Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression

Rapid factor depletion highlights intricacies of nucleoplasmic RNA degradation

(2022) Maria Gockert et al.   NUCLEIC ACIDS RESEARCH

Integrator is a genome-wide attenuator of non-productive transcription

(2021) Søren Lykke-Andersen et al.   MOLECULAR CELL

m6A RNA methylation regulates the fate of endogenous retroviruses

(2021) Tomasz Chelmicki et al.   NATURE

MPP8 is essential for sustaining self-renewal of ground-state pluripotent stem cells

(2021) Iris Müller et al.   Nature Communications

RNA m6A meets transposable elements and chromatin

(2021) Chenxi He et al.   Protein & Cell

Crossroads between transposons and gene regulation

(2020) Miguel R. Branco et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The role of DNA demethylation in induction of stem cells

(2020) Mohammad H. Ghazimoradi et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

N6-methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription

(2020) Jun Liu et al.   SCIENCE

A Two-Layered Targeting Mechanism Underlies Nuclear RNA Sorting by the Human Exosome

(2020) Guifen Wu et al.   Cell Reports

N6-Methyladenosine co-transcriptionally directs the demethylation of histone H3K9me2

(2020) Yuan Li et al.   NATURE GENETICS

The RNA exosome shapes the expression of key protein-coding genes

(2020) Mengjun Wu et al.   NUCLEIC ACIDS RESEARCH

The Human Integrator Complex Facilitates Transcriptional Elongation by Endonucleolytic Cleavage of Nascent Transcripts

(2020) Felipe Beckedorff et al.   Cell Reports

Periphilin self-association underpins epigenetic silencing by the HUSH complex

(2020) Daniil M Prigozhin et al.   NUCLEIC ACIDS RESEARCH

TASOR is a pseudo-PARP that directs HUSH complex assembly and epigenetic transposon control

(2020) Christopher H. Douse et al.   Nature Communications

Regulation of transposable elements by DNA modifications

(2019) Özgen Deniz et al.   NATURE REVIEWS GENETICS

CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing

(2019) Kornel Labun et al.   NUCLEIC ACIDS RESEARCH

The MTR4 helicase recruits nuclear adaptors of the human RNA exosome using distinct arch-interacting motifs

(2019) Mahesh Lingaraju et al.   Nature Communications

A Functional Link between Nuclear RNA Decay and Transcriptional Control Mediated by the Polycomb Repressive Complex 2

(2019) William Garland et al.   Cell Reports

Nuclear Exosome Targeting Complex Core Factor Zcchc8 Regulates the Degradation of LINE1 RNA in Early Embryos and Embryonic Stem Cells

(2019) You Wu et al.   Cell Reports

Nuclear sorting of RNA

(2019) William Garland et al.   Wiley Interdisciplinary Reviews-RNA

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

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

The human ZC3H3 and RBM26/27 proteins are critical for PAXT-mediated nuclear RNA decay

(2019) Toomas Silla et al.   NUCLEIC ACIDS RESEARCH

The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes

(2018) Luisa Robbez-Masson et al.   GENOME RESEARCH

Controlling nuclear RNA levels

(2018) Manfred Schmid et al.   NATURE REVIEWS GENETICS

Structural basis for MTR4–ZCCHC8 interactions that stimulate the MTR4 helicase in the nuclear exosome-targeting complex

(2018) M. Rhyan Puno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aminode: Identification of Evolutionary Constraints in the Human Proteome

(2018) Kevin T. Chang et al.   Scientific Reports

Characterizing ZC3H18, a Multi-domain Protein at the Interface of RNA Production and Destruction Decisions

(2018) Kinga Winczura et al.   Cell Reports

The splicing factor SRSF3 is functionally connected to the nuclear RNA exosome for intronless mRNA decay

(2018) Fabrice Mure et al.   Scientific Reports

Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells

(2018) Jiangping He et al.   Nature Communications

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators

(2017) Nian Liu et al.   NATURE

A heterochromatin-dependent transcription machinery drives piRNA expression

(2017) Peter Refsing Andersen et al.   NATURE

KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks

(2017) Michaël Imbeault et al.   NATURE

Mutually Exclusive CBC-Containing Complexes Contribute to RNA Fate

(2017) Simone Giacometti et al.   Cell Reports

Hide and seek: how chromatin-based pathways silence retroelements in the mammalian germline

(2016) Antoine Molaro et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The RNA-induced transcriptional silencing complex targets chromatin exclusively via interacting with nascent transcripts

(2016) Yukiko Shimada et al.   GENES & DEVELOPMENT

Identification of a Nuclear Exosome Decay Pathway for Processed Transcripts

(2016) Nicola Meola et al.   MOLECULAR CELL

ATF7IP-Mediated Stabilization of the Histone Methyltransferase SETDB1 Is Essential for Heterochromatin Formation by the HUSH Complex

(2016) Richard T. Timms et al.   Cell Reports

Restricting retrotransposons: a review

(2016) John L. Goodier   Mobile DNA

TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets

(2015) Ying Jin et al.   BIOINFORMATICS

MPP8 and SIRT1 crosstalk in E-cadherin gene silencing and epithelial-mesenchymal transition

(2015) L. Sun et al.   EMBO REPORTS

RBM7 subunit of the NEXT complex binds U-rich sequences and targets 3′-end extended forms of snRNAs

(2015) Dominika Hrossova et al.   NUCLEIC ACIDS RESEARCH

A HUSH for transgene expression

(2015) T. R. Brummelkamp et al.   SCIENCE

Epigenetic silencing by the HUSH complex mediates position-effect variegation in human cells

(2015) I. A. Tchasovnikarova et al.   SCIENCE

The Human Nuclear Exosome Targeting Complex Is Loaded onto Newly Synthesized RNA to Direct Early Ribonucleolysis

(2015) Michal Lubas et al.   Cell Reports

Human Telomerase RNA Processing and Quality Control

(2015) Chi-Kang Tseng et al.   Cell Reports

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

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

Gene Silencing Triggers Polycomb Repressive Complex 2 Recruitment to CpG Islands Genome Wide

(2014) Eva Madi Riising et al.   MOLECULAR CELL

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

(2014) Frank M. J. Jacobs et al.   NATURE

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

O-GlcNAcylation regulates EZH2 protein stability and function

(2014) C.-S. Chu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mtr4-like Protein Coordinates Nuclear RNA Processing for Heterochromatin Assembly and for Telomere Maintenance

(2013) Nathan N. Lee et al.   CELL

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

The human cap-binding complex is functionally connected to the nuclear RNA exosome

(2013) Peter Refsing Andersen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Mmi1 RNA surveillance machinery directs RNAi complex RITS to specific meiotic genes in fission yeast

(2012) Edwige Hiriart et al.   EMBO JOURNAL

A unique regulatory phase of DNA methylation in the early mammalian embryo

(2012) Zachary D. Smith et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs

(2011) Mohammad M. Karimi et al.   Cell Stem Cell

Interaction Profiling Identifies the Human Nuclear Exosome Targeting Complex

(2011) Michal Lubas et al.   MOLECULAR CELL

RNA Elimination Machinery Targeting Meiotic mRNAs Promotes Facultative Heterochromatin Formation

(2011) M. Zofall et al.   SCIENCE

MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a

(2011) Yanqi Chang et al.   Nature Communications

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

LINE-1 Retrotransposition Activity in Human Genomes

(2010) Christine R. Beck et al.   CELL

Methyl-H3K9-binding protein MPP8 mediates E-cadherin gene silencing and promotes tumour cell motility and invasion

(2010) Kenji Kokura et al.   EMBO JOURNAL

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET

(2010) Toshiyuki Matsui et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

Retrotransposons Revisited: The Restraint and Rehabilitation of Parasites

(2008) John L. Goodier et al.   CELL

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY