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Altemose N, Maslan A, Smith OK, Sundararajan K, Brown RR, Mishra R, Detweiler AM, Neff N, Miga KH, Straight AF, Streets A. DiMeLo-seq: a long-read, single-molecule method for mapping protein-DNA interactions genome wide. Nat Methods 2022; 19:711-723. [PMID: 35396487 PMCID: PMC9189060 DOI: 10.1038/s41592-022-01475-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 03/24/2022] [Indexed: 12/13/2022]
Abstract
Studies of genome regulation routinely use high-throughput DNA sequencing approaches to determine where specific proteins interact with DNA, and they rely on DNA amplification and short-read sequencing, limiting their quantitative application in complex genomic regions. To address these limitations, we developed directed methylation with long-read sequencing (DiMeLo-seq), which uses antibody-tethered enzymes to methylate DNA near a target protein's binding sites in situ. These exogenous methylation marks are then detected simultaneously with endogenous CpG methylation on unamplified DNA using long-read, single-molecule sequencing technologies. We optimized and benchmarked DiMeLo-seq by mapping chromatin-binding proteins and histone modifications across the human genome. Furthermore, we identified where centromere protein A localizes within highly repetitive regions that were unmappable with short sequencing reads, and we estimated the density of centromere protein A molecules along single chromatin fibers. DiMeLo-seq is a versatile method that provides multimodal, genome-wide information for investigating protein-DNA interactions.
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Affiliation(s)
- Nicolas Altemose
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Annie Maslan
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Owen K Smith
- Department of Biochemistry, Stanford University, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | | | - Rachel R Brown
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Reet Mishra
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Karen H Miga
- Department of Molecular & Cell Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University, Stanford, CA, USA.
| | - Aaron Streets
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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Kan KKW, Rudd JA, Wai MK. Differential action of anti-emetic drugs on defecation and emesis induced by prostaglandin E2 in the ferret. Eur J Pharmacol 2006; 544:153-9. [PMID: 16844111 DOI: 10.1016/j.ejphar.2006.06.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Revised: 06/14/2006] [Accepted: 06/19/2006] [Indexed: 11/15/2022]
Abstract
In the present studies we investigated the mechanism of action of prostaglandin E2 (1 mg/kg, i.p.) to induce emesis and defecation and/or tenesmus in the ferret. The emesis was antagonized significantly (P<0.05) by ondansetron (0.3 and 1 mg/kg, i.p.) and (+)-(2S,3S)-3-(2-methoxybenzylamino)-2-phenlypiperidine hydrochloride (CP-99,994; 10 mg/kg, i.p.), but neither compound reduced defecations and/or tenesmus, with ondansetron (0.3 mg/kg) actually producing a slight increase (P<0.05). Droperidol (1 and 3 mg/kg), metoclopramide (0.3 and 3 mg/kg), domperidone (0.3 and 3 mg/kg), promethazine (0.3 and 3 mg/kg) and scopolamine (0.3 and 3 mg/kg) failed to reduce prostaglandin E2 induced emesis. However, droperidol (1 and 3 mg/kg) and scopolamine (0.3 and 3 mg/kg) reduced significantly the defecatory and/or tenesmus response (P<0.05). Bilateral abdominal vagotomy was ineffective to reduce emesis and defecations and/or tenesmus. The data suggests that 5-HT3 receptor and NK1 tachykinin receptor antagonists could be useful in the clinic to prevent emesis but not defecations induced by prostaglandin E2.
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Affiliation(s)
- Kelvin K W Kan
- Emesis Research Group, Department of Pharmacology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
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