ReviewMolecular cell2023
Deciphering the multi-scale, quantitative cis-regulatory code.
Review in Molecular cell, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 191 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
191 citing papers in PubMed, 286 citations in OpenAlex.
- Developmental contexts of gene-regulatory evolution following whole genome duplication in salmonids.Nature ecology & evolution · 2026Article
- UnlockingNAR genomics and bioinformatics · 2026Article
- Foundation Models for Microbiome Research: From Sequence Semantics to Community Dynamics and Multimodal World Models.Advanced genetics (Hoboken, N.J.) · 2026Review
- CRISPR-Cas9 and precision editing technologies linking functional genomics to clinical translation in genetic diseases.Clinical and translational medicine · 2026Review
- Adaptation of eukaryotic membrane homeostasis to species-specific cellular lipid landscapes.Genes & development · 2026Article
- Enhancer control of promoter activity and variability via frequency modulation of clustered transcriptional bursts.Nature genetics · 2026Article
- Article
- Cumulative transcription factor binding and p300-mediated histone acetylation drive enhancer activation frequency.Nature genetics · 2026Article
- Promoter strength and position govern promoter competition through transcript-dependent insulation.Nature genetics · 2026Article
- Toward generalizable and interpretable AI in regulatory genomics.Nature genetics · 2026Review
- Maize ZmBES1/BZR1-7 Transcription Factor Positively Regulates Drought Tolerance in TransgenicPlants (Basel, Switzerland) · 2026Article
- Nonconsensus flanking sequence of hundreds of base pairs around in vivo binding sites: statistical beacons for transcription factor scanning.Nucleic acids research · 2026Article
- Gene Expression and Alternative Splicing Regulate Phenotypic Plasticity of a Social Wasp.Ecology and evolution · 2026Article
- Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers.bioRxiv : the preprint server for biology · 2026Article
- Spatially resolved profiling of steroid nuclear receptors reveals a role for the disordered N-terminal domains in genome targeting and AP-1 interaction.Genome research · 2026Article
- Antibody-trapping presents a widespread pitfall for microscopy and genomics in the nucleus.Nucleic acids research · 2026Article
- Protocol to predict gene expression from transcriptomic data using PREDICT.STAR protocols · 2026Article
- Systemic degradation of repressive transcription factors gates gene expression and cell fate specification.bioRxiv : the preprint server for biology · 2026Article
- Transcription clusters and developmental pathways - nature, nurture, noise.Journal of cell science · 2026Review
- Predicting gene-specific regulation with transcriptomic and epigenetic single-cell data.Bioinformatics (Oxford, England) · 2026Article
131 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
2 authors at 2 institutions in 1 country.
Funding
Abstract
Uncovering the cis-regulatory code that governs when and how much each gene is transcribed in a given genome and cellular state remains a central goal of biology. Here, we discuss major layers of regulation that influence how transcriptional outputs are encoded by DNA sequence and cellular context. We first discuss how transcription factors bind specific DNA sequences in a dosage-dependent and cooperative manner and then proceed to the cofactors that facilitate transcription factor function and mediate the activity of modular cis-regulatory elements such as enhancers, silencers, and promoters. We then consider the complex and poorly understood interplay of these diverse elements within regulatory landscapes and its relationships with chromatin states and nuclear organization. We propose that a mechanistically informed, quantitative model of transcriptional regulation that integrates these multiple regulatory layers will be the key to ultimately cracking the cis-regulatory code.
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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.