ArticleGenome research2014
Genome-wide map of regulatory interactions in the human genome.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 180 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
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Who cites it
180 citing papers in PubMed, 298 citations in OpenAlex.
- TM-Loop: Transformer multi-omics hierarchical detection of chromatin loop.Scientific reports · 2026Article
- Accurate and efficient HiChIP interaction detection by modeling restriction enzyme cut site density as biological signal.Briefings in bioinformatics · 2026Article
- Transposable elements shape stemness in normal and leukemic hematopoiesis.Nature genetics · 2026Article
- Effects of topological domain disruption on transcriptional regulation are chromatin context dependent.Epigenetics & chromatin · 2026Article
- A split luciferase biosensing platform for detection and imaging of chromatin loops in individual live cells.Nucleic acids research · 2025Article
- Joint analysis of sQTL and Hi-C reveals spatial proximity between sQTLs and target genes in cancer tissues.Scientific reports · 2025Article
- EPIPDLF: a pretrained deep learning framework for predicting enhancer-promoter interactions.Bioinformatics (Oxford, England) · 2025Article
- DconnLoop: a deep learning model for predicting chromatin loops based on multi-source data integration.BMC bioinformatics · 2025Article
- Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements.Genome research · 2025Article
- ZNF143 binds DNA and stimulates transcription initiation to activate and repress direct target genes.Nucleic acids research · 2025Article
- Identification of a distal enhancer of Ucp1 essential for thermogenesis and mitochondrial function in brown fat.Communications biology · 2025Article
- ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF.Molecular cell · 2025Article
- Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function.Molecular cell · 2025Article
- DeepEPI: CNN-transformer-based model for extracting TF interactions through predicting enhancer-promoter interactions.Bioinformatics advances · 2025Article
- Genome structural dynamics: insights from Gaussian network analysis of Hi-C data.Briefings in functional genomics · 2024Article
- ZNF143 binds DNA and stimulates transcripstion initiation to activate and repress direct target genes.bioRxiv : the preprint server for biology · 2024Article
- BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies.Nucleic acids research · 2024Article
- ADNP modulates SINE B2-derived CTCF-binding sites during blastocyst formation in mice.Genes & development · 2024Article
- Structural insights into the HDAC4-MEF2A-DNA complex and its implication in long-range transcriptional regulation.Nucleic acids research · 2024Article
- MMCT-Loop: a mix model-based pipeline for calling targeted 3D chromatin loops.Nucleic acids research · 2024Article
120 more citing papers are in PubMed but not listed here.
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 5 institutions in 2 countries.
Funding
Abstract
Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. Bound regions covered 80% of DNase I hypersensitive sites including 99.7% of TSS and 98% of enhancers. Correlating this map with ChIP-seq and RNA-seq data sets revealed cohesin, CTCF, and ZNF143 as key components of three-dimensional chromatin structure and revealed how the distal chromatin state affects gene transcription. Comparison of interactions between cell types revealed that enhancer-promoter interactions were highly cell-type-specific. Construction and comparison of distal and proximal regulatory networks revealed stark differences in structure and biological function. Proximal binding events are enriched at genes with housekeeping functions, while distal binding events interact with genes involved in dynamic biological processes including response to stimulus. This study reveals new mechanistic and functional insights into regulatory region organization in the nucleus.
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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.