik Huseynov, Michele Bortolomeazzi, Sina Jasmin Wille, Sabrina Schumacher, Pooja Sant, Denise Keitel, Konstantin Okonechnikov, David R. Ghasemi, Kristian W. Pajtler, Jan-Philipp Mallm, Karsten Rippe   +11 more
doaj   +1 more source

Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) analysis uncovers broad changes in chromatin structure resulting from hexavalent chromium exposure. [PDF]

PLoS ONE, 2014
The ability of chromatin to switch back and forth from open euchromatin to closed heterochromatin is vital for transcriptional regulation and genomic stability, but its dynamic structure is subject to disruption by exposure to environmental agents such ...
Jerald L Ovesen, Yunxia Fan, Xiang Zhang, Jing Chen, Mario Medvedovic, Ying Xia, Alvaro Puga   +6 more
doaj   +1 more source

Gut microbiome and aging—A dynamic interplay of microbes, metabolites, and the immune system

FEBS Letters, EarlyView.
Age‐dependent shifts in microbial communities engender shifts in microbial metabolite profiles. These in turn drive shifts in barrier surface permeability of the gut and brain and induce immune activation. When paired with preexisting age‐related chronic inflammation this increases the risk of neuroinflammation and neurodegenerative diseases.
Aaron Mehl, Eran Blacher
wiley   +1 more source

Modelling stem cell differentiation related processes—A practical overview for biologists

FEBS Letters, EarlyView.
Stem cell differentiation is complex and difficult to control experimentally. This review introduces suitable computational modelling approaches that can support stem cell research, from mechanistic ODE and abstract models to multiscale and deep learning methods.
Ricco Zeegelaar, Xinqi Yan, Lucas F. Jansen Klomp, Stefano Schivo, Janine N. Post   +4 more
wiley   +1 more source

The NuRD complex cooperates with SALL4 to orchestrate reprogramming

Nature Communications, 2023
Cell fate decision involves rewiring of the genome, but remains poorly understood at the chromatin level. Here, we report that chromatin remodeling complex NuRD participates in closing open chromatin in the early phase of somatic reprogramming.
Bo Wang, Chen Li, Jin Ming, Linlin Wu, Shicai Fang, Yi Huang, Lihui Lin, He Liu, Junqi Kuang, Chengchen Zhao, Xingnan Huang, Huijian Feng, Jing Guo, Xuejie Yang, Liman Guo, Xiaofei Zhang, Jiekai Chen, Jing Liu, Ping Zhu, Duanqing Pei   +19 more
doaj   +1 more source