ArticleNucleic acids research2021
Cell-free genomics reveal intrinsic, cooperative and competitive determinants of chromatin interactions.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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Who cites it
8 citing papers in PubMed, 10 citations in OpenAlex.
- Eukaryotic cell-free protein synthesis: Chassis diversification, system engineering, and emerging applications.Synthetic and systems biotechnology · 2026Review
- Dosage compensation defects due to roX RNA loss are rescued by recalibration of X/autosome stoichiometry.Nucleic acids research · 2026Article
- Differential chromatin looping regulated by two GA-binding transcription factors creates an X-specific chromatin environment for dosage compensation.bioRxiv : the preprint server for biology · 2026Article
- Reciprocal targeting of the unfolded protein response regulator Xbp1 and the DOM-A nucleosome remodeler in Drosophila.Nucleic acids research · 2026Article
- The Quartet of Core Oncogenic Drivers in Neuroendocrine Prostate Cancer: Multi-Omics Dataset Integration to Forge a Translational Link Between Biology and Precision Therapy.International journal of biological sciences · 2026Review
- Physical interaction between MSL2 and CLAMP assures direct cooperativity and prevents competition at composite binding sites.Nucleic acids research · 2023Article
- Article
- Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory.Nature structural & molecular biology · 2022Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metazoan transcription factors distinguish their response elements from a large excess of similar sequences. We explored underlying principles of DNA shape read-out and factor cooperativity in chromatin using a unique experimental system. We reconstituted chromatin on Drosophila genomes in extracts of preblastoderm embryos, mimicking the naïve state of the zygotic genome prior to developmental transcription activation. We then compared the intrinsic binding specificities of three recombinant transcription factors, alone and in combination, with GA-rich recognition sequences genome-wide. For MSL2, all functional elements reside on the X chromosome, allowing to distinguish physiological elements from non-functional 'decoy' sites. The physiological binding profile of MSL2 is approximated through interaction with other factors: cooperativity with CLAMP and competition with GAF, which sculpts the profile by occluding non-functional sites. An extended DNA shape signature is differentially read out in chromatin. Our results reveal novel aspects of target selection in a complex chromatin environment.
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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.