XL-DNase-Seq: Footprinting Analysis of Dynamic Transcription Factors.

Kyu-Seon Oh, Mohammad Aqdas, Myong-Hee Sung

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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4 · The record

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5 · Who and what money

Authors and funding

3 authors.

Kyu-Seon OhLaboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.

Mohammad AqdasLaboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.

Myong-Hee SungLaboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA. sungm@nih.gov.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

We have developed a novel method for genomic footprinting of transcription factors (TFs) that detects potential gene regulatory relationships from DNase-seq data at the nucleotide level. We introduce an assay termed cross-link (XL)-DNase-seq, designed to capture chromatin interactions of dynamic TFs. A mild cross-linking step in XL-DNase-seq improves the detection of DNase-based footprints of dynamic TFs. The footprint strengths and detectability depend on an optimal cross-linking procedure. This method may help extract novel gene regulatory circuits involving previously undetectable TFs. The XL-DNase-seq method is illustrated here for activated mouse macrophage-like cells, which share several features with inflammatory macrophages.

Indexed as

DNA FootprintingTranscription FactorsAnimalsChromatinDeoxyribonucleasesHigh-Throughput Nucleotide SequencingMacrophagesMiceSequence Analysis, DNAChromatinDeoxyribonucleasesTranscription FactorsChromatin accessibilityDNase-seqGenomic footprintingHigh-throughput sequencingTranscription factor footprinting

Identifiers

PMID39141240

DOI10.1186/1756-8935-5-10

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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.