ArticleCell reports2018
Fine-Resolution Mapping of TF Binding and Chromatin Interactions.
Article in Cell reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 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.
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Who cites it
36 citing papers in PubMed, 57 citations in OpenAlex.
- Reciprocal, methylation-dependent binding of Zfp57 and Gzf1 safeguards Dlk1-Dio3 imprinting during developmental reprogramming.Nature communications · 2026Article
- Sequence and chemical specificity define the functional landscape of intrinsically disordered regions.Nature cell biology · 2026Article
- High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion.Nature communications · 2025Article
- Experimental approaches to investigate biophysical interactions between homeodomain transcription factors and DNA.Biochimica et biophysica acta. Gene regulatory mechanisms · 2025Review
- General regulatory factors exert differential effects on nucleosome sliding activity of the ISW1a complex.Biological research · 2024Article
- Yeast heterochromatin stably silences only weak regulatory elements by altering burst duration.Cell reports · 2024Article
- In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization.Nature genetics · 2024Article
- A single fiber view of the nucleosome organization in eukaryotic chromatin.Nucleic acids research · 2024Article
- Yeast Heterochromatin Only Stably Silences Weak Regulatory Elements by Altering Burst Duration.bioRxiv : the preprint server for biology · 2023Article
- Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries.Nature communications · 2023Article
- Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells.Nature communications · 2023Article
- Single-cell technologies in multiple myeloma: new insights into disease pathogenesis and translational implications.Biomarker research · 2023Review
- SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors.Genome biology · 2023Article
- The chromatin factor ROW cooperates with BEAF-32 in regulating long-range inducible genes.EMBO reports · 2022Article
- Generating specificity in genome regulation through transcription factor sensitivity to chromatin.Nature reviews. Genetics · 2022Review
- nMOWChIP-seq: low-input genome-wide mapping of non-histone targets.NAR genomics and bioinformatics · 2022Article
- The MuvB complex binds and stabilizes nucleosomes downstream of the transcription start site of cell-cycle dependent genes.Nature communications · 2022Article
- A regulatory phosphorylation site on Mec1 controls chromatin occupancy of RNA polymerases during replication stress.The EMBO journal · 2021Article
- Measurement of histone replacement dynamics with genetically encoded exchange timers in yeast.Nature biotechnology · 2021Article
- Genome information processing by the INO80 chromatin remodeler positions nucleosomes.Nature communications · 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
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription factor (TF) binding to DNA is crucial for transcriptional regulation. There are multiple methods for mapping such binding. These methods balance between input requirements, spatial resolution, and compatibility with high-throughput automation. Here, we describe SLIM-ChIP (short-fragment-enriched, low-input, indexed MNase ChIP), which combines enzymatic fragmentation of chromatin and on-bead indexing to address these desiderata. SLIM-ChIP reproduces a high-resolution binding map of yeast Reb1 comparable with existing methods, yet with less input material and full compatibility with high-throughput procedures. We demonstrate the robustness and flexibility of SLIM-ChIP by probing additional factors in yeast and mouse. Finally, we show that SLIM-ChIP provides information on the chromatin landscape surrounding the bound transcription factor. We identify a class of Reb1 sites where the proximal -1 nucleosome tightly interacts with Reb1 and maintains unidirectional transcription. SLIM-ChIP is an attractive solution for mapping DNA binding proteins and charting the surrounding chromatin occupancy landscape at a single-cell level.
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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.