Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

A Mortazavi, S Pepke, C Jansen, GK Marinov… - Genome …, 2013 - genome.cshlp.org
… New candidate cell-type-specific enhancers were identified for multiple ENCODE cell types
in … We conclude that large SOMs trained on chromatin data from multiple cell types provide a …

Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation

MI Love, MR Huska, M Jurk, R Schöpflin… - Nucleic acids …, 2017 - academic.oup.com
… by GR across cell types than for cell type-specific target genes. … accessible chromatin,
we propose that cell type-specific … , whose chromatin accessibility is typically cell type-specific, …

[HTML][HTML] The accessible chromatin landscape of the human genome

RE Thurman, E Rynes, R Humbert, J Vierstra… - Nature, 2012 - nature.com
… active in one or more cell types. Of these DHSs, 970,100 were specific to a single cell type,
1,920,642 were active in 2 or more cell types, and a small minority (3,692) was detected in all …

Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns

D Srivastava, S Mahony - Biochimica et Biophysica Acta (BBA)-Gene …, 2020 - Elsevier
… We then describe the chromatin landscape at cell type-specific enhancer elements, and we
review computational advances in imputing TF binding patterns from sequence information …

Chromatin plasticity: a versatile landscape that underlies cell fate and identity

T Yadav, JP Quivy, G Almouzni - Science, 2018 - science.org
… after fertilization to reach totipotency, and finally a progressive gain of specific chromatin
marks and higher organization in line with the diversity of cell types forming the adult organism. …

Engineering cell identity: establishing new gene regulatory and chromatin landscapes

C Guo, SA Morris - Current opinion in genetics & development, 2017 - Elsevier
chromatin landscape, considering how the mechanistic relationship between nuclear
organization and cell … Tissue-specific and cell type-specific interactions occur on various scales, …

[HTML][HTML] The chromatin landscape of healthy and injured cell types in the human kidney

DL Gisch, M Brennan, BB Lake, J Basta… - Nature …, 2024 - nature.com
Cell-type specific open chromatin in the reference cell state … data to better understand the
cell type-specific open chromatin signature across the kidney’s diverse range of cell types. The …

[HTML][HTML] Cell-type specialization is encoded by specific chromatin topologies

W Winick-Ng, A Kukalev, I Harabula, L Zea-Redondo… - Nature, 2021 - nature.com
… Future studies can explore the relationship between DN-specific chromatin landscapes
and the regulation of these critical genes, with potential implications for the onset of addiction. …

[HTML][HTML] A single-cell map of dynamic chromatin landscapes of immune cells in renal cell carcinoma

N Kourtis, Q Wang, B Wang, E Oswald, C Adler… - Nature cancer, 2022 - nature.com
… -cell assay technology for transposase-accessible chromatin … Through surveying the
chromatin landscapes of T cells of … , we observe cell-type-specific and tissue-specific chromatin

[HTML][HTML] Cell-of-origin chromatin organization shapes the mutational landscape of cancer

P Polak, R Karlić, A Koren, R Thurman, R Sandstrom… - Nature, 2015 - nature.com
… The comprehensive representation of different cell types in the Epigenome … chromatin
marks and gene expression to regional mutation density, and the extent of cell type specificity