[PDF][PDF] Sequence-directed action of RSC remodeler and general regulatory factors modulates+ 1 nucleosome position to facilitate transcription

S Kubik, E O'Duibhir, WJ de Jonge, S Mattarocci… - Molecular cell, 2018 - cell.com
Accessible chromatin is important for RNA polymerase II recruitment and transcription initiation
at eukaryotic promoters. We investigated the mechanistic links between promoter DNA …

[PDF][PDF] Following the tracks: How transcription factor binding dynamics control transcription

WJ de Jonge, HP Patel, JVW Meeussen, TL Lenstra - Biophysical journal, 2022 - cell.com
Transcription, the process of copying genetic information from DNA to messenger RNA, is
regulated by sequence-specific DNA-binding proteins known as transcription factors (TFs). …

Transcription factor clusters enable target search but do not contribute to target gene activation

…, W Pomp, I Brouwer, WJ de Jonge… - Nucleic Acids …, 2023 - academic.oup.com
Many transcription factors (TFs) localize in nuclear clusters of locally increased concentrations,
but how TF clustering is regulated and how it influences gene expression is not well …

Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

WJ de Jonge, E O'Duibhir, P Lijnzaad… - The EMBO …, 2017 - embopress.org
An important distinction is frequently made between constitutively expressed housekeeping
genes versus regulated genes. Although generally characterized by different DNA elements, …

[HTML][HTML] An optimized chromatin immunoprecipitation protocol for quantification of protein-DNA interactions

WJ de Jonge, M Brok, P Kemmeren, FCP Holstege - STAR protocols, 2020 - Elsevier
Transcription factors are important regulators of cell fate and function. Knowledge about where
transcription factors are bound in the genome is crucial for understanding their function. A …

Genome‐wide off‐rates reveal how DNA binding dynamics shape transcription factor function

WJ de Jonge, M Brok, P Lijnzaad… - Molecular systems …, 2020 - embopress.org
Protein– DNA interactions are dynamic, and these dynamics are an important aspect of
chromatin‐associated processes such as transcription or replication. Due to a lack of methods to …

Neural reflex pathways in intestinal inflammation: hypotheses to viable therapy

…, MD Luyer, WA Buurman, WJ De Jonge - Nature Reviews …, 2015 - nature.com
Studies in neuroscience and immunology have clarified much of the anatomical and cellular
basis for bidirectional interactions between the nervous and immune systems. As with other …

An extensively optimized chromatin immunoprecipitation protocol for quantitatively comparable and robust results

WJ de Jonge, M Brok, P Kemmeren, FCP Holstege - BioRxiv, 2019 - biorxiv.org
Chromatin immunoprecipitation (ChIP) is a commonly used technique to investigate which
parts of a genome are bound by a particular protein. The result of ChIP is often interpreted in …

Comparison of treatment strategies in early rheumatoid arthritis: a randomized trial

…, AJ Peeters, JM de Jonge-Bok… - Annals of internal …, 2007 - acpjournals.org
Background: In patients with early rheumatoid arthritis, initial combination therapies provide
earlier clinical improvement and less progression of joint damage after 1 year compared …

Beyond unfavorable thinking: the illness cognition questionnaire for chronic diseases.

…, W van Lankveld, PJH Jongen… - Journal of consulting …, 2001 - psycnet.apa.org
The literature on chronic diseases recognizes the role of illness cognition as a mediator
between stress and illness. Few conceptualizations and instruments, however, give an …