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Article: Dam mutants provide improved sensitivity and spatial resolution for profiling transcription factor binding
Title | Dam mutants provide improved sensitivity and spatial resolution for profiling transcription factor binding |
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Authors | |
Keywords | Dam DamID Tcf7l2 Transcription factor |
Issue Date | 2019 |
Publisher | BioMed Central Ltd. The Journal's web site is located at http://www.epigeneticsandchromatin.com |
Citation | Epigenetics & Chromatin, 2019, v. 12, p. article no. 36 How to Cite? |
Abstract | DamID, in which a protein of interest is fused to Dam methylase, enables mapping of protein-DNA binding through readout of adenine methylation in genomic DNA. DamID offers a compelling alternative to chromatin immunoprecipitation sequencing (ChIP-Seq), particularly in cases where cell number or antibody availability is limiting. This comes at a cost, however, of high non-specific signal and a lowered spatial resolution of several kb, limiting its application to transcription factor-DNA binding. Here we show that mutations in Dam, when fused to the transcription factor Tcf7l2, greatly reduce non-specific methylation. Combined with a simplified DamID sequencing protocol, we find that these Dam mutants allow for accurate detection of transcription factor binding at a sensitivity and spatial resolution closely matching that seen in ChIP-seq. |
Persistent Identifier | http://hdl.handle.net/10722/271377 |
ISSN | 2023 Impact Factor: 4.2 2023 SCImago Journal Rankings: 2.062 |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Szczesnik, T | - |
dc.contributor.author | Ho, JWK | - |
dc.contributor.author | Sherwood, R | - |
dc.date.accessioned | 2019-06-24T01:08:42Z | - |
dc.date.available | 2019-06-24T01:08:42Z | - |
dc.date.issued | 2019 | - |
dc.identifier.citation | Epigenetics & Chromatin, 2019, v. 12, p. article no. 36 | - |
dc.identifier.issn | 1756-8935 | - |
dc.identifier.uri | http://hdl.handle.net/10722/271377 | - |
dc.description.abstract | DamID, in which a protein of interest is fused to Dam methylase, enables mapping of protein-DNA binding through readout of adenine methylation in genomic DNA. DamID offers a compelling alternative to chromatin immunoprecipitation sequencing (ChIP-Seq), particularly in cases where cell number or antibody availability is limiting. This comes at a cost, however, of high non-specific signal and a lowered spatial resolution of several kb, limiting its application to transcription factor-DNA binding. Here we show that mutations in Dam, when fused to the transcription factor Tcf7l2, greatly reduce non-specific methylation. Combined with a simplified DamID sequencing protocol, we find that these Dam mutants allow for accurate detection of transcription factor binding at a sensitivity and spatial resolution closely matching that seen in ChIP-seq. | - |
dc.language | eng | - |
dc.publisher | BioMed Central Ltd. The Journal's web site is located at http://www.epigeneticsandchromatin.com | - |
dc.relation.ispartof | Epigenetics & Chromatin | - |
dc.rights | Epigenetics & Chromatin. Copyright © BioMed Central Ltd. | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.subject | Dam | - |
dc.subject | DamID | - |
dc.subject | Tcf7l2 | - |
dc.subject | Transcription factor | - |
dc.title | Dam mutants provide improved sensitivity and spatial resolution for profiling transcription factor binding | - |
dc.type | Article | - |
dc.identifier.email | Ho, JWK: jwkho@hku.hk | - |
dc.identifier.authority | Ho, JWK=rp02436 | - |
dc.description.nature | published_or_final_version | - |
dc.identifier.doi | 10.1186/s13072-019-0273-x | - |
dc.identifier.scopus | eid_2-s2.0-85067278597 | - |
dc.identifier.hkuros | 298180 | - |
dc.identifier.volume | 12 | - |
dc.identifier.spage | article no. 36 | - |
dc.identifier.epage | article no. 36 | - |
dc.identifier.isi | WOS:000471697300002 | - |
dc.publisher.place | United Kingdom | - |
dc.identifier.issnl | 1756-8935 | - |