ArticlePLoS computational biology2017
Uncovering direct and indirect molecular determinants of chromatin loops using a computational integrative approach.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 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
7 citing papers in PubMed, 8 citations in OpenAlex.
- Targeting 3D chromosomal architecture at the RANK loci to suppress myeloma-driven osteoclastogenesis.Oncoimmunology · 2022Article
- The Myc-associated zinc finger protein (MAZ) works together with CTCF to control cohesin positioning and genome organization.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Insulator-based loops mediate the spreading of H3K27me3 over distant micro-domains repressing euchromatin genes.Genome biology · 2020Article
- 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs.BMC genomics · 2019Article
- The Role of Systems Biologic Approach in Cell Signaling and Drug Development Responses-A Mini Review.Medical sciences (Basel, Switzerland) · 2018Review
- High-resolution TADs reveal DNA sequences underlying genome organization in flies.Nature communications · 2018Article
- Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation.Genome biology · 2017Article
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 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chromosomal organization in 3D plays a central role in regulating cell-type specific transcriptional and DNA replication timing programs. Yet it remains unclear to what extent the resulting long-range contacts depend on specific molecular drivers. Here we propose a model that comprehensively assesses the influence on contacts of DNA-binding proteins, cis-regulatory elements and DNA consensus motifs. Using real data, we validate a large number of predictions for long-range contacts involving known architectural proteins and DNA motifs. Our model outperforms existing approaches including enrichment test, random forests and correlation, and it uncovers numerous novel long-range contacts in Drosophila and human. The model uncovers the orientation-dependent specificity for long-range contacts between CTCF motifs in Drosophila, highlighting its conserved property in 3D organization of metazoan genomes. Our model further unravels long-range contacts depending on co-factors recruited to DNA indirectly, as illustrated by the influence of cohesin in stabilizing long-range contacts between CTCF sites. It also reveals asymmetric contacts such as enhancer-promoter contacts that highlight opposite influences of the transcription factors EBF1, EGR1 or MEF2C depending on RNA Polymerase II pausing.
Indexed as
Identifiers
What OpenQuestion holds
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.