Hijacking of transcriptional condensates by endogenous retroviruses

Roles of transposable elements in the regulation of mammalian transcription

(2022) Raquel Fueyo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

m6A RNA methylation regulates the fate of endogenous retroviruses

(2021) Tomasz Chelmicki et al.   NATURE

METTL3 regulates heterochromatin in mouse embryonic stem cells

(2021) Wenqi Xu et al.   NATURE

The RNA m6A reader YTHDC1 silences retrotransposons and guards ES cell identity

(2021) Jiadong Liu et al.   NATURE

RNA promotes the formation of spatial compartments in the nucleus

(2021) Sofia A. Quinodoz et al.   CELL

Diverse epigenetic mechanisms maintain parental imprints within the embryonic and extraembryonic lineages

(2021) Daniel Andergassen et al.   DEVELOPMENTAL CELL

RNA in formation and regulation of transcriptional condensates

(2021) Phillip A. Sharp et al.   RNA

KRAB-zinc finger protein gene expansion in response to active retrotransposons in the murine lineage

(2020) Gernot Wolf et al.   eLife

Epigenetic regulator function through mouse gastrulation

(2020) Stefanie Grosswendt et al.   NATURE

RNA contributions to the form and function of biomolecular condensates

(2020) Christine Roden et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Silencing and Transcriptional Regulation of Endogenous Retroviruses: An Overview

(2020) Franziska K. Geis et al.   Viruses-Basel

Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukaemia

(2020) Özgen Deniz et al.   Nature Communications

A Field Guide to Eukaryotic Transposable Elements

(2020) Jonathan N. Wells et al.   Annual Review of Genetics

RNA-Mediated Feedback Control of Transcriptional Condensates

(2020) Jonathan E. Henninger et al.   CELL

TRIM28 haploinsufficiency predisposes to Wilms tumor

(2019) Illja J. Diets et al.   INTERNATIONAL JOURNAL OF CANCER

Molecular recording of mammalian embryogenesis

(2019) Michelle M. Chan et al.   NATURE

Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets

(2019) Tobias Neumann et al.   BMC BIOINFORMATICS

Time-Resolved Small RNA Sequencing Unravels the Molecular Principles of MicroRNA Homeostasis

(2019) Brian Reichholf et al.   MOLECULAR CELL

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

(2019) Yang Eric Guo et al.   NATURE

Transposable elements in human genetic disease

(2019) Lindsay M. Payer et al.   NATURE REVIEWS GENETICS

The Nuclear Matrix Protein SAFB Cooperates with Major Satellite RNAs to Stabilize Heterochromatin Architecture Partially through Phase Separation

(2019) Xiangru Huo et al.   MOLECULAR CELL

The dTAG system for immediate and target-specific protein degradation

(2018) Behnam Nabet et al.   Nature Chemical Biology

SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis

(2018) Matthias Muhar et al.   SCIENCE

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells

(2018) J. O. Andrews et al.   Scientific Reports

RNA polymerase II clustering through carboxy-terminal domain phase separation

(2018) Marc Boehning et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

Loss of maternalTrim28causes male-predominant early embryonic lethality

(2017) Abhishek Sampath Kumar et al.   GENES & DEVELOPMENT

DiAna, an ImageJ tool for object-based 3D co-localization and distance analysis

(2017) Jean-François Gilles et al.   METHODS

Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer

(2017) Zachary D. Smith et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo

(2017) Joanna W Jachowicz et al.   NATURE GENETICS

Trim28 Haploinsufficiency Triggers Bi-stable Epigenetic Obesity

(2016) Kevin Dalgaard et al.   CELL

Long Terminal Repeats: From Parasitic Elements to Building Blocks of the Transcriptional Regulatory Repertoire

(2016) Peter J. Thompson et al.   MOLECULAR CELL

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

Regulatory evolution of innate immunity through co-option of endogenous retroviruses

(2016) E. B. Chuong et al.   SCIENCE

RNA Polymerase II cluster dynamics predict mRNA output in living cells

(2016) Won-Ki Cho et al.   eLife

Systematic Identification of Factors for Provirus Silencing in Embryonic Stem Cells

(2015) Bin Xia Yang et al.   CELL

The KRAB zinc finger protein ZFP809 is required to initiate epigenetic silencing of endogenous retroviruses

(2015) Gernot Wolf et al.   GENES & DEVELOPMENT

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

(2015) Edward J. Grow et al.   NATURE

Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells

(2015) Simon J. Elsässer et al.   NATURE

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

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

(2014) S. Anders et al.   BIOINFORMATICS

Suv39h-Dependent H3K9me3 Marks Intact Retrotransposons and Silences LINE Elements in Mouse Embryonic Stem Cells

(2014) Aydan Bulut-Karslioglu et al.   MOLECULAR CELL

Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells

(2014) Jichang Wang et al.   NATURE

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Defending the genome from the enemy within: mechanisms of retrotransposon suppression in the mouse germline

(2013) James H. Crichton et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA

(2013) Anas Fadloun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells

(2013) I. I. Cisse et al.   SCIENCE

TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells

(2012) H. M. Rowe et al.   GENOME RESEARCH

Embryonic stem cell potency fluctuates with endogenous retrovirus activity

(2012) Todd S. Macfarlan et al.   NATURE

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Trim28 Is Required for Epigenetic Stability During Mouse Oocyte to Embryo Transition

(2012) D. M. Messerschmidt et al.   SCIENCE

Dynamic control of endogenous retroviruses during development

(2011) Helen M. Rowe et al.   VIROLOGY

KAP1 controls endogenous retroviruses in embryonic stem cells

(2010) Helen M. Rowe et al.   NATURE

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET

(2010) Toshiyuki Matsui et al.   NATURE

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal

(2009) G. Hu et al.   GENES & DEVELOPMENT

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

Endogenous retroviruses

(2008) C. Stocking et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

A drug-inducible transgenic system for direct reprogramming of multiple somatic cell types

(2008) Marius Wernig et al.   NATURE BIOTECHNOLOGY

Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes

(2008) Arnauld Sergé et al.   NATURE METHODS