Transcriptional regulatory control of mammalian nephron progenitors revealed by multi-factor cistromic analysis and genetic studies

Differential regulation of mouse and human nephron progenitors by the Six family of transcriptional regulators

(2016) Lori L. O'Brien et al.   DEVELOPMENT

Sp7/Osterix Is Restricted to Bone-Forming Vertebrates where It Acts as a Dlx Co-factor in Osteoblast Specification

(2016) Hironori Hojo et al.   DEVELOPMENTAL CELL

Kidney disease in children: latest advances and remaining challenges

(2016) John F. Bertram et al.   Nature Reviews Nephrology

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

(2016) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments

(2016) Ramya Raviram et al.   PLoS Computational Biology

Osr1 Interacts Synergistically with Wt1 to Regulate Kidney Organogenesis

(2016) Jingyue Xu et al.   PLoS One

Recurrent DGCR8, DROSHA, and SIX Homeodomain Mutations in Favorable Histology Wilms Tumors

(2015) Amy L. Walz et al.   CANCER CELL

Mutations in the SIX1/2 Pathway and the DROSHA/DGCR8 miRNA Microprocessor Complex Underlie High-Risk Blastemal Type Wilms Tumors

(2015) Jenny Wegert et al.   CANCER CELL

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

WT1 targets Gas1 to maintain nephron progenitor cells by modulating FGF signals

(2015) M. Kann et al.   DEVELOPMENT

A Synthetic Niche for Nephron Progenitor Cells

(2015) Aaron C. Brown et al.   DEVELOPMENTAL CELL

Eya-six are necessary for survival of nephrogenic cord progenitors and inducing nephric duct development before ureteric bud formation

(2015) Jinshu Xu et al.   DEVELOPMENTAL DYNAMICS

Genome-Wide Analysis of Wilms' Tumor 1-Controlled Gene Expression in Podocytes Reveals Key Regulatory Mechanisms

(2015) M. Kann et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Kidney organoids from human iPS cells contain multiple lineages and model human nephrogenesis

(2015) Minoru Takasato et al.   NATURE

Nephron organoids derived from human pluripotent stem cells model kidney development and injury

(2015) Ryuji Morizane et al.   NATURE BIOTECHNOLOGY

Sall1 in renal stromal progenitors non-cell autonomously restricts the excessive expansion of nephron progenitors

(2015) Tomoko Ohmori et al.   Scientific Reports

Osr1 acts downstream of and interacts synergistically with Six2 to maintain nephron progenitor cells during kidney organogenesis

(2014) J. Xu et al.   DEVELOPMENT

Eya1 Interacts with Six2 and Myc to Regulate Expansion of the Nephron Progenitor Pool during Nephrogenesis

(2014) Jinshu Xu et al.   DEVELOPMENTAL CELL

ASox2distal enhancer cluster regulates embryonic stem cell differentiation potential

(2014) Harry Y. Zhou et al.   GENES & DEVELOPMENT

Sall1 Maintains Nephron Progenitors and Nascent Nephrons by Acting as Both an Activator and a Repressor

(2014) S. Kanda et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells

(2014) Yan Li et al.   PLoS One

WT1 controls antagonistic FGF and BMP-pSMAD pathways in early renal progenitors

(2014) Fariba Jian Motamedi et al.   Nature Communications

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

(2014) Benoit Ballester et al.   eLife

Identification of a Multipotent Self-Renewing Stromal Progenitor Population during Mammalian Kidney Organogenesis

(2014) Akio Kobayashi et al.   Stem Cell Reports

Redefining the In Vivo Origin of Metanephric Nephron Progenitors Enables Generation of Complex Kidney Structures from Pluripotent Stem Cells

(2013) Atsuhiro Taguchi et al.   Cell Stem Cell

HNF1B controls proximal-intermediate nephron segment identity in vertebrates by regulating Notch signalling components and Irx1/2

(2013) C. Heliot et al.   DEVELOPMENT

The transcription factor sry-related HMG box-4 (SOX4) is required for normal renal developmentin vivo

(2013) Jez Huang et al.   DEVELOPMENTAL DYNAMICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

BMP signaling and its modifiers in kidney development

(2013) Ryuichi Nishinakamura et al.   PEDIATRIC NEPHROLOGY

Role for compartmentalization in nephron progenitor differentiation

(2013) A. C. Brown et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Gene Regulatory Networks Mediating Canonical Wnt Signal-Directed Control of Pluripotency and Differentiation in Embryo Stem Cells

(2013) Xiaoxiao Zhang et al.   STEM CELLS

FGF9 and FGF20 Maintain the Stemness of Nephron Progenitors in Mice and Man

(2012) Hila Barak et al.   DEVELOPMENTAL CELL

Six2 and Wnt Regulate Self-Renewal and Commitment of Nephron Progenitors through Shared Gene Regulatory Networks

(2012) Joo-Seop Park et al.   DEVELOPMENTAL CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Robust 4C-seq data analysis to screen for regulatory DNA interactions

(2012) Harmen J G van de Werken et al.   NATURE METHODS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

The GUDMAP database - an online resource for genitourinary research

(2011) S. D. Harding et al.   DEVELOPMENT

Nephron formation adopts a novel spatial topology at cessation of nephrogenesis

(2011) Bree A. Rumballe et al.   DEVELOPMENTAL BIOLOGY

A Wt1-Controlled Chromatin Switching Mechanism Underpins Tissue-Specific Wnt4 Activation and Repression

(2011) Abdelkader Essafi et al.   DEVELOPMENTAL CELL

A conditional knockout resource for the genome-wide study of mouse gene function

(2011) William C. Skarnes et al.   NATURE

Embryonic stem cell–based mapping of developmental transcriptional programs

(2011) Esteban O Mazzoni et al.   NATURE METHODS

Human nephron number: implications for health and disease

(2011) John F. Bertram et al.   PEDIATRIC NEPHROLOGY

Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart

(2011) A. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo

(2011) Graciana Diez-Roux et al.   PLOS BIOLOGY

Genomic characterization of Wilms' tumor suppressor 1 targets in nephron progenitor cells during kidney development

(2010) S. Hartwig et al.   DEVELOPMENT

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

TSC-22 contributes to hematopoietic precursor cell proliferation and repopulation and is epigenetically silenced in large granular lymphocyte leukemia

(2009) J. Yu et al.   BLOOD

Non-homeodomain regions of Hox proteins mediate activation versus repression of Six2 via a single enhancer site in vivo

(2009) Alisha R. Yallowitz et al.   DEVELOPMENTAL BIOLOGY

C-myc as a modulator of renal stem/progenitor cell population

(2009) Martin Couillard et al.   DEVELOPMENTAL DYNAMICS

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Six2 Defines and Regulates a Multipotent Self-Renewing Nephron Progenitor Population throughout Mammalian Kidney Development

(2008) Akio Kobayashi et al.   Cell Stem Cell

The sine oculis homeobox (SIX) family of transcription factors as regulators of development and disease

(2008) J. P. Kumar   CELLULAR AND MOLECULAR LIFE SCIENCES

Osr1 expression demarcates a multi-potent population of intermediate mesoderm that undergoes progressive restriction to an Osr1-dependent nephron progenitor compartment within the mammalian kidney

(2008) Joshua W. Mugford et al.   DEVELOPMENTAL BIOLOGY

Hoxd11 specifies a program of metanephric kidney development within the intermediate mesoderm of the mouse embryo

(2008) Joshua W. Mugford et al.   DEVELOPMENTAL BIOLOGY

Misexpression ofSix2is associated with heritable frontonasal dysplasia and renal hypoplasia in 3H1Brmice

(2008) Ben Fogelgren et al.   DEVELOPMENTAL DYNAMICS

R-spondin1 plays an essential role in ovarian development through positively regulating Wnt-4 signaling

(2008) Kazuma Tomizuka et al.   HUMAN MOLECULAR GENETICS

SIX2 and BMP4 Mutations Associate With Anomalous Kidney Development

(2008) S. Weber et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

GUDMAP: The Genitourinary Developmental Molecular Anatomy Project

(2008) A. P. McMahon et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

(2008) Anton Valouev et al.   NATURE METHODS