ArticleCell reports2019
High Sensitivity Profiling of Chromatin Structure by MNase-SSP.
Article in Cell reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed, 44 citations in OpenAlex.
- Article
- A Scalable MNase-seq Framework for Reproducible Nucleosome Profiling across Pluripotent Stem Cell and Cardiomyocyte Models.Computational and structural biotechnology journal · 2026Article
- Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy.Genome research · 2025Article
- MAX inactivation deregulates the MYC network and induces neuroendocrine neoplasia in multiple tissues.Science advances · 2025Article
- The histone chaperone Spn1 preserves chromatin protections at promoters and nucleosome positioning in open reading frames.G3 (Bethesda, Md.) · 2025Article
- Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2.PLoS computational biology · 2025Article
- Article
- cBAF generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers.Nature structural & molecular biology · 2024Article
- Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy.bioRxiv : the preprint server for biology · 2024Article
- A germline point mutation in the MYC-FBW7 phosphodegron initiates hematopoietic malignancies.Genes & development · 2024Article
- Transcriptional regulation of FACT involves Coordination of chromatin accessibility and CTCF binding.The Journal of biological chemistry · 2024Article
- RNase H genes cause distinct impacts on RNA:DNA hybrid formation and mutagenesis genome wide.Science advances · 2023Article
- PGEProceedings of the National Academy of Sciences of the United States of America · 2023Article
- RNase H genes cause distinct impacts on RNA:DNA hybrid formation and mutagenesis genome-wide.bioRxiv : the preprint server for biology · 2023Article
- The esBAF and ISWI nucleosome remodeling complexes influence occupancy of overlapping dinucleosomes and fragile nucleosomes in murine embryonic stem cells.BMC genomics · 2023Article
- Chromatin accessibility: methods, mechanisms, and biological insights.Nucleus (Austin, Tex.) · 2022Review
- A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function.Molecular cell · 2022Article
- The glucose-sensing transcription factor MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis.PLoS biology · 2021Article
- The Genome-Wide Binding Profile for Human RE1 Silencing Transcription Factor Unveils a Unique Genetic Circuitry in Hippocampus.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2021Article
- The native cistrome and sequence motif families of the maize ear.PLoS genetics · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 3 institutions in 1 country.
Funding
Abstract
A complete view of eukaryotic gene regulation requires that we accurately delineate how transcription factors (TFs) and nucleosomes are arranged along linear DNA in a sensitive, unbiased manner. Here we introduce MNase-SSP, a single-stranded sequencing library preparation method for nuclease-digested chromatin that enables simultaneous mapping of TF and nucleosome positions. As a proof of concept, we apply MNase-SSP toward the genome-wide, high-resolution mapping of nucleosome and TF occupancy in murine embryonic stem cells (mESCs). Compared with existing MNase-seq protocols, MNase-SSP markedly enriches for short DNA fragments, enabling detection of binding by subnucleosomal particles and TFs, in addition to nucleosomes. From these same data, we identify multiple, sequence-dependent binding modes of the architectural TF Ctcf and extend this analysis to the TF Nrsf/Rest. Looking forward, we anticipate that single stranded protocol (SSP) adaptations of any protein-DNA interaction mapping technique (e.g., ChIP-exo and CUT&RUN) will enhance the information content of the resulting data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.