Clinical relevance of blood-based ctDNA analysis: mutation detection and beyond

L Keller, Y Belloum, H Wikman, K Pantel - British journal of cancer, 2021‏ - nature.com
Cell-free DNA (cfDNA) derived from tumours is present in the plasma of cancer patients. The
majority of currently available studies on the use of this circulating tumour DNA (ctDNA) deal …

CTCF shapes chromatin structure and gene expression in health and disease

B Dehingia, M Milewska, M Janowski, A Pękowska - EMBO reports, 2022‏ - embopress.org
CCCTC‐binding factor (CTCF) is an eleven zinc finger (ZF), multivalent transcriptional
regulator, that recognizes numerous motifs thanks to the deployment of distinct combinations …

Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization

EP Nora, A Goloborodko, AL Valton, JH Gibcus… - Cell, 2017‏ - cell.com
The molecular mechanisms underlying folding of mammalian chromosomes remain poorly
understood. The transcription factor CTCF is a candidate regulator of chromosomal …

Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin

MW Snyder, M Kircher, AJ Hill, RM Daza, J Shendure - Cell, 2016‏ - cell.com
Nucleosome positioning varies between cell types. By deep sequencing cell-free DNA
(cfDNA), isolated from circulating blood plasma, we generated maps of genome-wide in vivo …

Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming

A Soufi, MF Garcia, A Jaroszewicz, N Osman… - Cell, 2015‏ - cell.com
Pioneer transcription factors (TFs) access silent chromatin and initiate cell-fate changes,
using diverse types of DNA binding domains (DBDs). FoxA, the paradigm pioneer TF, has a …

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors

D Barisic, MB Stadler, M Iurlaro, D Schübeler - Nature, 2019‏ - nature.com
Chromatin remodelling complexes evict, slide, insert or replace nucleosomes, which
represent an intrinsic barrier for access to DNA. These remodellers function in most aspects …

Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation

T Baubec, DF Colombo, C Wirbelauer, J Schmidt… - Nature, 2015‏ - nature.com
DNA methylation is an epigenetic modification associated with transcriptional repression of
promoters and is essential for mammalian development. Establishment of DNA methylation …

Highly cooperative chimeric super-SOX induces naive pluripotency across species

CM MacCarthy, G Wu, V Malik, Y Menuchin-Lasowski… - Cell Stem Cell, 2024‏ - cell.com
Our understanding of pluripotency remains limited: iPSC generation has only been
established for a few model species, pluripotent stem cell lines exhibit inconsistent …

Gene silencing triggers polycomb repressive complex 2 recruitment to CpG islands genome wide

EM Riising, I Comet, B Leblanc, X Wu, JV Johansen… - Molecular cell, 2014‏ - cell.com
Polycomb group (PcG) proteins are required for normal differentiation and development and
are frequently deregulated in cancer. PcG proteins are involved in gene silencing; however …

Structural features of transcription factors associating with nucleosome binding

MF Garcia, CD Moore, KN Schulz, O Alberto… - Molecular cell, 2019‏ - cell.com
Fate-changing transcription factors (TFs) scan chromatin to initiate new genetic programs
during cell differentiation and reprogramming. Yet the protein structure domains that allow …