AbstractWe recently developed directed methylation with long-read sequencing (DiMeLo-seq) to map protein–DNA interactions genome wide. DiMeLo-seq is capable of mapping multiple interaction sites on single DNA molecules, profiling protein binding in the context of endogenous DNA methylation, identifying haplotype-specific protein–DNA interactions and mapping protein–DNA interactions in repetitive regions of the genome that are difficult to study with short-read methods.

摘要我们最近开发了长读测序（DiMeLo-seq）定向甲基化，以绘制全基因组蛋白质与DNA的相互作用。DiMeLo-seq能够绘制单个DNA分子上的多个相互作用位点，在内源性DNA甲基化的背景下分析蛋白质结合，鉴定单倍型特异性蛋白质-DNA相互作用，并绘制基因组重复区域中难以用短读方法研究的蛋白质-DNA相互作用。

With DiMeLo-seq, adenines in the vicinity of a protein of interest are methylated in situ by tethering the Hia5 methyltransferase to an antibody using protein A. Protein–DNA interactions are then detected by direct readout of adenine methylation with long-read, single-molecule DNA sequencing platforms such as Nanopore sequencing.

使用DiMeLo-seq，通过使用蛋白a将Hia5甲基转移酶束缚在抗体上，将目标蛋白质附近的腺嘌呤原位甲基化。然后通过长读单分子DNA测序平台（例如纳米孔测序）直接读取腺嘌呤甲基化来检测蛋白质与DNA的相互作用。

Here we present a detailed protocol and practical guidance for performing DiMeLo-seq. This protocol can be run on nuclei from fresh, lightly fixed or frozen cells. The protocol requires 1–2 d for performing in situ targeted methylation, 1–5 d for library preparation depending on desired fragment length and 1–3 d for Nanopore sequencing depending on desired sequencing depth.

在这里，我们提供了执行DiMeLo-seq的详细协议和实用指南。该方案可以在新鲜，轻度固定或冷冻细胞的细胞核上运行。该方案需要1-2天进行原位靶向甲基化，1-5天用于文库制备，具体取决于所需的片段长度，1-3天用于纳米孔测序，具体取决于所需的测序深度。

The protocol requires basic molecular biology skills and equipment, as well as access to a Nanopore sequencer. We also provide a Python package, dimelo, for analysis of DiMeLo-seq data.Key points.

该协议需要基本的分子生物学技能和设备，以及使用纳米孔测序仪。我们还提供了一个Python包dimelo，用于分析dimelo-seq数据。关键点。

DiMeLo-seq uses long-read, single-molecule sequencing to map protein–DNA interactions genome wide, in nuclei from fresh, fixed or frozen cells, and from primary tissues or intact organisms.

DiMeLo-seq使用长读单分子测序来绘制全基因组蛋白质与DNA的相互作用，从新鲜，固定或冷冻的细胞以及原代组织或完整生物体的细胞核中绘制蛋白质与DNA的相互作用。

Compared with short-read methods, this enables mapping of multiple interaction sites on single DNA molecules, profiling protein binding in the context of endogenous DNA methylation, identifying haplotype-specific protein–DNA interactions and mapping protein–DNA interactions in repetitive regions of the genome..

与短读方法相比，这可以绘制单个DNA分子上的多个相互作用位点，在内源性DNA甲基化的背景下分析蛋白质结合，鉴定单倍型特异性蛋白质-DNA相互作用，并绘制基因组重复区域中的蛋白质-DNA相互作用。。

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Fig. 1: DiMeLo-seq protocol overview.Fig. 2: Experimental QC.Fig. 3: Analysis pipeline overview.Fig. 4: Sequencing QC.Fig. 5: Validation of targeted methylation in GM12878 cells.Fig. 6: Evaluating protein binding at regions of interest.Fig. 7: H3K9me3-targeted DiMeLo-seq in D. melanogaster embryos.

图1:DiMeLo-seq协议概述。。图3：分析管道概述。图4：测序QC。图5:GM12878细胞中靶向甲基化的验证。图6：评估感兴趣区域的蛋白质结合。图7:H3K9me3靶向黑腹果蝇胚胎中的DiMeLo-seq。

Data availability

数据可用性

Data generated for this protocol: raw sequencing data are available in the Sequence Read Archive (SRA) under BioProject accession PRJNA855257 and processed data are available on Gene Expression Omnibus (GEO) under accession GSE208125. All raw fast5 sequencing data from the accompanying Altemose et al.

为该协议生成的数据：原始测序数据可在BioProject登录号PRJNA855257下的序列读取档案（SRA）中获得，处理后的数据可在登录号GSE208125下的Gene Expression Omnibus（GEO）上获得。来自伴随的Altemose等人的所有原始fast5测序数据。

manuscript are available in the SRA under BioProject accession PRJNA752170. External data sources used in this protocol: H3K27ac ChIP-seq data in GM12878 available from ENCODE Project Consortium under accession ENCFF218QBO (https://www.encodeproject.org/files/ENCFF218QBO/). H3K27me3 ChIP-seq data in GM12878 available from ENCODE Project Consortium under accession ENCFF119CAV (https://www.encodeproject.org/files/ENCFF119CAV/).

手稿可在SRA的BioProject登录号PRJNA752170下获得。本协议中使用的外部数据源：GM12878中的H3K27ac ChIP-seq数据可从ENCODE项目联盟获得，登录号为ENCFF218QBO(https://www.encodeproject.org/files/ENCFF218QBO/)。GM12878中的H3K27me3 ChIP-seq数据可从ENCODE项目联盟获得，登录号为ENCFF119CAV(https://www.encodeproject.org/files/ENCFF119CAV/)。

H3K4me3 ChIP-seq data in GM12878 available from ENCODE Project Consortium under accession ENCFF228TWF (https://www.encodeproject.org/files/ENCFF228TWF/). H3K27ac CUT&Tag data in GM12878 available on Gene Expression Omnibus (GEO) under accession GSM5530639. H3K27me3 CUT&Tag data in GM12878 available on GEO under accession GSM5530673.

GM12878中的H3K4me3 ChIP-seq数据可从ENCODE项目联盟获得，登录号为ENCFF228TWF(https://www.encodeproject.org/files/ENCFF228TWF/)。GM12878中的H3K27ac切割和标记数据可在Gene Expression Omnibus（GEO）上获得，登录号为GSM5530639。GM12878中的H3K27me3切割和标记数据可在GEO上获得，登录号为GSM5530673。

ATAC-seq data in GM12878 available from ENCODE Project Consortium under accession ENCFF603BJO (https://www.encodeproject.org/files/ENCFF603BJO/). TSS and gene annotations from NCBI RefSeq downloaded from UCSC Genome Browser (https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=refSeqComposite&db=hg38). RNA-seq data in GM12878 available from ENCODE Project Consortium under accession ENCFF978HIY (https://www.encodeproject.org/files/ENCFF978HIY/).

GM12878中的ATAC-seq数据可从ENCODE项目联盟获得，登录号为ENCFF603BJO(https://www.encodeproject.org/files/ENCFF603BJO/)。从UCSC基因组浏览器下载的NCBI RefSeq的TSS和基因注释(https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=refSeqComposite&db=hg38)。GM12878中的RNA-seq数据可从ENCODE项目联盟获得，登录号为ENCFF978HIY(https://www.encodeproject.org/files/ENCFF978HIY/)。

D. melanogaster H3K9me3 ChIP-seq data available on GEO under accession GSE140539. File GSE140539_H3K9me3_sorted_deepnorm_log2_smooth.bw was used..

D、 黑腹果蝇H3K9me3 ChIP-seq数据可在GEO上获得，登录号为GSE140539。使用了文件GSE140539\u H3K9me3\u sorted\u deepnorm\u log2\u smooth.bw。。

Code availability

代码可用性

The dimelo Python package for analysis of DiMeLo-seq data is available on Github: https://github.com/streetslab/dimelo.

Github上提供了用于分析dimelo-seq数据的dimelo Python包：https://github.com/streetslab/dimelo.

ReferencesMikkelsen, T. S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007).Article

参考文献Mikkelsen，T.S。等人。多能和谱系定型细胞中染色质状态的全基因组图谱。自然448553-560（2007）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Robertson, G. et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4, 651–657 (2007).Article

Robertson，G。等人。使用染色质免疫沉淀和大规模平行测序的STAT1 DNA关联的全基因组谱。《自然方法》4651-657（2007）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Johnson, D. S., Mortazavi, A., Myers, R. M. & Wold, B. Genome-wide mapping of in vivo protein–DNA interactions. Science 316, 1497–1502 (2007).Article

Johnson，D.S.，Mortazavi，A.，Myers，R.M。＆Wold，B。体内蛋白质-DNA相互作用的全基因组作图。科学3161497-1502（2007）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).Article

Barski，A。等人。人类基因组中组蛋白甲基化的高分辨率分析。细胞129823-837（2007）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Kaya-Okur, H. S. et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat. Commun. 10, 1930 (2019).Article

Kaya Okur，H.S.等人的CUT＆Tag用于小样本和单细胞的有效表观基因组分析。国家公社。101930（2019）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Skene, P. J., Henikoff, J. G. & Henikoff, S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat. Protoc. 13, 1006–1019 (2018).Article

Skene，P.J.，Henikoff，J.G。＆Henikoff，S。靶向全基因组原位分析，对低细胞数具有高效率。自然协议。131006-1019（2018）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat. Biotechnol. 18, 424–428 (2000).Article

van Steensel，B。＆Henikoff，S。使用栓系dam甲基转移酶鉴定染色质蛋白的体内DNA靶标。美国国家生物技术公司。18424-428（2000）。文章

PubMed

PubMed

Google Scholar

谷歌学者

ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).Article

。人类基因组中DNA元素的综合百科全书。《自然》489,57-74（2012）。文章

Google Scholar

谷歌学者

Altemose, N. et al. DiMeLo-seq: a long-read, single-molecule method for mapping protein–DNA interactions genome wide. Nat. Methods 19, 711–723 (2022).Article

Altemose，N.等人，《DiMeLo-seq：一种用于绘制全基因组蛋白质与DNA相互作用的长读本单分子方法》。自然方法19711-723（2022）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

van Schaik, T., Vos, M., Peric-Hupkes, D., Hn Celie, P. & van Steensel, B. Cell cycle dynamics of lamina-associated DNA. EMBO Rep. 21, e50636 (2020).Article

van Schaik，T.，Vos，M.，Peric-Hupkes，D.，Hn-Celie，P。＆van Steensel，B。薄层相关DNA的细胞周期动力学。。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Stergachis, A. B., Debo, B. M., Haugen, E., Churchman, L. S. & Stamatoyannopoulos, J. A. Single-molecule regulatory architectures captured by chromatin fiber sequencing. Science 368, 1449–1454 (2020).Article

Stergachis，A.B.，Debo，B.M.，Haugen，E.，Churchman，L.S。和Stamatoyannopoulos，J.A。通过染色质纤维测序捕获的单分子调控结构。科学3681449-1454（2020）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Shipony, Z. et al. Long-range single-molecule mapping of chromatin accessibility in eukaryotes. Nat. Methods 17, 319–327 (2020).Article

Shipony，Z.等人。真核生物染色质可及性的远程单分子定位。自然方法17319-327（2020）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Abdulhay, N. J. et al. Massively multiplex single-molecule oligonucleosome footprinting. eLife 9, e59404 (2020).Article

Abdulhay，N.J.等人。大规模多重单分子寡核苷酸足迹。eLife 9，e59404（2020）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Lee, I. et al. Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing. Nat. Methods 17, 1191–1199 (2020).Article

Lee，I.等人。通过纳米孔测序同时分析人类细胞系上的染色质可及性和甲基化。自然方法171191-1199（2020）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Wang, Y. et al. Single-molecule long-read sequencing reveals the chromatin basis of gene expression. Genome Res. 29, 1329–1342 (2019).Article

Wang，Y.等人。单分子长读测序揭示了基因表达的染色质基础。基因组研究291329-1342（2019）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Weng, Z. et al. BIND&MODIFY: a long-range method for single-molecule mapping of chromatin modifications in eukaryotes. Genome Biol. 24, 61 (2023).Article

Weng，Z.等人，《结合与修饰：真核生物染色质修饰单分子作图的远程方法》。基因组生物学。24，61（2023）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Yue, X. et al. Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing. Nat. Commun. 13, 1–14 (2022).Article

Yue，X。等人。通过纳米孔测序同时分析组蛋白修饰和DNA甲基化。国家公社。13，1-14（2022）。文章

Google Scholar

谷歌学者

Statham, A. L. et al. Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA. Genome Res. 22, 1120–1127 (2012).Article

Statham，A.L.等人，染色质免疫沉淀DNA（BisChIP-seq）的亚硫酸氢盐测序直接告知组蛋白修饰DNA的甲基化状态。基因组研究221120-1127（2012）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Brinkman, A. B. et al. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res. 22, 1128–1138 (2012).Article

Brinkman，A.B.等人，序列芯片亚硫酸氢盐测序可以直接进行染色质和DNA甲基化串扰的基因组规模研究。基因组研究221128-1138（2012）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Gamba, R. et al. Enrichment of centromeric DNA from human cells. PLoS Genet. 18, e1010306 (2022).Article

Gamba，R.等人。从人类细胞中富集着丝粒DNA。PLoS Genet。18，e1010306（2022）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Payne, A. et al. Readfish enables targeted nanopore sequencing of gigabase-sized genomes. Nat. Biotechnol. 39, 442–450 (2021).Article

Payne，A。等人Readfish能够对千兆碱基大小的基因组进行靶向纳米孔测序。美国国家生物技术公司。。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Kovaka, S., Fan, Y., Ni, B., Timp, W. & Schatz, M. C. Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED. Nat. Biotechnol. 39, 431–441 (2021).Article

Kovaka，S.，Fan，Y.，Ni，B.，Timp，W。＆Schatz，M.C。通过实时映射未调用的原始电信号来靶向纳米孔测序。美国国家生物技术公司。39431-441（2021）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Hoffman, E. A., Frey, B. L., Smith, L. M. & Auble, D. T. Formaldehyde crosslinking: a tool for the study of chromatin complexes. J. Biol. Chem. 290, 26404–26411 (2015).Article

Hoffman，E.A.，Frey，B.L.，Smith，L.M。＆Auble，D.T。甲醛交联：研究染色质复合物的工具。J、 生物。化学。29026404-26411（2015）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Vogel, M. J., Peric-Hupkes, D. & van Steensel, B. Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nat. Protoc. 2, 1467–1478 (2007).Article

Vogel，M.J.，Peric-Hupkes，D。和van Steensel，B。在哺乳动物细胞中使用DamID检测体内蛋白质-DNA相互作用。自然协议。21467-1478（2007）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Altemose, N. et al. DiMeLo-Seq: directed methylation with long-read sequencing v2. Protocols.io https://www.protocols.io/view/dimelo-seq-directed-methylation-with-long-read-seq-b2u8qezw (2021).De Coster, W., Stovner, E. B. & Strazisar, M. Methplotlib: analysis of modified nucleotides from nanopore sequencing.

Altemose，N。等人DiMeLo-Seq：长读测序的定向甲基化v2。协议.iohttps://www.protocols.io/view/dimelo-seq-directed-methylation-with-long-read-seq-b2u8qezw（2021年）。De Coster，W.，Stovner，E.B。＆Strazisar，M.Methplotlib：从纳米孔测序中分析修饰的核苷酸。

Bioinformatics 36, 3236–3238 (2020).Article .

生物信息学363236-3238（2020）。文章。

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Jain, M. et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat. Biotechnol. 36, 338–345 (2018).Article

Jain，M.等人。具有超长读数的人类基因组的纳米孔测序和组装。美国国家生物技术公司。36338-345（2018）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Brothers, M. & Rine, J. Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae. eLife 11, e75653 (2022).Article

Brothers，M。＆Rine，J。区分酿酒酵母中沉默染色质结构的募集和扩散。eLife 11，e75653（2022）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Srinivasan, M., Sedmak, D. & Jewell, S. Effect of fixatives and tissue processing on the content and integrity of nucleic acids. Am. J. Pathol. 161, 1961–1971 (2002).Article

Srinivasan，M.，Sedmak，D。＆Jewell，S。固定剂和组织加工对核酸含量和完整性的影响。美国J.Pathol。1611961-1971（2002）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Altemose, N. et al. PA-Hia5 protein expression and purification v1. Protocols.io https://www.protocols.io/view/pa-hia5-protein-expression-and-purification-bv82n9ye (2021).Altemose, N. et al. AlphaHOR-RES: a method for enriching centromeric DNA v1. Protocols.io https://www.protocols.io/view/alphahor-res-a-method-for-enriching-centromeric-dn-bv9vn966 (2021).Kim, B.

Altemose，N。等人，PA-Hia5蛋白表达和纯化v1。协议.iohttps://www.protocols.io/view/pa-hia5-protein-expression-and-purification-bv82n9ye（2021年）。Altemose，N。等人。AlphaHOR RES：富集着丝粒DNA v1的方法。协议.iohttps://www.protocols.io/view/alphahor-res-a-method-for-enriching-centromeric-dn-bv9vn966（2021年）。金，B。

Y. et al. Highly contiguous assemblies of 101 drosophilid genomes. eLife 10, e66405 (2021).Article .

Y、 等人。101个果蝇基因组的高度连续组装。eLife 10，e66405（2021）。文章。

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Kim, B. Y., Miller, D. E. & Wang, J. DNA extraction and nanopore library prep from 15-30 whole flies v1. Protocols.io https://www.protocols.io/view/dna-extraction-and-nanopore-library-prep-from-15-3-bdfqi3mw (2021).Luo, Y. et al. New developments on the Encyclopedia of DNA Elements (ENCODE) data portal.

Kim，B.Y.，Miller，D.E。＆Wang，J。DNA提取和纳米孔文库制备，来自15-30只全蝇v1。协议.iohttps://www.protocols.io/view/dna-extraction-and-nanopore-library-prep-from-15-3-bdfqi3mw（2021年）。Luo，Y.等人。DNA元素百科全书（ENCODE）数据门户的新发展。

Nucleic Acids Res. 48, D882–D889 (2020).Article .

核酸研究48，D882–D889（2020）。文章。

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Zhao, L. et al. FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers. Nucleic Acids Res. 49, e125 (2021).Article

Zhao，L。等人。FACT-seq：分析福尔马林固定石蜡包埋的低细胞数样品中的组蛋白修饰。核酸研究49，e125（2021）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Karlić, R., Chung, H.-R., Lasserre, J., Vlahovicek, K. & Vingron, M. Histone modification levels are predictive for gene expression. Proc. Natl Acad. Sci. USA 107, 2926–2931 (2010).Article

Karlić，R.，Chung，H.-R.，Lasserre，J.，Vlahovicek，K。＆Vingron，M。组蛋白修饰水平可预测基因表达。程序。国家科学院。科学。美国1072926–2931（2010）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Cedar, H. & Bergman, Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat. Rev. Genet. 10, 295–304 (2009).Article

Cedar，H。＆Bergman，Y。连接DNA甲基化和组蛋白修饰：模式和范例。Genet自然Rev。10295-304（2009）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Zenk, F. et al. HP1 drives de novo 3D genome reorganization in early Drosophila embryos. Nature 593, 289–293 (2021).Article

Zenk，F。等人，HP1驱动果蝇早期胚胎中的从头3D基因组重组。自然593289-293（2021）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Download referencesAcknowledgementsResearch reported in this publication was supported by the Chan Zuckerberg Biohub, San Francisco, and by the National Human Genome Research Institute and the National Institute of General Medical Sciences of the National Institutes of Health under award number R01HG012383 to A.S., R01GM074728 to A.F.S.

下载参考文献致谢本出版物中报道的研究得到了旧金山Chan Zuckerberg Biohub以及美国国家人类基因组研究所和美国国立卫生研究院国家普通医学科学研究所的支持，授予A.S.的奖项编号为R01HG012383，授予A.F.S.的奖项编号为R01GM074728。

and R35GM139653 to G.K. A.M. is supported by a NSF GRFP award. L.D.B. is supported by Volkswagen Stiftung (98196). N.A. is an HHMI Hanna H. Gray Fellow. A.S. is a Chan Zuckerberg Biohub Investigator and a Pew Scholar in the Biomedical Sciences. The sequencing was carried out by the DNA Technologies and Expression Analysis Core at the UC Davis Genome Center, supported by NIH Shared Instrumentation Grant 1S10OD010786-01.

G.K.A.M.的R35GM139653得到了NSF GRFP奖的支持。五十、 D.B.由大众汽车公司（98196）支持。N、 A.是HHMI Hanna H.Gray的同事。A、 S.是Chan Zuckerberg Biohub的研究员，也是生物医学领域的皮尤学者。。

This project has been made possible in part by grant number 2022-253563 from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation.Author informationAuthor notesNicolas AltemosePresent address: Department of Genetics, Stanford University, Stanford, CA, USAAuthors and AffiliationsDepartment of Bioengineering, University of California, Berkeley, Berkeley, CA, USAAnnie Maslan, Reet Mishra & Aaron StreetsUC Berkeley–UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USAAnnie Maslan & Aaron StreetsCenter for Computational Biology, University of California, Berkeley, Berkeley, CA, USAAnnie Maslan, Jeremy Marcus & Aaron StreetsDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USANicolas Altemose, Lucy D.

该项目部分是由硅谷社区基金会的顾问基金ChanZuckerberg Initiative DAF的2022-253563号赠款实现的。作者信息作者注释Nicolas Altemoseppresent address：斯坦福大学遗传学系，加利福尼亚州斯坦福，美国作者和附属机构加利福尼亚大学伯克利分校生物工程系，加利福尼亚州伯克利，美国安妮·马斯兰，里特·米什拉和亚伦街Suc Berkeley–加州大学伯克利分校生物工程研究生课程，加利福尼亚州伯克利，美国加利福尼亚大学伯克利分校，加利福尼亚州伯克利分校，美国安妮·马斯兰和亚伦街计算生物学系，美国安妮·马斯兰，杰里米·马库斯和亚伦街加利福尼亚大学分子与细胞生物学系伯克利，加利福尼亚州伯克利，美国尼古拉斯·阿尔特摩斯，露西·D。

Brennan & Gary KarpenDepartment of Biochemistry, Stanford University, Stanford, CA, USAKousik Sundararajan & Aaron F. StraightDepartment of BioEngineering and BioMedical Sciences, Lawrence Berkel.

Brennan和Gary KarpenDepartment of Biochemistry，Stanford University，Stanford，CA，USAKousik Sundararajan和Aaron F.Straighted Department of BioEngineering and BioMedical Sciences，Lawrence Berkel。

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PubMed Google ScholarContributionsA.M., N.A. and A.S. designed the study. A.M., N.A. and L.D.B. performed the experiments. A.M., R.M. and J.M. developed dimelo software package. A.M. and N.A. analyzed and interpreted the data. A.M., N.A. and R.M. made the figures. A.M. and J.M.

PubMed谷歌学术贡献。M、 ，N.A.和A.S.设计了这项研究。A、 M.，N.A.和L.D.B.进行了实验。A、 M.，R.M.和J.M.开发了dimelo软件包。A、 M.和N.A.分析并解释了数据。A、 M.，N.A.和R.M.制作了这些数字。A、 M.和J.M。

wrote the manuscript, with input from N.A., R.M., L.D.B., K.S., G.K., A.F.S. and A.S. A.S. and N.A. supervised the study.Corresponding authorCorrespondence to.

在N.A.，R.M.，L.D.B.，K.S.，G.K.，A.F.S.和A.S.A.S.的投入下撰写了手稿，N.A.监督了这项研究。对应作者对应。

Aaron Streets.Ethics declarations

亚伦街。道德宣言

Competing interests

相互竞争的利益

N.A., A.M., K.S., A.F.S. and A.S. are co-inventors on a patent application related to this work. The remaining authors declare no competing interests.

N、 A.，A.M.，K.S.，A.F.S.和A.S.是与这项工作相关的专利申请的共同发明人。其余作者声明没有利益冲突。

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同行评审

Peer review information

同行评审信息

Nature Protocols thanks the anonymous reviewer(s) for their contribution to the peer review of this work.

Nature Protocols感谢匿名审稿人对这项工作的同行评审做出的贡献。

Additional informationPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.Related linksKey reference using this protocolAltemose, N. et al. Nat. Methods 19, 711–723 (2022): https://doi.org/10.1038/s41592-022-01475-6Supplementary informationSupplementary InformationSupplementary Methods and Table 1.Rights and permissionsSpringer Nature or its licensor (e.g.

。使用此协议的相关linksKey参考，N.等人，《自然方法》19711–723（2022）：https://doi.org/10.1038/s41592-022-01475-6Supplementary信息补充信息补充方法和表1。权利和许可原告性质或其许可人（例如。

a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.Reprints and permissionsAbout this articleCite this articleMaslan, A., Altemose, N., Marcus, J.

协会或其他合作伙伴）根据与作者或其他权利持有人的出版协议对本文拥有专有权；本文接受稿件版本的作者自行存档仅受此类出版协议和适用法律的条款管辖。转载和许可本文引用本文Maslan，A.，Altemose，N.，Marcus，J。

et al. Mapping protein–DNA interactions with DiMeLo-seq..

等人。用DiMeLo-seq绘制蛋白质-DNA相互作用图。。

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