Results 51 to 60 of about 94,335 (243)

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

Proteins driving liquid-liquid phase separation and histone modifications cooperatively associate with chromatin looping and transcriptional regulation

Epigenetics & Chromatin
Background Although liquid-liquid phase separation (LLPS) proteins are known to participate in genome organization and transcriptional regulation through the formation of biomolecular condensates, their functional interplay with other regulatory proteins
Xue Ji, Yumin Nie
doaj   +1 more source

SATB1 Mediates Long-Range Chromatin Interactions: A Dual Regulator of Anti-Apoptotic BCL2 and Pro-Apoptotic NOXA Genes. [PDF]

PLoS ONE, 2015
Aberrant expression of special AT-rich binding protein 1 (SATB1), a global genomic organizer, has been associated with various cancers, which raises the question of how higher-order chromatin structure contributes to carcinogenesis.
Yin Yang, Zongdan Wang, Luan Sun, Lipei Shao, Nan Yang, Dawei Yu, Xin Zhang, Xiao Han, Yujie Sun   +8 more
doaj   +1 more source

Tumour–host interactions in Drosophila: mechanisms in the tumour micro‐ and macroenvironment

Molecular Oncology, EarlyView.
This review examines how tumour–host crosstalk takes place at multiple levels of biological organisation, from local cell competition and immune crosstalk to organism‐wide metabolic and physiological collapse. Here, we integrate findings from Drosophila melanogaster studies that reveal conserved mechanisms through which tumours hijack host systems to ...
José Teles‐Reis, Tor Erik Rusten
wiley   +1 more source

Linking Differential Chromatin Loops to Transcriptional Decisions [PDF]

Molecular Cell, 2008
GATA-1 and GATA-2 control proliferation and differentiation of hematopoietic progenitor cells via transcriptional regulation. In this issue of Molecular Cell, Jing et al. (2008) demonstrate that GATA factor exchange on the Kit locus directs a transcriptional switch by reconfiguring chromatin loops.
Apostolou, Effie, Thanos, Dimitris
openaire   +2 more sources

CellLoop: Identifying single-cell 3D genome chromatin loops

Nature Communications
Single-cell 3D genome technologies provide unprecedented views of chromatin architecture, but the extreme sparsity and noise of contact maps limit robust detection of chromatin loops at the individual cell level. Here we present CellLoop, a computational
Yusen Ye, Yiheng Wang, Shiji Liu, Yuxuan Hu, Liang Yu, Weibing Wang, Shihua Zhang, Hebing Chen, Lin Gao   +8 more
doaj   +1 more source

Cohesin and condensin extrude DNA loops in a cell cycle-dependent manner

eLife, 2020
Loop extrusion by structural maintenance of chromosomes (SMC) complexes has been proposed as a mechanism to organize chromatin in interphase and metaphase. However, the requirements for chromatin organization in these cell cycle phases are different, and
Stefan Golfier, Thomas Quail, Hiroshi Kimura, Jan Brugués   +3 more
doaj   +1 more source

Metastasis on pause: How dormant tumor cells stay hidden within the tumor microenvironment and evade immune surveillance

Molecular Oncology, EarlyView.
Dormant cancer cells can hide in distant organs for years, evading treatment and the immune system. This review highlights how signals from the surrounding tissue and immune environment keep these cells inactive or trigger their reawakening. Understanding these mechanisms may help develop therapies to eliminate or control dormant cells and prevent ...
Kanishka Tiwary, Jose Javier Bravo‐Cordero   +1 more
wiley   +1 more source

Alterations in 3D chromatin organization contribute to tumorigenesis of EGFR-amplified glioblastoma

Computational and Structural Biotechnology Journal, 2022
Background: EGFR amplification and/or mutation are found in more than half of the cases with glioblastoma. Yet, the role of chromatin interactions and its regulation of gene expression in EGFR-amplified glioblastoma remains unclear.
Qi Yang, Nian Jiang, Han Zou, Xuning Fan, Tao Liu, Xi Huang, Siyi Wanggou, Xuejun Li   +7 more
doaj   +1 more source

ZW4864‐mediated inhibition of the β‐catenin/BCL9/BCL9L complex reveals therapeutic potential in bladder cancer

Molecular Oncology, EarlyView.
BCL9 and BCL9L drive bladder cancer progression by enhancing β‐catenin signaling, promoting proliferation, migration, invasion, and organoid growth. Genetic depletion of BCL9(L) suppresses malignant phenotypes, while pharmacological disruption of the β‐catenin/BCL9(L) complex with ZW4864 inhibits canonical Wnt signaling and tumor‐associated cellular ...
Roland Kotolloshi, Mandy Berndt‐Paetz, Eileen Lerner, Gregoire Najjar, Anca Azoitei, Krishna Pal Singh, Shailendra Kumar Gupta, Olaf Wolkenhauer, Cagatay Günes, Otmar Huber, Marc‐Oliver Grimm, Daniel Steinbach   +11 more
wiley   +1 more source