Epigenetic remodelling licences adult cholangiocytes for organoid formation and liver regeneration

YAP, but Not RSPO-LGR4/5, Signaling in Biliary Epithelial Cells Promotes a Ductular Reaction in Response to Liver Injury

(2019) Lara Planas-Paz et al.   Cell Stem Cell

Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration

(2019) Brian J. Pepe-Mooney et al.   Cell Stem Cell

Lgr5+ stem/progenitor cells reside at the apex of a heterogeneous embryonic hepatoblast pool

(2019) Nicole Prior et al.   DEVELOPMENT

Self-organization and symmetry breaking in intestinal organoid development

(2019) Denise Serra et al.   NATURE

Concerted cell divisions in embryonic visceral endoderm guide anterior visceral endoderm migration

(2019) Francesco Antonica et al.   DEVELOPMENTAL BIOLOGY

Chronic Liver Injury Induces Conversion of Biliary Epithelial Cells into Hepatocytes

(2018) Xing Deng et al.   Cell Stem Cell

Distributed hepatocytes expressing telomerase repopulate the liver in homeostasis and injury

(2018) Shengda Lin et al.   NATURE

Postnatal DNA demethylation and its role in tissue maturation

(2018) Yitzhak Reizel et al.   Nature Communications

A Critical Role of TET1/2 Proteins in Cell-Cycle Progression of Trophoblast Stem Cells

(2018) Stephanie Chrysanthou et al.   Stem Cell Reports

Targeted DamID reveals differential binding of mammalian pluripotency factors

(2018) Seth W. Cheetham et al.   DEVELOPMENT

Hepatocyte-specific β-catenin deletion during severe liver injury provokes cholangiocytes to differentiate into hepatocytes

(2018) Jacquelyn O Russell et al.   HEPATOLOGY

Epigenetic reprogramming enables the transition from primordial germ cell to gonocyte

(2018) Peter W. S. Hill et al.   NATURE

Regulators of Cholangiocyte Proliferation

(2017) Chad Hall et al.   GENE EXPRESSION

A single-cell transcriptomic analysis reveals precise pathways and regulatory mechanisms underlying hepatoblast differentiation

(2017) Li Yang et al.   HEPATOLOGY

Cholangiocytes act as facultative liver stem cells during impaired hepatocyte regeneration

(2017) Alexander Raven et al.   NATURE

Adult Mouse Liver Contains Two Distinct Populations of Cholangiocytes

(2017) Bin Li et al.   Stem Cell Reports

Loss of Tet1-Associated 5-Hydroxymethylcytosine Is Concomitant with Aberrant Promoter Hypermethylation in Liver Cancer

(2016) J. P. Thomson et al.   CANCER RESEARCH

Multi-organ Mapping of Cancer Risk

(2016) Liqin Zhu et al.   CELL

Epigenetic regulation of intestinal stem cells by Tet1-mediated DNA hydroxymethylation

(2016) Rinho Kim et al.   GENES & DEVELOPMENT

Role of TET enzymes in DNA methylation, development, and cancer

(2016) Kasper Dindler Rasmussen et al.   GENES & DEVELOPMENT

The plastic cellular states of liver cells: Are EpCAM and Lgr5 fit for purpose?

(2016) Meritxell Huch et al.   HEPATOLOGY

Cell-type-specific profiling of protein–DNA interactions without cell isolation using targeted DamID with next-generation sequencing

(2016) Owen J Marshall et al.   Nature Protocols

Culture and establishment of self-renewing human and mouse adult liver and pancreas 3D organoids and their genetic manipulation

(2016) Laura Broutier et al.   Nature Protocols

5-Hydroxymethylcytosine Marks Sites of DNA Damage and Promotes Genome Stability

(2016) Georgia Rose Kafer et al.   Cell Reports

Heterogeneity and stochastic growth regulation of biliary epithelial cells dictate dynamic epithelial tissue remodeling

(2016) Kenji Kamimoto et al.   eLife

damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets: Fig. 1.

(2015) Owen J. Marshall et al.   BIOINFORMATICS

Hybrid Periportal Hepatocytes Regenerate the Injured Liver without Giving Rise to Cancer

(2015) Joan Font-Burgada et al.   CELL

Long-Term Culture of Genome-Stable Bipotent Stem Cells from Adult Human Liver

(2015) Meritxell Huch et al.   CELL

Modeling mouse and human development using organoid cultures

(2015) M. Huch et al.   DEVELOPMENT

The Cholangiopathies

(2015) Konstantinos N. Lazaridis et al.   MAYO CLINIC PROCEEDINGS

Self-renewing diploid Axin2+ cells fuel homeostatic renewal of the liver

(2015) Bruce Wang et al.   NATURE

Hepatic progenitor cells of biliary origin with liver repopulation capacity

(2015) Wei-Yu Lu et al.   NATURE CELL BIOLOGY

EpiFactors: a comprehensive database of human epigenetic factors and complexes

(2015) Yulia A. Medvedeva et al.   Database-The Journal of Biological Databases and Curation

The Liver Is a Peculiar Organ When It Comes to Stem Cells

(2014) George K. Michalopoulos   AMERICAN JOURNAL OF PATHOLOGY

Hippo Pathway Activity Influences Liver Cell Fate

(2014) Dean Yimlamai et al.   CELL

Fucci2a:A bicistronic cell cycle reporter that allows Cre mediated tissue specific expression in mice

(2014) Richard Lester Mort et al.   CELL CYCLE

Zrf1 is required to establish and maintain neural progenitor identity

(2014) L. Aloia et al.   GENES & DEVELOPMENT

DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos

(2014) D. M. Messerschmidt et al.   GENES & DEVELOPMENT

5-Hydroxymethylcytosine: A stable or transient DNA modification?

(2014) Maria A. Hahn et al.   GENOMICS

DNA demethylation, Tet proteins and 5-hydroxymethylcytosine in epigenetic reprogramming: An emerging complex story

(2014) Peter W.S. Hill et al.   GENOMICS

Clonal tracing of Sox9+liver progenitors in mouse oval cell injury

(2014) Branden D. Tarlow et al.   HEPATOLOGY

Preparing the ground for tissue regeneration: from mechanism to therapy

(2014) Stuart J Forbes et al.   NATURE MEDICINE

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Plasticity of epithelial stem cells in tissue regeneration

(2014) C. Blanpain et al.   SCIENCE

DNA Methylation in Mammals

(2014) E. Li et al.   Cold Spring Harbor Perspectives in Biology

Extensive Conversion of Hepatic Biliary Epithelial Cells to Hepatocytes After Near Total Loss of Hepatocytes in Zebrafish

(2013) Tae–Young Choi et al.   GASTROENTEROLOGY

TET enzymes, TDG and the dynamics of DNA demethylation

(2013) Rahul M. Kohli et al.   NATURE

In vitro expansion of single Lgr5+ liver stem cells induced by Wnt-driven regeneration

(2013) Meritxell Huch et al.   NATURE

Role of Tet1 in erasure of genomic imprinting

(2013) Shinpei Yamaguchi et al.   NATURE

NANOG-dependent function of TET1 and TET2 in establishment of pluripotency

(2013) Yael Costa et al.   NATURE

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription

(2013) William A. Pastor et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Diabetes Risk Gene and Wnt Effector Tcf7l2/TCF4 Controls Hepatic Response to Perinatal and Adult Metabolic Demand

(2012) Sylvia F. Boj et al.   CELL

Liver Progenitor Cells Yield Functional Hepatocytes in Response to Chronic Liver Injury in Mice

(2012) Regina Español–Suñer et al.   GASTROENTEROLOGY

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

5-Hydroxymethylcytosine Is Strongly Depleted in Human Cancers but Its Levels Do Not Correlate with IDH1 Mutations

(2011) S.-G. Jin et al.   CANCER RESEARCH

The Cellular Basis for Animal Regeneration

(2011) Elly M. Tanaka et al.   DEVELOPMENTAL CELL

Foxl1-Cre-marked adult hepatic progenitors have clonogenic and bilineage differentiation potential

(2011) S. Shin et al.   GENES & DEVELOPMENT

Prospective isolation of a bipotential clonogenic liver progenitor cell in adult mice

(2011) C. Dorrell et al.   GENES & DEVELOPMENT

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation

(2011) Gabriella Ficz et al.   NATURE

Uncovering the role of 5-hydroxymethylcytosine in the epigenome

(2011) Miguel R. Branco et al.   NATURE REVIEWS GENETICS

Redefining CpG islands using hidden Markov models

(2010) H. Wu et al.   BIOSTATISTICS

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Lrig1 Expression Defines a Distinct Multipotent Stem Cell Population in Mammalian Epidermis

(2009) Kim B. Jensen et al.   Cell Stem Cell

Potential hepatic stem cells reside in EpCAM+ cells of normal and injured mouse liver

(2009) M. Okabe et al.   DEVELOPMENT

Stem Cells and Liver Regeneration

(2009) Andrew W. Duncan et al.   GASTROENTEROLOGY

Epigenetic inheritance during the cell cycle

(2009) Aline V. Probst et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

Foxl1 is a marker of bipotential hepatic progenitor cells in mice

(2008) Sara D. Sackett et al.   HEPATOLOGY