ArticleeLife2018
Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts.
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Article in eLife, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 123 papers.
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0cells of the map it votes in
123citing papers in PubMed
6.8field-weighted citation impact, top 2% of its field
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Who cites it
123 citing papers in PubMed, 165 citations in OpenAlex.
- Role of Chromatin-Associated RNAs in Eye Physiology and Pathology.Methods in molecular biology (Clifton, N.J.) · 2027Review
- Decoding chromatin-associated RNA (caRNA) interaction networks: from genome-wide dynamic capture to epigenetic mechanisms in plants and animals.Epigenetics · 2026Review
- PCRD-seq: proximity crosslinking-induced RNA depletion sequencing for low-input chromatin-associated transcriptome profiling.Nucleic acids research · 2026Article
- EBER-associated promoter contacts mark accessible but transcriptionally constrained RNAPII promoter hubs in EBV-positive B cells.Epigenetics & chromatin · 2026Article
- CAD-C: An engineered nuclease enables repair-freebioRxiv : the preprint server for biology · 2026Article
- Improved RNA-DNA interaction calling suggests RNA-based gene regulation of phenotypic transitions.Nucleic acids research · 2026Article
- RNA modifications and epigenetic regulation in plants.aBIOTECH · 2026Review
- Widespread DNA off-targeting confounds RNA chromatin occupancy studies.Nature biotechnology · 2026Article
- Metamorphosis and lncRNAs: A Close Relationship.Genesis (New York, N.Y. : 2000) · 2026Review
- A comparative analysis of topological domain callers over RNA-associated interactome.BMC bioinformatics · 2026Article
- Microfluidic low-input profiling reveals lncRNA roles in disease.bioRxiv : the preprint server for biology · 2026Article
- A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest.Genome research · 2026Review
- Deciphering the regulatory landscape of enhancer RNAs in health and disease.Signal transduction and targeted therapy · 2026Review
- 3D Chromatin Architecture During Early Development: New Methods and New Findings.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Noncoding RNAs: A Novel Frontier in Liver Cancer Research and Therapy: Implications for Precision Oncology.Sub-cellular biochemistry · 2026Review
- Protein-Centric Mapping of RNA-DNA Interactions with RedChIP.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Chromatin-Associated RNAs Regulate Gene Expression and Chromatin Structure.Non-coding RNA · 2025Review
- Coordinated regulation by lncRNAs results in tight lncRNA-target couplings.Cell genomics · 2025Article
- A U3 snoRNA is required for the regulation of chromatin dynamics and antiviral response in Drosophila melanogaster.Nucleic acids research · 2025Article
- Identification of chromatin-associated RNAs at human centromeres.bioRxiv : the preprint server for biology · 2025Article
63 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Jason C BellDepartment of Biochemistry, Stanford University, Stanford, United States.ORCID https://orcid.org/0000-0001-5480-7975
David JukamDepartment of Biology, Stanford University, Stanford, United States.ORCID http://orcid.org/0000-0003-4167-2754
Nicole A TeranDepartment of Biochemistry, Stanford University, Stanford, United States.ORCID http://orcid.org/0000-0002-9625-5010
Viviana I RiscaDepartment of Genetics, Stanford University, Stanford, United States.ORCID http://orcid.org/0000-0003-2670-8704
Owen K SmithDepartment of Biochemistry, Stanford University, Stanford, United States.ORCID http://orcid.org/0000-0003-0880-2801
Whitney L JohnsonDepartment of Biochemistry, Stanford University, Stanford, United States.
Jan M SkotheimDepartment of Biology, Stanford University, Stanford, United States.
William James GreenleafDepartment of Genetics, Stanford University, Stanford, United States.
Aaron F StraightDepartment of Biochemistry, Stanford University, Stanford, United States.ORCID http://orcid.org/0000-0001-5885-7881
Stanford University · US
Funding
Supplement to Enhance Wellness and Resiliency in the Graduate EnvironmentT32GM007276 · NIGMS · STANFORD UNIVERSITY · PI MORRISON, ASHBY J. · 1985 to 2023
$32.9MINSTITUTIONAL TRAINING GRANT IN GENOME SCIENCET32HG000044 · NHGRI · STANFORD UNIVERSITY · PI MICHAEL P. SNYDER · 1995 to 2026
$32.2MTRAINING & OUTREACH COREP50GM107615 · NIGMS · STANFORD UNIVERSITY · PI COVERT, MARKUS W · 2013 to 2017
$10.9MDROSOPHILA GENOMICS RESOURCE CENTERP40OD010949 · OD · TRUSTEES OF INDIANA UNIVERSITY · PI Andrew Zelhof · 2012 to 2026
$9.4MGenome wide identification and functional analysis of chromatin regulatory RNAsR01HG009909 · NHGRI · STANFORD UNIVERSITY · PI GREENLEAF, WILLIAM JAMES, STRAIGHT, AARON F · 2018 to 2021
$2.5MControl and coordination of the maternal-to-zygotic transitionR01HD085135 · NICHD · STANFORD UNIVERSITY · PI SKOTHEIM, JAN M, STRAIGHT, AARON F · 2016 to 2020
$1.6MCTCF dependent chromatin looping dynamicsR01GM106005 · NIGMS · STANFORD UNIVERSITY · PI MABUCHI, HIDEO, STRAIGHT, AARON F · 2013 to 2016
$1.1MMolecular Pharmacology Training GrantT32GM113854 · NIGMS · STANFORD UNIVERSITY · PI MOCHLY-ROSEN, DARIA · 2015 to 2019
$1.1MMapping chromatin secondary structure by sequencing correlated DNA strand breaksR21HG007726 · NHGRI · STANFORD UNIVERSITY · PI GREENLEAF, WILLIAM JAMES · 2014 to 2015
$441kDetermining the dynamic mechanisms regulating the maternal-to-zygotic transitionF32GM108295 · NIGMS · STANFORD UNIVERSITY · PI JUKAM, DAVID M · 2013 to 2016
$161kChromatin looping by CTCF, the dynamic scaffold of genomic architectureF32GM116338 · NIGMS · STANFORD UNIVERSITY · PI BELL, JASON C · 2015 to 2016
$116kHoward Hughes Medical Institute HHMI-Simons Faculty Scholar AwardNHGRI NIH HHS R01 HG009909NHGRI NIH HHS R21 HG007726NHGRI NIH HHS T32 HG000044NICHD NIH HHS R01 HD085135NIGMS NIH HHS F32 GM108295NIGMS NIH HHS F32 GM116338NIGMS NIH HHS P50 GM107615NIGMS NIH HHS R01 GM106005NIGMS NIH HHS T32 GM007276NIGMS NIH HHS T32 GM113854NIH HHS Molecular Pharmacology Training Grant (NIH T32-GM113854-02)NIH HHS NIH Ruth Kirchstein National Research Service Award (F32GM108295 )NIH HHS NIH Ruth Kirchstein National Research Service Award (F32GM116338)NIH HHS NIH T32 Training Fellowship (GM007276)NIH HHS P40 OD010949NIH HHS P50HG00773501NIH HHS R01GM106005NIH HHS R01HG009909NIH HHS R21HG007726NIH HHS RO1 HD085135NIH HHS Stanford Center for Systems Biology (NIH P50 GM107615) Seed GrantNIH HHS Stanford Genetics Training Program (5T32HG000044-19)
Abstract
RNA is a critical component of chromatin in eukaryotes, both as a product of transcription, and as an essential constituent of ribonucleoprotein complexes that regulate both local and global chromatin states. Here, we present a proximity ligation and sequencing method called
Indexed as
AnimalsChromatinDNADosage Compensation, GeneticDrosophila melanogasterDrosophila ProteinsFemaleHigh-Throughput Nucleotide SequencingMaleRNATranscription FactorsTranscription, GeneticChromatinDNADrosophila ProteinsRNATranscription FactorschromatinchromosomesD. melanogasterdosage compensationgene expressiongenomicsnon-coding RNARNAtranscription
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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.