Heterochromatin rewiring and domain disruption-mediated chromatin compaction during erythropoiesis

Erythrocytes 3D genome organization in vertebrates

(2021) Anastasia Ryzhkova et al.   Scientific Reports

Regulation of RNA Polymerase II Activity is Essential for Terminal Erythroid Maturation

(2021) Zachary Murphy et al.   BLOOD

Coolpup.py: versatile pile-up analysis of Hi-C data

(2020) Ilya M Flyamer et al.   BIOINFORMATICS

Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis

(2020) Mark A. Gillespie et al.   MOLECULAR CELL

Comparative targeting analysis of KLF1, BCL11A, and HBG1/2 in CD34+ HSPCs by CRISPR/Cas9 for the induction of fetal hemoglobin

(2020) Andrés Lamsfus-Calle et al.   Scientific Reports

Disruption of erythroid nuclear opening and histone release in myelodysplastic syndromes

(2019) Baobing Zhao et al.   Cancer Medicine

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors

(2019) Darko Barisic et al.   NATURE

Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling

(2019) Michael P. Meers et al.   Epigenetics & Chromatin

Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis

(2019) Leif S. Ludwig et al.   Cell Reports

Chromatin structure dynamics during the mitosis-to-G1 phase transition

(2019) Haoyue Zhang et al.   NATURE

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

Functional profiling of single CRISPR/Cas9-edited human long-term hematopoietic stem cells

(2019) Elvin Wagenblast et al.   Nature Communications

Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch

(2018) Nan Liu et al.   CELL

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

(2018) Ralph Stadhouders et al.   NATURE GENETICS

hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data

(2018) Caleb A Lareau et al.   NATURE METHODS

Targeted in situ genome-wide profiling with high efficiency for low cell numbers

(2018) Peter J Skene et al.   Nature Protocols

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   CELL

Coaching from the sidelines: the nuclear periphery in genome regulation

(2018) Abigail Buchwalter et al.   NATURE REVIEWS GENETICS

3D organization of chicken genome demonstrates evolutionary conservation of topologically associated domains and highlights unique architecture of erythrocytes’ chromatin

(2018) Veniamin Fishman et al.   NUCLEIC ACIDS RESEARCH

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment

(2017) Jonathan A. Beagan et al.   GENOME RESEARCH

Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation

(2017) Kyong-Rim Kieffer-Kwon et al.   MOLECULAR CELL

Ten principles of heterochromatin formation and function

(2017) Robin C. Allshire et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Thyroid hormone receptor beta and NCOA4 regulate terminal erythrocyte differentiation

(2017) Xiaofei Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

CAM: A quality control pipeline for MNase-seq data

(2017) Sheng’en Hu et al.   PLoS One

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

3D Chromosome Regulatory Landscape of Human Pluripotent Cells

(2016) Xiong Ji et al.   Cell Stem Cell

Immunophenotypic analysis of erythroid dysplasia in myelodysplastic syndromes. A report from the IMDSFlow working group

(2016) Theresia M. Westers et al.   HAEMATOLOGICA

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon et al.   MOLECULAR CELL

The landscape of accessible chromatin in mammalian preimplantation embryos

(2016) Jingyi Wu et al.   NATURE

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Immunophenotypic analysis of erythroid dysplasia in myelodysplastic syndromes. A report from the IMDSFlow working group

(2016) Theresia M. Westers et al.   HAEMATOLOGICA

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

PPAR-α and glucocorticoid receptor synergize to promote erythroid progenitor self-renewal

(2015) Hsiang-Ying Lee et al.   NATURE

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Global transcriptome analyses of human and murine terminal erythroid differentiation

(2014) X. An et al.   BLOOD

Reactivation of Developmentally Silenced Globin Genes by Forced Chromatin Looping

(2014) Wulan Deng et al.   CELL

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Isolation and functional characterization of human erythroblasts at distinct stages: implications for understanding of normal and disordered erythropoiesis in vivo

(2013) J. Hu et al.   BLOOD

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Overlapping chromatin-remodeling systems collaborate genome wide at dynamic chromatin transitions

(2013) Stephanie A Morris et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor

(2012) Wulan Deng et al.   CELL

A novel role for survivin in erythroblast enucleation

(2012) G. Keerthivasan et al.   HAEMATOLOGICA

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

Gene induction and repression during terminal erythropoiesis are mediated by distinct epigenetic changes

(2011) P. Wong et al.   BLOOD

From stem cell to red cell: regulation of erythropoiesis at multiple levels by multiple proteins, RNAs, and chromatin modifications

(2011) S. M. Hattangadi et al.   BLOOD

Autophagy Driven by a Master Regulator of Hematopoiesis

(2011) Y.-A. Kang et al.   MOLECULAR AND CELLULAR BIOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Global DNA Demethylation During Mouse Erythropoiesis in Vivo

(2011) J. R. Shearstone et al.   SCIENCE

Formation of mammalian erythrocytes: chromatin condensation and enucleation

(2011) Peng Ji et al.   TRENDS IN CELL BIOLOGY

Erythroblast Enucleation

(2011) Ganesan Keerthivasan et al.   Stem Cells International

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Vesicle trafficking plays a novel role in erythroblast enucleation

(2010) G. Keerthivasan et al.   BLOOD

The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation

(2010) E. Soler et al.   GENES & DEVELOPMENT

Histone deacetylase 2 is required for chromatin condensation and subsequent enucleation of cultured mouse fetal erythroblasts

(2010) P. Ji et al.   HAEMATOLOGICA

From stem cell to erythroblast: Regulation of red cell production at multiple levels by multiple hormones

(2010) Harvey Lodish et al.   IUBMB LIFE

Down-regulation of Myc Is Essential for Terminal Erythroid Maturation

(2010) Senthil Raja Jayapal et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2010) Sven Heinz et al.   MOLECULAR CELL

A Key Commitment Step in Erythropoiesis Is Synchronized with the Cell Cycle Clock through Mutual Inhibition between PU.1 and S-Phase Progression

(2010) Ramona Pop et al.   PLOS BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Chromatin condensation in terminally differentiating mouse erythroblasts does not involve special architectural proteins but depends on histone deacetylation

(2009) Evgenya Y. Popova et al.   CHROMOSOME RESEARCH

Discovering Hematopoietic Mechanisms through Genome-wide Analysis of GATA Factor Chromatin Occupancy

(2009) Tohru Fujiwara et al.   MOLECULAR CELL

Insights into GATA-1-Mediated Gene Activation versus Repression via Genome-wide Chromatin Occupancy Analysis

(2009) Ming Yu et al.   MOLECULAR CELL

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Enucleation of cultured mouse fetal erythroblasts requires Rac GTPases and mDia2

(2008) Peng Ji et al.   NATURE CELL BIOLOGY

CTCF physically links cohesin to chromatin

(2008) E. D. Rubio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY