{"id":["DOI:10.1126/sciadv.adu3308"],"title":["Combinatorial profiling of multiple histone modifications and transcriptome in single cells using scMTR-seq"],"publication_date":["2025-08-06"],"authors":{"ORCID:0000-0003-2802-5392":{"id":["ORCID:0000-0003-2802-5392"],"family_name":["Wang"],"personal_name":["Yang"],"affiliations":{"ROR:01d5qpn59":{"organization_name":["Babraham Institute"]}},"HDBItheme":["Early"]},"ORCID:0000-0001-9677-7532":{"id":["ORCID:0000-0001-9677-7532"],"family_name":["Li"],"personal_name":["Jingyu"],"affiliations":{"ROR:01d5qpn59":{"organization_name":["Babraham Institute"]}}},"ORCID:0000-0001-6240-7701":{"id":["ORCID:0000-0001-6240-7701"],"family_name":["Malcolm"],"personal_name":["Andrew A."],"affiliations":{"ROR:01d5qpn59":{"organization_name":["Babraham Institute"]},"ROR:05nz0zp31":{"organization_name":["Wellcome/MRC Cambridge Stem Cell Institute"]}}},"AUTHTEMP:00075":{"id":["AUTHTEMP:00075"],"family_name":["Mansfield"],"personal_name":["William"],"affiliations":{"ROR:01d5qpn59":{"organization_name":["Babraham Institute"]}}},"ORCID:0000-0002-6183-491X":{"id":["ORCID:0000-0002-6183-491X"],"family_name":["Clark"],"personal_name":["Stephen J."],"affiliations":{"ROR:01d5qpn59":{"organization_name":["Babraham Institute"]}}},"ORCID:0000-0003-3199-3722":{"id":["ORCID:0000-0003-3199-3722"],"family_name":["Argelaguet"],"personal_name":["Ricard"],"affiliations":{"ROR:01d5qpn59":{"organization_name":["Babraham Institute"]}}},"ORCID:0000-0002-0975-1121":{"id":["ORCID:0000-0002-0975-1121"],"family_name":["Biggins"],"personal_name":["Laura"],"affiliations":{"ROR:01d5qpn59":{"organization_name":["Babraham Institute"]}}},"ORCID:0000-0002-2574-9611":{"id":["ORCID:0000-0002-2574-9611"],"family_name":["Acton"],"personal_name":["Richard J."],"affiliations":{"ROR:01d5qpn59":{"organization_name":["Babraham Institute"]}},"HDBItheme":["Data Management"]},"ORCID:0000-0002-5006-3507":{"id":["ORCID:0000-0002-5006-3507"],"family_name":["Andrews"],"personal_name":["Simon"],"affiliations":{"ROR:01d5qpn59":{"organization_name":["Babraham Institute"]}}},"ORCID:0000-0003-0216-9881":{"id":["ORCID:0000-0003-0216-9881"],"family_name":["Reik"],"personal_name":["Wolf"],"affiliations":{"ROR:01d5qpn59":{"organization_name":["Babraham Institute"]},"ROR:05467hx49":{"organization_name":["Altos Labs"]}}},"ORCID:0000-0002-9762-5634":{"id":["ORCID:0000-0002-9762-5634"],"family_name":["Kelsey"],"personal_name":["Gavin"],"affiliations":{"ROR:01d5qpn59":{"organization_name":["Babraham Institute"]},"ROR:02hmmse52":{"organization_name":["The Loke Centre for Trophoblast Research"]},"ROR:013meh722":{"organization_name":["University of Cambridge"]}},"HDBItheme":["Early"]},"ORCID:0000-0002-9601-5949":{"id":["ORCID:0000-0002-9601-5949"],"family_name":["Rugg-Gunn"],"personal_name":["Peter J."],"affiliations":{"1":{}},"HDBItheme":["Early"]}},"abstract":["Profiling combinations of histone modifications identifies gene regulatory elements in different states and discovers features controlling transcriptional and epigenetic programs. However, efforts to map chromatin states in complex, heterogeneous samples are hindered by the lack of methods that can profile multiple histone modifications together with transcriptomes in individual cells. Here, we describe single-cell multitargets and mRNA sequencing (scMTR-seq), a high-throughput method that enables simultaneous profiling of six histone modifications and transcriptome in single cells. We apply scMTR-seq to uncover dynamic and coordinated changes in chromatin states and transcriptomes during human endoderm differentiation. We also use scMTR-seq to produce lineage-resolved chromatin maps and gene regulatory networks in mouse blastocysts, revealing epigenetic asymmetries at gene regulatory regions between the three embryo lineages and identifying Trps1 as a potential repressor in epiblast cells of trophectoderm-associated enhancer networks and their target genes. Together, scMTR-seq enables investigation of combinatorial chromatin landscapes in a broad range of heterogeneous samples, providing insights into epigenetic regulatory systems."],"HDBItheme":["Early"],"protocols":{"DOI:10.17504/protocols.io.yxmvmb7dog3p/v1":{"id":["DOI:10.17504/protocols.io.yxmvmb7dog3p/v1"],"title":["scMTR-seq"],"description":["Here, we describe a protocol for scMTR-seq (single cell multi-targets and mRNA sequencing), which is a multi-omics sequencing technology that can simultaneously profile multiple histone modifications or other chromatin-bound proteins and transcriptome in the same single cells. scMTR-seq has high sensitivity, high cell recovery and is highly scalable in terms of starting material requirement. The protocol has the following steps: i) pre-assemble antibodies specific for each target histone modification or protein with indexed proteinA-Tn5-adapters; ii) perform in situ Tn5-mediated tagmentation with indexed complexes; iii) capture nuclear mRNA with a barcoded poly-T primer followed by in situ reverse transcription; iv) label single cells using split-pool combinatorial barcoding. We have applied scMTR-seq to profile histone modifications and transcriptomes in single cells from a broad range of heterogeneous samples including pluripotent stem cell differentiation and mouse pre-implantation embryos."],"authors":{"ORCID:0000-0003-2802-5392":{"id":["ORCID:0000-0003-2802-5392"],"family_name":["Wang"],"personal_name":["Yang"],"affiliations":{"ROR:01d5qpn59":{"organization_name":["Babraham Institute"]}},"HDBItheme":["Early"]},"ORCID:0000-0002-9601-5949":{"id":["ORCID:0000-0002-9601-5949"],"family_name":["Rugg-Gunn"],"personal_name":["Peter J."],"affiliations":{"1":{}},"HDBItheme":["Early"]}}}},"datasets":{"GEO:GSE277856":{"id":["GEO:GSE277856"],"title":["Combinatorial profiling of multiple histone modifications and transcriptome in single cells using scMTR-seq"],"description":["Profiling combinations of histone modifications identifies gene regulatory elements in different states and discovers features controlling transcriptional and epigenetic programmes. However, efforts to map chromatin states in defined cell types are hindered by the lack of methods that can profile multiple histone modifications together with transcriptome in individual cells. Here we describe single-cell Multi-Targets and mRNA sequencing (scMTR-seq), which enables simultaneous profiling of six histone modifications and transcriptome in single cells. As a proof of concept, we apply scMTR-seq to uncover the dynamics of chromatin state change during human endoderm differentiation. We also use scMTR-seq to produce lineage-resolved chromatin maps and gene regulatory networks in mouse blastocysts, revealing striking epigenetic asymmetries at gene regulatory regions between the three embryo lineages. We identify the transcription factor Trps1 as a potential repressor in epiblast cells of trophectoderm-associated enhancer networks and their target genes. Together, scMTR-seq enables investigation of combinatorial epigenetic modalities in low-cell number and heterogeneous samples."],"tags":["sequencing"]}},"code":{"DOI:10.5281/zenodo.15046901":{"id":["DOI:10.5281/zenodo.15046901"],"title":["A Nextflow pipeline for analysing scMTR-seq data (a single cell multiomics method)"],"description":["A Nextflow pipeline for analysing scMTR-seq data (a single cell multiomics method)"]},"DOI:10.5281/zenodo.15046989":{"id":["DOI:10.5281/zenodo.15046989"],"title":["Code for reproducing the analysis / figures in the manuscript: Combinatorial profiling of multiple histone modifications and transcriptome in single cells using scMTR-seq"],"description":["Code for reproducing the analysis / figures in the manuscript: Combinatorial profiling of multiple histone modifications and transcriptome in single cells using scMTR-seq"]}}}