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Chromatin accessibility dynamics of myogenesis at single cell resolution

https://doi.org/10.1101/155473
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What this work says

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

inferredcites →https://doi.org/10.1016/0092-8674(90)90214-yopenalex-snapshot
The protein Id: A negative regulator of helix-loop-helix DNA binding proteins
inferredcites →https://doi.org/10.1016/0092-8674(95)90139-6openalex-snapshot
Cooperative activation of muscle gene expression by MEF2 and myogenic bHLH proteins
inferredcites →https://doi.org/10.1016/0092-8674(95)90385-2openalex-snapshot
The retinoblastoma protein and cell cycle control
inferredcites →https://doi.org/10.1016/j.ajhg.2014.10.004openalex-snapshot
Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases
inferredcites →https://doi.org/10.1016/j.cell.2014.11.021openalex-snapshot
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
inferredcites →https://doi.org/10.1016/j.cell.2015.11.024openalex-snapshot
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription
inferredcites →https://doi.org/10.1016/j.celrep.2015.02.055openalex-snapshot
Conversion of MyoD to a Neurogenic Factor: Binding Site Specificity Determines Lineage
inferredcites →https://doi.org/10.1016/j.devcel.2010.02.014openalex-snapshot
Genome-wide MyoD Binding in Skeletal Muscle Cells: A Potential for Broad Cellular Reprogramming
inferredcites →https://doi.org/10.1016/j.molcel.2007.08.021openalex-snapshot
Functional Interdependence at the Chromatin Level between the MKK6/p38 and IGF1/PI3K/AKT Pathways during Muscle Differentiation
inferredcites →https://doi.org/10.1016/s1097-2765(00)80005-2openalex-snapshot
Differential Roles of p300 and PCAF Acetyltransferases in Muscle Differentiation
inferredcites →https://doi.org/10.1016/s1097-2765(02)00781-5openalex-snapshot
Looping and Interaction between Hypersensitive Sites in the Active β-globin Locus
inferredcites →https://doi.org/10.1016/s1097-2765(04)00260-6openalex-snapshot
Pbx Marks Genes for Activation by MyoD Indicating a Role for a Homeodomain Protein in Establishing Myogenic Potential
inferredcites →https://doi.org/10.1023/a:1024922626726openalex-snapshot
Spatial organization of gene expression: the active chromatin hub
inferredcites →https://doi.org/10.1038/nature11232openalex-snapshot
The accessible chromatin landscape of the human genome
inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot
An integrated encyclopedia of DNA elements in the human genome
inferredcites →https://doi.org/10.1038/nbt.2859openalex-snapshot
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
inferredcites →https://doi.org/10.1038/nbt.3199openalex-snapshot
Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers
inferredcites →https://doi.org/10.1038/ng1378openalex-snapshot
p38 pathway targets SWI-SNF chromatin-remodeling complex to muscle-specific loci
inferredcites →https://doi.org/10.1038/nmeth.3033openalex-snapshot
Sets and intersections
inferredcites →https://doi.org/10.1038/nmeth.4402openalex-snapshot
Reversed graph embedding resolves complex single-cell trajectories
inferredcites →https://doi.org/10.1038/nprot.2012.101openalex-snapshot
Identifying ChIP-seq enrichment using MACS
inferredcites →https://doi.org/10.1038/nrg3454openalex-snapshot
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data
inferredcites →https://doi.org/10.1073/pnas.0404192101openalex-snapshot
In vitro transcription system delineates the distinct roles of the coactivators pCAF and p300 during MyoD/E47-dependent transactivation
inferredcites →https://doi.org/10.1073/pnas.1518552112openalex-snapshot
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
inferredcites →https://doi.org/10.1073/pnas.93.18.9384openalex-snapshot
Chromatin structure and gene expression.
inferredcites →https://doi.org/10.1080/01621459.2012.737745openalex-snapshot
Optimal Detection of Changepoints With a Linear Computational Cost
inferredcites →https://doi.org/10.1088/1742-5468/2008/10/p10008openalex-snapshot
Fast unfolding of communities in large networks
inferredcites →https://doi.org/10.1093/bib/bbu034openalex-snapshot
Predictive modelling of gene expression from transcriptional regulatory elements
inferredcites →https://doi.org/10.1093/bioinformatics/btr064openalex-snapshot
FIMO: scanning for occurrences of a given motif
inferredcites →https://doi.org/10.1093/biostatistics/kxm045openalex-snapshot
Sparse inverse covariance estimation with the graphical lasso
inferredcites →https://doi.org/10.1093/nar/27.18.3752openalex-snapshot
A conserved motif N-terminal to the DNA-binding domains of myogenic bHLH transcription factors mediates cooperative DNA binding with Pbx-Meis1/Prep1
inferredcites →https://doi.org/10.1093/nar/gkt111openalex-snapshot
Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods
inferredcites →https://doi.org/10.1093/nar/gkt374openalex-snapshot
Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers
inferredcites →https://doi.org/10.1093/nar/gkv1176openalex-snapshot
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles
inferredcites →https://doi.org/10.1101/086025openalex-snapshot
A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types
inferredcites →https://doi.org/10.1111/j.1467-9868.2005.00503.xopenalex-snapshot
Regularization and Variable Selection Via the Elastic Net
inferredcites →https://doi.org/10.1126/science.1222794openalex-snapshot
Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
inferredcites →https://doi.org/10.1126/science.aab1601openalex-snapshot
Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
inferredcites →https://doi.org/10.1128/mcb.00916-12openalex-snapshot
Comparison of Genome-Wide Binding of MyoD in Normal Human Myogenic Cells and Rhabdomyosarcomas Identifies Regional and Local Suppression of Promyogenic Transcription Factors
inferredcites →https://doi.org/10.1128/mcb.17.2.1010openalex-snapshot
Molecular Mechanisms of Myogenic Coactivation by p300: Direct Interaction with the Activation Domain of MyoD and with the MADS Box of MEF2C
inferredcites →https://doi.org/10.1128/mcb.25.10.3997-4009.2005openalex-snapshot
MyoD Targets Chromatin Remodeling Complexes to the Myogenin Locus Prior to Forming a Stable DNA-Bound Complex
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/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1242/dev.003905openalex-snapshot
Pbx homeodomain proteins direct Myod activity to promote fast-muscle differentiation
inferredcites →https://doi.org/10.1242/jcs.111.6.769openalex-snapshot
Cell heterogeneity upon myogenic differentiation: down-regulation of MyoD and Myf-5 generates ‘reserve cells’
inferredcites →https://doi.org/10.1242/jcs.114.2.303openalex-snapshot
A calcineurin- and NFAT-dependent pathway regulates Myf5 gene expression in skeletal muscle reserve cells
inferredcites →https://doi.org/10.1371/journal.pone.0009425openalex-snapshot
The Core Binding Factor CBF Negatively Regulates Skeletal Muscle Terminal Differentiation
inferredcites →https://doi.org/10.1371/journal.pone.0013984openalex-snapshot
Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

What points at this work

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

inferred← citeshttps://doi.org/10.1007/978-1-4939-9802-9_3openalex-snapshot
Chromatin Epigenomics in Muscle Development and Disease
inferred← citeshttps://doi.org/10.1016/j.cels.2020.02.003openalex-snapshot
Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe
inferred← citeshttps://doi.org/10.1016/j.tig.2018.06.001openalex-snapshot
Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation
inferred← citeshttps://doi.org/10.1038/nature25981openalex-snapshot
The cis-regulatory dynamics of embryonic development at single-cell resolution
inferred← citeshttps://doi.org/10.1038/s41467-018-04629-3openalex-snapshot
Unsupervised clustering and epigenetic classification of single cells
inferred← citeshttps://doi.org/10.1038/s41467-019-09483-5openalex-snapshot
Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory
inferred← citeshttps://doi.org/10.1038/s41467-019-09670-4openalex-snapshot
Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM
inferred← citeshttps://doi.org/10.1038/s41586-019-0969-xopenalex-snapshot
The single-cell transcriptional landscape of mammalian organogenesis
inferred← citeshttps://doi.org/10.1038/s41586-021-03933-1openalex-snapshot
Genetic and epigenetic coordination of cortical interneuron development
inferred← citeshttps://doi.org/10.1093/bfgp/elx046openalex-snapshot
Mapping gene regulatory networks from single-cell omics data
inferred← citeshttps://doi.org/10.1093/nar/gky950openalex-snapshot
Classifying cells with Scasat, a single-cell ATAC-seq analysis tool
inferred← citeshttps://doi.org/10.1101/370346openalex-snapshot
Cis-topic modelling of single-cell epigenomes
inferred← citeshttps://doi.org/10.1101/438937openalex-snapshot
Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self-Organizing Maps
inferred← citeshttps://doi.org/10.1186/s43556-020-00009-wopenalex-snapshot
Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1006555openalex-snapshot
Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps
inferred← citeshttps://doi.org/10.15252/msb.20178046openalex-snapshot
Using single‐cell genomics to understand developmental processes and cell fate decisions
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