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Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification

https://doi.org/10.1101/519207

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Methylation status of CpG-rich islands on active and inactive mouse X chromosomes

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Neural differentiation of Xenopus laevis ectoderm takes place after disaggregation and delayed reaggregation without inducer

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Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development

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A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

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Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation

inferredcites →https://doi.org/10.1016/j.devcel.2012.06.011openalex-snapshot

Smchd1-Dependent and -Independent Pathways Determine Developmental Dynamics of CpG Island Methylation on the Inactive X Chromosome

inferredcites →https://doi.org/10.1016/j.devcel.2013.10.009openalex-snapshot

A Common Set of DNA Regulatory Elements Shapes Drosophila Appendages

inferredcites →https://doi.org/10.1016/j.devcel.2016.02.020openalex-snapshot

Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo

inferredcites →https://doi.org/10.1016/j.devcel.2016.09.012openalex-snapshot

Single-Cell Approaches: Pandora’s Box of Developmental Mechanisms

inferredcites →https://doi.org/10.1016/j.molcel.2010.05.004openalex-snapshot

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

inferredcites →https://doi.org/10.1016/j.molcel.2013.01.038openalex-snapshot

Modification of Enhancer Chromatin: What, How, and Why?

inferredcites →https://doi.org/10.1016/j.stem.2008.06.018openalex-snapshot

Establishment of Endoderm Progenitors by SOX Transcription Factor Expression in Human Embryonic Stem Cells

inferredcites →https://doi.org/10.1016/j.stem.2014.05.005openalex-snapshot

Epigenomic Comparison Reveals Activation of “Seed” Enhancers during Transition from Naive to Primed Pluripotency

inferredcites →https://doi.org/10.1016/j.stem.2014.05.008openalex-snapshot

Reprogramming the Methylome: Erasing Memory and Creating Diversity

inferredcites →https://doi.org/10.1016/j.stem.2018.08.016openalex-snapshot

Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate

inferredcites →https://doi.org/10.1016/j.tcb.2017.10.008openalex-snapshot

Epigenome in Early Mammalian Development: Inheritance, Reprogramming and Establishment

inferredcites →https://doi.org/10.1016/j.tig.2016.12.003openalex-snapshot

Single-Cell Multiomics: Multiple Measurements from Single Cells

inferredcites →https://doi.org/10.1016/j.ydbio.2012.12.004openalex-snapshot

The mesenchymal architecture of the cranial mesoderm of mouse embryos is disrupted by the loss of Twist1 function

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DNA Methyltransferases Dnmt3a and Dnmt3b Are Essential for De Novo Methylation and Mammalian Development

inferredcites →https://doi.org/10.1016/s0896-6273(01)00263-xopenalex-snapshot

Direct Neural Fate Specification from Embryonic Stem Cells

inferredcites →https://doi.org/10.1038/cr.2017.82openalex-snapshot

Single-cell multi-omics sequencing of mouse early embryos and embryonic stem cells

inferredcites →https://doi.org/10.1038/emboj.2011.210openalex-snapshot

DNA methylation status predicts cell type‐specific enhancer activity

inferredcites →https://doi.org/10.1038/nature10960openalex-snapshot

A unique regulatory phase of DNA methylation in the early mammalian embryo

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The DNA methylation landscape of human early embryos

inferredcites →https://doi.org/10.1038/nature13581openalex-snapshot

DNA methylation dynamics of the human preimplantation embryo

inferredcites →https://doi.org/10.1038/nature18606openalex-snapshot

The landscape of accessible chromatin in mammalian preimplantation embryos

inferredcites →https://doi.org/10.1038/nature18633openalex-snapshot

Resolving early mesoderm diversification through single-cell expression profiling

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Allelic reprogramming of the histone modification H3K4me3 in early mammalian development

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TET-mediated DNA demethylation controls gastrulation by regulating Lefty–Nodal signalling

inferredcites →https://doi.org/10.1038/nature23891openalex-snapshot

Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer

inferredcites →https://doi.org/10.1038/nature25981openalex-snapshot

The cis-regulatory dynamics of embryonic development at single-cell resolution

inferredcites →https://doi.org/10.1038/nbt.3129openalex-snapshot

Integrated genome and transcriptome sequencing of the same cell

inferredcites →https://doi.org/10.1038/ncomms7315openalex-snapshot

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos

inferredcites →https://doi.org/10.1038/ng.3522openalex-snapshot

Active DNA demethylation at enhancers during the vertebrate phylotypic period

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nmeth.3035openalex-snapshot

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

inferredcites →https://doi.org/10.1038/nmeth.3317openalex-snapshot

HISAT: a fast spliced aligner with low memory requirements

inferredcites →https://doi.org/10.1038/nmeth.3370openalex-snapshot

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

inferredcites →https://doi.org/10.1038/nmeth.3728openalex-snapshot

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

inferredcites →https://doi.org/10.1038/nmeth.4236openalex-snapshot

SC3: consensus clustering of single-cell RNA-seq data

inferredcites →https://doi.org/10.1038/nprot.2014.006openalex-snapshot

Full-length RNA-seq from single cells using Smart-seq2

inferredcites →https://doi.org/10.1038/nprot.2016.138openalex-snapshot

Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq

inferredcites →https://doi.org/10.1038/nprot.2016.187openalex-snapshot

Genome-wide base-resolution mapping of DNA methylation in single cells using single-cell bisulfite sequencing (scBS-seq)

inferredcites →https://doi.org/10.1038/nrg2084openalex-snapshot

Gene function in mouse embryogenesis: get set for gastrulation

inferredcites →https://doi.org/10.1038/nrg3354openalex-snapshot

DNA methylation: roles in mammalian development

inferredcites →https://doi.org/10.1038/nrm2618openalex-snapshot

Making a commitment: cell lineage allocation and axis patterning in the early mouse embryo

inferredcites →https://doi.org/10.1038/nrn786openalex-snapshot

Neural induction, the default model and embryonic stem cells

inferredcites →https://doi.org/10.1038/s41467-018-03149-4openalex-snapshot

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

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Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation

inferredcites →https://doi.org/10.1038/s41556-018-0123-2openalex-snapshot

Single-cell multi-omics sequencing of human early embryos

inferredcites →https://doi.org/10.1038/s41586-018-0048-8openalex-snapshot

Pluripotency factors functionally premark cell-type-restricted enhancers in ES cells

inferredcites →https://doi.org/10.1038/s41586-019-1184-5openalex-snapshot

Molecular recording of mammalian embryogenesis

inferredcites →https://doi.org/10.1038/s41588-017-0003-xopenalex-snapshot

Dynamic epigenomic landscapes during early lineage specification in mouse embryos

inferredcites →https://doi.org/10.1038/s41588-017-0007-6openalex-snapshot

Single-cell DNA methylome sequencing of human preimplantation embryos

inferredcites →https://doi.org/10.1073/pnas.0401866101openalex-snapshot

Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome

inferredcites →https://doi.org/10.1073/pnas.0914005107openalex-snapshot

Independent filtering increases detection power for high-throughput experiments

inferredcites →https://doi.org/10.1073/pnas.1016071107openalex-snapshot

Histone H3K27ac separates active from poised enhancers and predicts developmental state

inferredcites →https://doi.org/10.1074/jbc.m117.780585openalex-snapshot

Single-cell analysis reveals lineage segregation in early post-implantation mouse embryos

inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot

edgeR : a Bioconductor package for differential expression analysis of digital gene expression data

inferredcites →https://doi.org/10.1093/bioinformatics/btr167openalex-snapshot

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

inferredcites →https://doi.org/10.1093/bioinformatics/btt656openalex-snapshot

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

inferredcites →https://doi.org/10.1093/nar/gku818openalex-snapshot

TELP, a sensitive and versatile library construction method for next-generation sequencing

inferredcites →https://doi.org/10.1093/nar/gkv1157openalex-snapshot

Ensembl 2016

inferredcites →https://doi.org/10.1093/nar/gkx1126openalex-snapshot

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

inferredcites →https://doi.org/10.1101/gad.11.8.1061openalex-snapshot

Requirement of the transcription factor GATA4 for heart tube formation and ventral morphogenesis.

inferredcites →https://doi.org/10.1101/gad.234294.113openalex-snapshot

DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos

inferredcites →https://doi.org/10.1101/gr.226233.117openalex-snapshot

Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans

inferredcites →https://doi.org/10.1101/pdb.prot4358openalex-snapshot

Collecting Zygotes and Removing Cumulus Cells With Hyaluronidase

inferredcites →https://doi.org/10.1111/j.2517-6161.1995.tb02031.xopenalex-snapshot

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

inferredcites →https://doi.org/10.1126/science.aan3235openalex-snapshot

The Drosophila embryo at single-cell transcriptome resolution

inferredcites →https://doi.org/10.1126/science.aan6826openalex-snapshot

Single-cell epigenomics: Recording the past and predicting the future

inferredcites →https://doi.org/10.1126/science.aau0730openalex-snapshot

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

inferredcites →https://doi.org/10.1146/annurev-cellbio-092910-154043openalex-snapshot

Gastrulation: Making and Shaping Germ Layers

inferredcites →https://doi.org/10.1186/1471-2105-11-165openalex-snapshot

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot

Model-based Analysis of ChIP-Seq (MACS)

inferredcites →https://doi.org/10.1186/s13059-014-0545-5openalex-snapshot

Ontogeny of CpG island methylation and specificity of DNMT3 methyltransferases during embryonic development in the mouse

inferredcites →https://doi.org/10.1186/s13059-015-0844-5openalex-snapshot

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

inferredcites →https://doi.org/10.1186/s13059-016-0950-zopenalex-snapshot

Simultaneous profiling of transcriptome and DNA methylome from a single cell

inferredcites →https://doi.org/10.1242/dev.028415openalex-snapshot

Foxa2 regulates polarity and epithelialization in the endoderm germ layer of the mouse embryo

inferredcites →https://doi.org/10.1242/dev.147322openalex-snapshot

Functional characterisation of cis-regulatory elements governing dynamic Eomes expression in the early mouse embryo

inferredcites →https://doi.org/10.12688/f1000research.9501.2openalex-snapshot

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor

inferredcites →https://doi.org/10.15252/msb.20178046openalex-snapshot

Using single‐cell genomics to understand developmental processes and cell fate decisions

inferredcites →https://doi.org/10.15252/msb.20178124openalex-snapshot

Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets

inferredcites →https://doi.org/10.4252/wjsc.v6.i3.305openalex-snapshot

Sox2, a key factor in the regulation of pluripotency and neural differentiation

inferredcites →https://doi.org/10.7554/elife.02224openalex-snapshot

The transcription factor Pou3f1 promotes neural fate commitment via activation of neural lineage genes and inhibition of external signaling pathways

inferredcites →https://doi.org/10.7554/elife.23203openalex-snapshot

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/bs.ctdb.2019.11.012openalex-snapshot

Guts and gastrulation: Emergence and convergence of endoderm in the mouse embryo

inferred← citeshttps://doi.org/10.1016/j.omtm.2020.04.016openalex-snapshot

Vector Copy Distribution at a Single-Cell Level Enhances Analytical Characterization of Gene-Modified Cell Therapies

inferred← citeshttps://doi.org/10.1016/j.tibtech.2020.02.013openalex-snapshot

Integrative Methods and Practical Challenges for Single-Cell Multi-omics

inferred← citeshttps://doi.org/10.1016/j.tplants.2020.04.016openalex-snapshot

Single-Cell Genomics and Epigenomics: Technologies and Applications in Plants

inferred← citeshttps://doi.org/10.1038/s41556-019-0423-1openalex-snapshot

Eomes and Brachyury control pluripotency exit and germ-layer segregation by changing the chromatin state

inferred← citeshttps://doi.org/10.1093/bib/bbab024openalex-snapshot

Advances in bulk and single-cell multi-omics approaches for systems biology and precision medicine

inferred← citeshttps://doi.org/10.1093/bib/bbz070openalex-snapshot

Consistency and overfitting of multi-omics methods on experimental data

inferred← citeshttps://doi.org/10.1101/768507openalex-snapshot

Xmas ESC: A new female embryonic stem cell system that reveals the BAF complex as a key regulator of the establishment of X chromosome inactivation

inferred← citeshttps://doi.org/10.1186/s13059-020-02015-1openalex-snapshot

MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data

inferred← citeshttps://doi.org/10.1242/dev.179788openalex-snapshot

Cellular diversity and lineage trajectory: insights from mouse single cell transcriptomes

inferred← citeshttps://doi.org/10.70675/7612d87bz4c9ez49e6z87d4zb159d5924480openalex-snapshot

Deciphering the role of DNA methylation in early cellular transitions

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