Transcription factor competition at the γ-globin promoters controls hemoglobin switching

Reactivation of γ-globin expression through Cas9 or base editor to treat β-hemoglobinopathies

(2020) Liren Wang et al.   CELL RESEARCH

Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation

(2020) Anindita Basak et al.   NATURE GENETICS

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

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

Dynamics of the 4D genome during in vivo lineage specification and differentiation

(2020) A. Marieke Oudelaar et al.   Nature Communications

Reversible Disruption of Specific Transcription Factor-DNA Interactions Using CRISPR/Cas9

(2019) S. Ali Shariati et al.   MOLECULAR CELL

The Integrator Complex Attenuates Promoter-Proximal Transcription at Protein-Coding Genes

(2019) Nathan D. Elrod et al.   MOLECULAR CELL

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

(2018) Nan Liu et al.   CELL

Natural regulatory mutations elevate the fetal globin gene via disruption of BCL11A or ZBTB7A binding

(2018) Gabriella E. Martyn et al.   NATURE GENETICS

Easy quantification of template-directed CRISPR/Cas9 editing

(2018) Eva K Brinkman et al.   NUCLEIC ACIDS RESEARCH

MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast

(2018) Di Luo et al.   NUCLEIC ACIDS RESEARCH

Fetal γ-globin genes are regulated by the BGLT3 long non-coding RNA locus

(2018) Maria Soledad Ivaldi et al.   BLOOD

Engineered CRISPR-Cas9 nuclease with expanded targeting space

(2018) Hiroshi Nishimasu et al.   SCIENCE

CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data

(2018) Jonathan Y. Hsu et al.   NATURE METHODS

Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element

(2017) Peng Huang et al.   GENES & DEVELOPMENT

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

A promiscuous split intein with expanded protein engineering applications

(2017) Adam J. Stevens et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved split fluorescent proteins for endogenous protein labeling

(2017) Siyu Feng et al.   Nature Communications

Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens

(2017) David W. Morgens et al.   Nature Communications

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

(2017) Peter J Skene et al.   eLife

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

Genetic dissection of the α-globin super-enhancer in vivo

(2016) Deborah Hay et al.   NATURE GENETICS

A genome-editing strategy to treat β-hemoglobinopathies that recapitulates a mutation associated with a benign genetic condition

(2016) Elizabeth A Traxler et al.   NATURE MEDICINE

Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells

(2016) Gaelen T Hess et al.   NATURE METHODS

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

(2016) Dig Bijay Mahat et al.   Nature Protocols

A high definition look at the NF-Y regulome reveals genome-wide associations with selected transcription factors

(2016) Diletta Dolfini et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin

(2016) T. Masuda et al.   SCIENCE

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver et al.   NATURE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging

(2014) Marvin E. Tanenbaum et al.   CELL

Histone-Fold Domain Protein NF-Y Promotes Chromatin Accessibility for Cell Type-Specific Master Transcription Factors

(2014) Andrew J. Oldfield et al.   MOLECULAR CELL

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

Easy quantitative assessment of genome editing by sequence trace decomposition

(2014) Eva K. Brinkman et al.   NUCLEIC ACIDS RESEARCH

In search of the determinants of enhancer–promoter interaction specificity

(2014) Joris van Arensbergen et al.   TRENDS IN CELL BIOLOGY

Sequence-Specific Transcription Factor NF-Y Displays Histone-like DNA Binding and H2B-like Ubiquitination

(2013) Marco Nardini et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors

(2013) J. D. Fleming et al.   GENOME RESEARCH

Establishment of Immortalized Human Erythroid Progenitor Cell Lines Able to Produce Enucleated Red Blood Cells

(2013) Ryo Kurita et al.   PLoS One

Corepressor-dependent silencing of fetal hemoglobin expression by BCL11A

(2013) J. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

NF-Y Recruits Both Transcription Activator and Repressor to Modulate Tissue- and Developmental Stage-Specific Expression of Human γ-Globin Gene

(2012) Xingguo Zhu et al.   PLoS One

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao et al.   GENOME BIOLOGY

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Transcriptional regulation of fetal to adult hemoglobin switching: new therapeutic opportunities

(2011) A. Wilber et al.   BLOOD

A Functional Element Necessary for Fetal Hemoglobin Silencing

(2011) Vijay G. Sankaran et al.   NEW ENGLAND JOURNAL OF MEDICINE

Transcriptional silencing of  -globin by BCL11A involves long-range interactions and cooperation with SOX6

(2010) J. Xu et al.   GENES & DEVELOPMENT

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Developmental and species-divergent globin switching are driven by BCL11A

(2009) Vijay G. Sankaran et al.   NATURE

Human Fetal Hemoglobin Expression Is Regulated by the Developmental Stage-Specific RepressorBCL11A

(2008) Vijay G. Sankaran et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY