相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development
Sergio Martin Espinola et al.
NATURE GENETICS (2021)
3D genome organisation in Drosophila
Charlotte Moretti et al.
BRIEFINGS IN FUNCTIONAL GENOMICS (2020)
TADs or no TADS: Lessons From Single-cell Imaging of Chromosome Architecture
Andres M. Cardozo Gizzil et al.
JOURNAL OF MOLECULAR BIOLOGY (2020)
Orchestrating single-cell analysis with Bioconductor
Robert A. Amezquita et al.
NATURE METHODS (2020)
The role of 3D chromatin domains in gene regulation: a multi-facetted view on genome organization
Daniel M. Ibrahim et al.
CURRENT OPINION IN GENETICS & DEVELOPMENT (2020)
Dynamics of the 4D genome during in vivo lineage specification and differentiation
A. Marieke Oudelaar et al.
NATURE COMMUNICATIONS (2020)
Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding
Tsung-Han S. Hsieh et al.
MOLECULAR CELL (2020)
Ultrastructural Details of Mammalian Chromosome Architecture
Nils Krietenstein et al.
MOLECULAR CELL (2020)
CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction
Silvia Galan et al.
NATURE GENETICS (2020)
Regulation of single-cell genome organization into TADs and chromatin nanodomains
Quentin Szabo et al.
NATURE GENETICS (2020)
FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data
Kai Kruse et al.
GENOME BIOLOGY (2020)
pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools
Pierre-Luc Germain et al.
GENOME BIOLOGY (2020)
Dynamics of transcriptional enhancers and chromosome topology in gene regulation
Moe Yokoshi et al.
DEVELOPMENT GROWTH & DIFFERENTIATION (2019)
Chromatin architecture reorganization during neuronal cell differentiation in Drosophila genome
Keerthi T. Chathoth et al.
GENOME RESEARCH (2019)
Visualizing DNA folding and RNA in embryos at single-cell resolution
Leslie J. Mateo et al.
NATURE (2019)
Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation
Leighton Core et al.
GENES & DEVELOPMENT (2019)
ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm
Marta Bozek et al.
GENOME RESEARCH (2019)
Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity
Jeffrey M. Alexander et al.
ELIFE (2019)
Comprehensive Integration of Single-Cell Data
Tim Stuart et al.
CELL (2019)
Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression
Yad Ghavi-Helm et al.
NATURE GENETICS (2019)
Functional dissection of the Sox9-Kcnj2 locus identifies nonessential and instructive roles of TAD architecture
Alexandra Despang et al.
NATURE GENETICS (2019)
Large distances separate coregulated genes in living Drosophila embryos
Tyler Heist et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
Developmentally regulated Shh expression is robust to TAD perturbations
Iain Williamson et al.
DEVELOPMENT (2019)
Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation
Nezha S. Benabdallah et al.
MOLECULAR CELL (2019)
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
Daehwan Kim et al.
NATURE BIOTECHNOLOGY (2019)
The Role of Insulation in Patterning Gene Expression
Isa Oezdemir et al.
GENES (2019)
Chromatin features constrain structural variation across evolutionary timescales
Geoff Fudenberg et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
Visualization of Transvection in Living Drosophila Embryos
Bomyi Lim et al.
MOLECULAR CELL (2018)
Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development
Yuki Ogiyama et al.
MOLECULAR CELL (2018)
Integrating single-cell transcriptomic data across different conditions, technologies, and species
Andrew Butler et al.
NATURE BIOTECHNOLOGY (2018)
Structural variation in the 3D genome
Malte Spielmann et al.
NATURE REVIEWS GENETICS (2018)
Imaging dynamic and selective low-complexity domain interactions that control gene transcription
Shasha Chong et al.
SCIENCE (2018)
Coactivator condensation at super-enhancers links phase separation and gene control
Benjamin R. Sabari et al.
SCIENCE (2018)
Principles of Chromosome Architecture Revealed by Hi-C
Kyle P. Eagen
TRENDS IN BIOCHEMICAL SCIENCES (2018)
High-resolution TADs reveal DNA sequences underlying genome organization in flies
Fidel Ramirez et al.
NATURE COMMUNICATIONS (2018)
Detection and removal of barcode swapping in single-cell RNA-seq data
Jonathan A. Griffiths et al.
NATURE COMMUNICATIONS (2018)
TADs are 3D structural units of higher-order chromosome organization in Drosophila
Quentin Szabo et al.
SCIENCE ADVANCES (2018)
Evolutionary stability of topologically associating domains is associated with conserved gene regulation
Jan Krefting et al.
BMC BIOLOGY (2018)
The cis-regulatory dynamics of embryonic development at single-cell resolution
Darren A. Cusanovich et al.
NATURE (2018)
Dynamic interplay between enhancer-promoter topology and gene activity
Hongtao Chen et al.
NATURE GENETICS (2018)
Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis
Bjort K. Kragesteen et al.
NATURE GENETICS (2018)
The Birth of the 3D Genome during Early Embryonic Development
Clemens B. Hug et al.
TRENDS IN GENETICS (2018)
Chromatin conformation analysis of primary patient tissue using a low input Hi-C method
Noelia Diaz et al.
NATURE COMMUNICATIONS (2018)
Regulatory principles governing the maternal-to-zygotic transition: insights from Drosophila melanogaster
Danielle C. Hamm et al.
OPEN BIOLOGY (2018)
Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos
Mustafa Mir et al.
ELIFE (2018)
Generation of Genome-wide Chromatin Conformation Capture Libraries from Tightly Staged Early Drosophila Embryos
Clemens B. Hug et al.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS (2018)
Developmental enhancers and chromosome topology
Eileen E. M. Furlong et al.
SCIENCE (2018)
HiGlass: web-based visual exploration and analysis of genome interaction maps
Peter Kerpedjiev et al.
GENOME BIOLOGY (2018)
Drosophila poised enhancers are generated during tissue patterning with the help of repression
Nina Koenecke et al.
GENOME RESEARCH (2017)
Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture
Caelin Cubenas-Potts et al.
NUCLEIC ACIDS RESEARCH (2017)
Evolutionarily Conserved Principles Predict 3D Chromatin Organization
M. Jordan Rowley et al.
MOLECULAR CELL (2017)
Two independent modes of chromatin organization revealed by cohesin removal
Wibke Schwarzer et al.
NATURE (2017)
Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition
Ilya M. Flyamer et al.
NATURE (2017)
3D structures of individual mammalian genomes studied by single-cell Hi-C
Tim J. Stevens et al.
NATURE (2017)
Cell-cycle dynamics of chromosomal organization at single-cell resolution
Takashi Nagano et al.
NATURE (2017)
Salmon provides fast and bias-aware quantification of transcript expression
Rob Patro et al.
NATURE METHODS (2017)
Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map
Kyle P. Eagen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
The Drosophila embryo at single-cell transcriptome resolution
Nikos Karaiskos et al.
SCIENCE (2017)
Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation
Nathan Harmston et al.
NATURE COMMUNICATIONS (2017)
Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions
Diego I. Cattoni et al.
NATURE COMMUNICATIONS (2017)
Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping
Stefanie L. Morgan et al.
NATURE COMMUNICATIONS (2017)
Nuclear microenvironments modulate transcription from low-affinity enhancers
Albert Tsai et al.
ELIFE (2017)
Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo
Michael R. Stadler et al.
ELIFE (2017)
Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins
Gordana Wutz et al.
EMBO JOURNAL (2017)
A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture
Johanna Gassler et al.
EMBO JOURNAL (2017)
YY1 Is a Structural Regulator of Enhancer-Promoter Loops
Abraham S. Weintraub et al.
CELL (2017)
Multiscale 3D Genome Rewiring during Mouse Neural Development
Boyan Bonev et al.
CELL (2017)
Cohesin Loss Eliminates All Loop Domains
Suhas S. P. Rao et al.
CELL (2017)
UpSetR: an R package for the visualization of intersecting sets and their properties
Jake R. Conway et al.
BIOINFORMATICS (2017)
Cell fixation and preservation for droplet-based single-cell transcriptomics
Jonathan Alles et al.
BMC BIOLOGY (2017)
Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization
Elphege P. Nora et al.
CELL (2017)
PRC2 Facilitates the Regulatory Topology Required for Poised Enhancer Function during Pluripotent Stem Cell Differentiation
Sara Cruz-Molina et al.
CELL STEM CELL (2017)
Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R
Davis J. McCarthy et al.
BIOINFORMATICS (2017)
Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription
Clemens B. Hug et al.
CELL (2017)
Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains
Sergey V. Ulianov et al.
GENOME RESEARCH (2016)
Insulator dysfunction and oncogene activation in IDH mutant gliomas
William A. Flavahan et al.
NATURE (2016)
csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows
Aaron T. L. Lun et al.
NUCLEIC ACIDS RESEARCH (2016)
Pioneer transcription factors, chromatin dynamics, and cell fate control
Kenneth S. Zaret et al.
CURRENT OPINION IN GENETICS & DEVELOPMENT (2016)
Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping
Caroline R. Bartman et al.
MOLECULAR CELL (2016)
Formation of new chromatin domains determines pathogenicity of genomic duplications
Martin Franke et al.
NATURE (2016)
Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome
Tsung-Han S. Hsieh et al.
NATURE METHODS (2016)
Initiation of diverse epigenetic states during nuclear programming of the Drosophila body plan
Ann Boija et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Activation of proto-oncogenes by disruption of chromosome neighborhoods
Denes Hnisz et al.
SCIENCE (2016)
Stepwise Progression of Embryonic Patterning
Jeremy E. Sandler et al.
TRENDS IN GENETICS (2016)
A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome
Anthony D. Schmitt et al.
CELL REPORTS (2016)
Third Chromosome Balancer Inversions Disrupt Protein-Coding Genes and Influence Distal Recombination Events in Drosophila melanogaster
Danny E. Miller et al.
G3-GENES GENOMES GENETICS (2016)
Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster
Hangnoh Lee et al.
PLOS GENETICS (2016)
Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis
Shelby A. Blythe et al.
ELIFE (2016)
Maternal AP determinants in the Drosophila oocyte and embryo
Jun Ma et al.
WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY (2016)
Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis
Nina Koenecke et al.
GENOME BIOLOGY (2016)
Sambamba: fast processing of NGS alignment formats
Artem Tarasov et al.
BIOINFORMATICS (2015)
Zygotic Genome Activation Triggers the DNA Replication Checkpoint at the Midblastula Transition
Shelby A. Blythe et al.
CELL (2015)
Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions
Dario G. Lupianez et al.
CELL (2015)
Dynamic Reorganization of Extremely Long-Range Promoter-Promoter Interactions between Two States of Pluripotency
Onkar Joshi et al.
CELL STEM CELL (2015)
TADs as modular and dynamic units for gene regulation by hormones
Francois Le Dily et al.
FEBS LETTERS (2015)
Condensin-driven remodelling of X chromosome topology during dosage compensation
Emily Crane et al.
NATURE (2015)
Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture
Matteo Vietri Rudan et al.
CELL REPORTS (2015)
Reactivation of Developmentally Silenced Globin Genes by Forced Chromatin Looping
Wulan Deng et al.
CELL (2014)
Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription
Luca Giorgetti et al.
CELL (2014)
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Suhas S. P. Rao et al.
CELL (2014)
Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation
Francois Le Dily et al.
GENES & DEVELOPMENT (2014)
Functional and topological characteristics of mammalian regulatory domains
Orsolya Symmons et al.
GENOME RESEARCH (2014)
UpSet: Visualization of Intersecting Sets
Alexander Lex et al.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS (2014)
Enhancer loops appear stable during development and are associated with paused polymerase
Yad Ghavi-Helm et al.
NATURE (2014)
Genome-scale functional characterization of Drosophila developmental enhancers in vivo
Evgeny Z. Kvon et al.
NATURE (2014)
De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly
Aaron T. L. Lun et al.
NUCLEIC ACIDS RESEARCH (2014)
deepTools: a flexible platform for exploring deep-sequencing data
Fidel Ramirez et al.
NUCLEIC ACIDS RESEARCH (2014)
Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition
Xiao-Yong Li et al.
ELIFE (2014)
Maternal control of the Drosophila dorsal-ventral body axis
David S. Stein et al.
WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY (2014)
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Michael I. Love et al.
GENOME BIOLOGY (2014)
Deletions of chromosomal regulatory boundaries are associated with congenital disease
Jonas Ibn-Salem et al.
GENOME BIOLOGY (2014)
Paused Pol II Coordinates Tissue Morphogenesis in the Drosophila Embryo
Mounia Lagha et al.
CELL (2013)
Single-Cell Dynamics of Genome-Nuclear Lamina Interactions
Jop Kind et al.
CELL (2013)
A fast algorithm for matrix balancing
Philip A. Knight et al.
IMA JOURNAL OF NUMERICAL ANALYSIS (2013)
A high-resolution map of the three-dimensional chromatin interactome in human cells
Fulai Jin et al.
NATURE (2013)
Organization of the Mitotic Chromosome
Natalia Naumova et al.
SCIENCE (2013)
Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor
Wulan Deng et al.
CELL (2012)
Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome
Tom Sexton et al.
CELL (2012)
Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation
Guoliang Li et al.
CELL (2012)
Dorsal-Ventral Gene Expression in the Drosophila Embryo Reflects the Dynamics and Precision of the Dorsal Nuclear Gradient
Gregory T. Reeves et al.
DEVELOPMENTAL CELL (2012)
Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains
Chunhui Hou et al.
MOLECULAR CELL (2012)
The long-range interaction landscape of gene promoters
Amartya Sanyal et al.
NATURE (2012)
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Jesse R. Dixon et al.
NATURE (2012)
Iterative correction of Hi-C data reveals hallmarks of chromosome organization
Maxim Imakaev et al.
NATURE METHODS (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
Identifying ChIP-seq enrichment using MACS
Jianxing Feng et al.
NATURE PROTOCOLS (2012)
clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
Guangchuang Yu et al.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2012)
Noncanonical Compensation of Zygotic X Transcription in Early Drosophila melanogaster Development Revealed through Single-Embryo RNA-Seq
Susan E. Lott et al.
PLOS BIOLOGY (2011)
Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition
Melissa M. Harrison et al.
PLOS GENETICS (2011)
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
Mark D. Robinson et al.
BIOINFORMATICS (2010)
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
Sushmita Roy et al.
SCIENCE (2010)
Neighbourhood Continuity Is Not Required for Correct Testis Gene Expression in Drosophila
Lisa A. Meadows et al.
PLOS BIOLOGY (2010)
Fast and accurate short read alignment with Burrows-Wheeler transform
Heng Li et al.
BIOINFORMATICS (2009)
How the Dorsal gradient works: Insights from postgenome technologies
Joung-Woo Hong et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Genomic regulatory blocks underlie extensive microsynteny conservation in insects
Par G. Engstrom et al.
GENOME RESEARCH (2007)
Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
Hiroshi Kikuta et al.
GENOME RESEARCH (2007)
Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo
Julia Zeitlinger et al.
GENES & DEVELOPMENT (2007)
The T-box-encoding Dorsocross genes function in amnioserosa development and the patterning of the dorsolateral germ band downstream of Dpp
I Reim et al.
DEVELOPMENT (2003)
Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo
A Stathopoulos et al.
CELL (2002)
Dorsal gradient networks in the Drosophila embryo
A Stathopoulos et al.
DEVELOPMENTAL BIOLOGY (2002)
分享论文
