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Chromatin architecture reorganisation during neuronal cell differentiation in Drosophila genome

https://doi.org/10.1101/395822
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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/j.cell.2012.01.010openalex-snapshot
Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome
inferredcites →https://doi.org/10.1016/j.cell.2013.04.053openalex-snapshot
Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment
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.2015.04.004openalex-snapshot
Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions
inferredcites →https://doi.org/10.1016/j.cell.2017.03.024openalex-snapshot
Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription
inferredcites →https://doi.org/10.1016/j.cell.2017.05.004openalex-snapshot
Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization
inferredcites →https://doi.org/10.1016/j.cell.2017.07.006openalex-snapshot
The Ground State and Evolution of Promoter Region Directionality
inferredcites →https://doi.org/10.1016/j.cell.2017.09.043openalex-snapshot
Multiscale 3D Genome Rewiring during Mouse Neural Development
inferredcites →https://doi.org/10.1016/j.celrep.2012.08.034openalex-snapshot
Defining the Status of RNA Polymerase at Promoters
inferredcites →https://doi.org/10.1016/j.celrep.2015.02.004openalex-snapshot
Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture
inferredcites →https://doi.org/10.1016/j.cels.2016.07.002openalex-snapshot
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
inferredcites →https://doi.org/10.1016/j.molcel.2012.08.031openalex-snapshot
Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains
inferredcites →https://doi.org/10.1016/j.molcel.2012.10.021openalex-snapshot
Order from Chaos in the Nucleus
inferredcites →https://doi.org/10.1016/j.molcel.2015.02.023openalex-snapshot
Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing
inferredcites →https://doi.org/10.1016/j.molcel.2017.07.022openalex-snapshot
Evolutionarily Conserved Principles Predict 3D Chromatin Organization
inferredcites →https://doi.org/10.1038/207785a0openalex-snapshot
Synthesis of Ribonucleic Acid by the X-Chromosomes of Drosophila melanogaster and the Problem of Dosage Compensation
inferredcites →https://doi.org/10.1038/emboj.2013.111openalex-snapshot
Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor
inferredcites →https://doi.org/10.1038/nature09725openalex-snapshot
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster
inferredcites →https://doi.org/10.1038/nature11049openalex-snapshot
Spatial partitioning of the regulatory landscape of the X-inactivation centre
inferredcites →https://doi.org/10.1038/nature11082openalex-snapshot
Topological domains in mammalian genomes identified by analysis of chromatin interactions
inferredcites →https://doi.org/10.1038/nature13417openalex-snapshot
Enhancer loops appear stable during development and are associated with paused polymerase
inferredcites →https://doi.org/10.1038/nature14222openalex-snapshot
Chromatin architecture reorganization during stem cell differentiation
inferredcites →https://doi.org/10.1038/nature21711openalex-snapshot
Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition
inferredcites →https://doi.org/10.1038/nature24281openalex-snapshot
Two independent modes of chromatin organization revealed by cohesin removal
inferredcites →https://doi.org/10.1038/ng2049openalex-snapshot
Using FlyAtlas to identify better Drosophila melanogaster models of human disease
inferredcites →https://doi.org/10.1038/nrg.2016.112openalex-snapshot
Organization and function of the 3D genome
inferredcites →https://doi.org/10.1038/nsmb.2509openalex-snapshot
Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures
inferredcites →https://doi.org/10.1038/s41467-017-00524-5openalex-snapshot
Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation
inferredcites →https://doi.org/10.1038/s41467-017-02525-wopenalex-snapshot
High-resolution TADs reveal DNA sequences underlying genome organization in flies
inferredcites →https://doi.org/10.1073/pnas.1317788111openalex-snapshot
Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells
inferredcites →https://doi.org/10.1073/pnas.1701291114openalex-snapshot
Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp698openalex-snapshot
Fast and accurate long-read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/genetics/165.3.1167openalex-snapshot
Study of Dosage Compensation in Drosophila
inferredcites →https://doi.org/10.1093/nar/gku1099openalex-snapshot
FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations
inferredcites →https://doi.org/10.1093/nar/gku1269openalex-snapshot
Estimating binding properties of transcription factors from genome-wide binding profiles
inferredcites →https://doi.org/10.1093/nar/gkw1114openalex-snapshot
Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture
inferredcites →https://doi.org/10.1093/nar/gkx716openalex-snapshot
Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S. pombe
inferredcites →https://doi.org/10.1101/130070openalex-snapshot
Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions
inferredcites →https://doi.org/10.1101/164590openalex-snapshot
Resolving systematic errors in widely-used enhancer activity assays in human cells enables genome-wide functional enhancer characterization
inferredcites →https://doi.org/10.1101/gr.110098.110openalex-snapshot
Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin
inferredcites →https://doi.org/10.1101/gr.112961.110openalex-snapshot
The transcriptional diversity of 25 Drosophila cell lines
inferredcites →https://doi.org/10.1101/gr.138156.112openalex-snapshot
Nature and function of insulator protein binding sites in the Drosophila genome
inferredcites →https://doi.org/10.1101/gr.169243.113openalex-snapshot
Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features
inferredcites →https://doi.org/10.1101/gr.196006.115openalex-snapshot
Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains
inferredcites →https://doi.org/10.1126/sciadv.1700944openalex-snapshot
Polycomb repressive complex 1 modifies transcription of active genes
inferredcites →https://doi.org/10.1126/science.1067799openalex-snapshot
Capturing Chromosome Conformation
inferredcites →https://doi.org/10.1126/science.1181369openalex-snapshot
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
inferredcites →https://doi.org/10.1126/science.1198374openalex-snapshot
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
inferredcites →https://doi.org/10.1126/science.1232542openalex-snapshot
Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq
inferredcites →https://doi.org/10.1126/science.287.5461.2185openalex-snapshot
The Genome Sequence of Drosophila melanogaster
inferredcites →https://doi.org/10.1186/gb-2007-8-7-r129openalex-snapshot
FlyMine: an integrated database for Drosophila and Anopheles genomics
inferredcites →https://doi.org/10.1186/gb-2014-15-5-r82openalex-snapshot
Insulator function and topological domain border strength scale with architectural protein occupancy
inferredcites →https://doi.org/10.1186/gb-2014-15-8-r70openalex-snapshot
DNA copy number evolution in Drosophila cell lines
inferredcites →https://doi.org/10.1371/journal.pgen.1003436openalex-snapshot
Insulators Target Active Genes to Transcription Factories and Polycomb-Repressed Genes to Polycomb Bodies
inferredcites →https://doi.org/10.1371/journal.pgen.1003529openalex-snapshot
Gene Expression Regulation by Upstream Open Reading Frames and Human Disease
inferredcites →https://doi.org/10.1371/journal.pgen.1004544openalex-snapshot
Chromatin Insulator Factors Involved in Long-Range DNA Interactions and Their Role in the Folding of the Drosophila Genome
inferredcites →https://doi.org/10.1371/journal.pone.0172725openalex-snapshot
Regions of very low H3K27me3 partition the Drosophila genome into topological domains
inferredcites →https://doi.org/10.1371/journal.pone.0179159openalex-snapshot
Polyamine transporter potABCD is required for virulence of encapsulated but not nonencapsulated Streptococcus pneumoniae
inferredcites →https://doi.org/10.15252/embj.201489923openalex-snapshot
Chromatin signatures at Notch‐regulated enhancers reveal large‐scale changes in H3K56ac upon activation
inferredcites →https://doi.org/10.4161/trns.25554openalex-snapshot
Divergent RNA transcription
inferredcites →https://doi.org/10.7554/elife.02557openalex-snapshot
Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci
inferredcites →https://doi.org/10.7554/elife.21926openalex-snapshot
Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells
inferredcites →https://doi.org/10.7554/elife.29550openalex-snapshot
Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo

What points at this work

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

inferred← citeshttps://doi.org/10.1016/j.conb.2019.05.006openalex-snapshot
From insects to mammals: regulation of genome architecture in neural development
inferred← citeshttps://doi.org/10.1101/634980openalex-snapshot
Mesoscale liquid model of chromatin recapitulates nuclear order of eukaryotes
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