Transcriptome-wide identification of the RNA-binding landscape of the chromatin-associated protein PARP1 reveals functions in RNA biogenesis

PAR-CLIP and streamlined small RNA cDNA library preparation protocol for the identification of RNA binding protein target sites

(2017) Daniel Benhalevy et al.   METHODS

rMAPS: RNA map analysis and plotting server for alternative exon regulation

(2016) Juw Won Park et al.   NUCLEIC ACIDS RESEARCH

Has land use pushed terrestrial biodiversity beyond the planetary boundary? A global assessment

(2016) Tim Newbold et al.   SCIENCE

Involvement of PARP1 in the regulation of alternative splicing

(2016) Elena Matveeva et al.   Cell Discovery

A chromatin code for alternative splicing involving a putative association between CTCF and HP1α proteins

(2015) Eneritz Agirre et al.   BMC BIOLOGY

RNA Regulation by Poly(ADP-Ribose) Polymerases

(2015) Florian J. Bock et al.   MOLECULAR CELL

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

Bookmarking promoters in mitotic chromatin: poly(ADP-ribose)polymerase-1 as an epigenetic mark

(2014) Niraj Lodhi et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Widespread Use of Non-productive Alternative Splice Sites in Saccharomyces cerevisiae

(2014) Tadashi Kawashima et al.   PLoS Genetics

A Transcriptome-wide Atlas of RNP Composition Reveals Diverse Classes of mRNAs and lncRNAs

(2013) Alex Charles Tuck et al.   CELL

Dynamic Integration of Splicing within Gene Regulatory Pathways

(2013) Ulrich Braunschweig et al.   CELL

Spliceosome-mediated decay (SMD) regulates expression of nonintronic genes in budding yeast

(2013) A. Volanakis et al.   GENES & DEVELOPMENT

Post-Transcriptional Regulation by Poly(ADP-ribosyl)ation of the RNA-Binding Proteins

(2013) Yingbiao Ji et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Interferon-Stimulated Poly(ADP-Ribose) Polymerases Are Potent Inhibitors of Cellular Translation and Virus Replication

(2013) S. Atasheva et al.   JOURNAL OF VIROLOGY

RIPiT-Seq: A high-throughput approach for footprinting RNA:protein complexes

(2013) Guramrit Singh et al.   METHODS

Proteome-wide Identification of Poly(ADP-Ribosyl)ation Targets in Different Genotoxic Stress Responses

(2013) Stephanie Jungmichel et al.   MOLECULAR CELL

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

The diverse roles and clinical relevance of PARPs in DNA damage repair: Current state of the art

(2012) Mike De Vos et al.   BIOCHEMICAL PHARMACOLOGY

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

Regulation of Poly(ADP-ribose) Polymerase-1-dependent Gene Expression through Promoter-directed Recruitment of a Nuclear NAD+Synthase

(2012) Tong Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Nuclear Matrix Factor hnRNP U/SAF-A Exerts a Global Control of Alternative Splicing by Regulating U2 snRNP Maturation

(2012) Rui Xiao et al.   MOLECULAR CELL

Inheritance of Silent rDNA Chromatin Is Mediated by PARP1 via Noncoding RNA

(2012) Claudio Guetg et al.   MOLECULAR CELL

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR CELL

PARP1 Represses PAP and Inhibits Polyadenylation during Heat Shock

(2012) Dafne Campigli Di Giammartino et al.   MOLECULAR CELL

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

New insights into the molecular and cellular functions of poly(ADP-ribose) and PARPs

(2012) Bryan A. Gibson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Guanine-Quadruplex Structure in the Human c-myc Gene's Promoter Is Converted into B-DNA Form by the Human Poly(ADP-Ribose)Polymerase-1

(2012) Anna Fekete et al.   PLoS One

Sequential RNA degradation pathways provide a fail-safe mechanism to limit the accumulation of unspliced transcripts in Saccharomyces cerevisiae

(2012) S. Sayani et al.   RNA

Overcoming the nucleosome barrier during transcript elongation

(2012) Steven J. Petesch et al.   TRENDS IN GENETICS

The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes

(2012) Minna-Liisa Änkö et al.   GENOME BIOLOGY

Transcriptome-wide Analysis of Regulatory Interactions of the RNA-Binding Protein HuR

(2011) Svetlana Lebedeva et al.   MOLECULAR CELL

Activator-Induced Spread of Poly(ADP-Ribose) Polymerase Promotes Nucleosome Loss at Hsp70

(2011) Steven J. Petesch et al.   MOLECULAR CELL

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins

(2011) Shivendra Kishore et al.   NATURE METHODS

Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43

(2011) Magdalini Polymenidou et al.   NATURE NEUROSCIENCE

Quality control of MAT a1 splicing and exon skipping by nuclear RNA degradation

(2011) Defne E. Egecioglu et al.   NUCLEIC ACIDS RESEARCH

Identification of RNA-protein interaction networks using PAR-CLIP

(2011) Manuel Ascano et al.   Wiley Interdisciplinary Reviews-RNA

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data

(2011) David L Corcoran et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Enhanced G4-DNA binding of 5,10,15,20 (N-propyl-4-pyridyl) porphyrin (TPrPyP4): A comparative study with TMPyP4

(2010) Susanna Cogoi et al.   CHEMICAL COMMUNICATIONS

Double-stranded DNA Binding Domain of Poly(ADP-ribose) Polymerase-1 and Molecular Insight into the Regulation of Its Activity

(2010) Orlando Huambachano et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Increased Foxp3+ Regulatory T Cells in Poly(ADP-Ribose) Polymerase-1 Deficiency

(2010) F. Nasta et al.   JOURNAL OF IMMUNOLOGY

PARP-1 Regulates Chromatin Structure and Transcription through a KDM5B-Dependent Pathway

(2010) Raga Krishnakumar et al.   MOLECULAR CELL

A Cytoplasmic ATM-TRAF6-cIAP1 Module Links Nuclear DNA Damage Signaling to Ubiquitin-Mediated NF-κB Activation

(2010) Michael Hinz et al.   MOLECULAR CELL

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Investigation of PARP-1, PARP-2, and PARG interactomes by affinity-purification mass spectrometry

(2010) Maxim Isabelle et al.   Proteome Science

Evidence-ranked motif identification

(2010) Stoyan Georgiev et al.   GENOME BIOLOGY

The Many Pathways of RNA Degradation

(2009) Jonathan Houseley et al.   CELL

PARP-1 Expression in the Mouse is Controlled by an Autoregulatory Loop: PARP-1 Binding to an Upstream S/MAR Element and to a Novel Recognition Motif in its Promoter Suppresses Transcription

(2009) Melita Vidaković et al.   JOURNAL OF MOLECULAR BIOLOGY

Poly(ADP-ribosyl)ation of heterogeneous nuclear ribonucleoproteins modulates splicing

(2009) Yingbiao Ji et al.   NUCLEIC ACIDS RESEARCH

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

First Evidence of a Functional Interaction between DNA Quadruplexes and Poly(ADP-ribose) Polymerase-1

(2008) V. A. Soldatenkov et al.   ACS Chemical Biology

EJCs at the Heart of Translational Control

(2008) Hervé Le Hir et al.   CELL

Rapid, Transcription-Independent Loss of Nucleosomes over a Large Chromatin Domain at Hsp70 Loci

(2008) Steven J. Petesch et al.   CELL

Poly(ADP-ribose) Binds to the Splicing Factor ASF/SF2 and Regulates Its Phosphorylation by DNA Topoisomerase I

(2008) Maria Malanga et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Widespread Impact of Nonsense-Mediated mRNA Decay on the Yeast Intronome

(2008) Shakir Sayani et al.   MOLECULAR CELL

Proteome-wide identification of poly(ADP-ribose) binding proteins and poly(ADP-ribose)-associated protein complexes

(2008) Jean-Philippe Gagné et al.   NUCLEIC ACIDS RESEARCH

Reciprocal Binding of PARP-1 and Histone H1 at Promoters Specifies Transcriptional Outcomes

(2008) R. Krishnakumar et al.   SCIENCE

The exosome: a multipurpose RNA-decay machine

(2008) Manfred Schmid et al.   TRENDS IN BIOCHEMICAL SCIENCES

The diverse biological roles of mammalian PARPS, a small but powerful family of poly-ADP-ribose polymerases

(2007) Paul et al.   Frontiers in Bioscience-Landmark