Comprehensive analysis of nucleocytoplasmic dynamics of mRNA in Drosophila cells

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

Interactome Mapping Reveals the Evolutionary History of the Nuclear Pore Complex

(2016) Samson O. Obado et al.   PLOS BIOLOGY

Control of Transcript Variability in Single Mammalian Cells

(2015) Nico Battich et al.   CELL

Genome-wide activities of Polycomb complexes control pervasive transcription

(2015) Hun-Goo Lee et al.   GENOME RESEARCH

Extensive cross-regulation of post-transcriptional regulatory networks inDrosophila

(2015) Marcus H. Stoiber et al.   GENOME RESEARCH

General and MicroRNA-Mediated mRNA Degradation Occurs on Ribosome Complexes in Drosophila Cells

(2015) Sanja Antic et al.   MOLECULAR AND CELLULAR BIOLOGY

Control of mammalian gene expression by selective mRNA export

(2015) Vihandha O. Wickramasinghe et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Dynamic profiling of the protein life cycle in response to pathogens

(2015) M. Jovanovic et al.   SCIENCE

Nuclear Retention of mRNA in Mammalian Tissues

(2015) Keren Bahar Halpern et al.   Cell Reports

Nuclear Export of Messenger RNA

(2015) Jun Katahira   Genes

High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

(2014) Michal Rabani et al.   CELL

Nucleoporin FG Domains Facilitate mRNP Remodeling at the Cytoplasmic Face of the Nuclear Pore Complex

(2014) Rebecca L. Adams et al.   GENETICS

Regulatory Interactions between RNA and Polycomb Repressive Complex 2

(2014) Catherine Cifuentes-Rojas et al.   MOLECULAR CELL

Periodic mRNA synthesis and degradation co-operate during cell cycle gene expression

(2014) P. Eser et al.   Molecular Systems Biology

Diversity and dynamics of the Drosophila transcriptome

(2014) James B. Brown et al.   NATURE

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

Selective nuclear export of specific classes of mRNA from mammalian nuclei is promoted by GANP

(2014) Vihandha O. Wickramasinghe et al.   NUCLEIC ACIDS RESEARCH

Easy quantitative assessment of genome editing by sequence trace decomposition

(2014) Eva K. Brinkman et al.   NUCLEIC ACIDS RESEARCH

Transcriptional Silencing by Polycomb-Group Proteins

(2014) U. Grossniklaus et al.   Cold Spring Harbor Perspectives in Biology

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

(2014) Iris Jonkers et al.   eLife

Cap-binding complex (CBC)

(2013) Thomas Gonatopoulos-Pournatzis et al.   BIOCHEMICAL JOURNAL

Gene Expression Is Circular: Factors for mRNA Degradation Also Foster mRNA Synthesis

(2013) Gal Haimovich et al.   CELL

The THO Complex Regulates Pluripotency Gene mRNA Export and Controls Embryonic Stem Cell Self-Renewal and Somatic Cell Reprogramming

(2013) Li Wang et al.   Cell Stem Cell

Human Inositol Polyphosphate Multikinase Regulates Transcript-Selective Nuclear mRNA Export to Preserve Genome Integrity

(2013) Vihandha O. Wickramasinghe et al.   MOLECULAR CELL

A Network Model of the Molecular Organization of Chromatin in Drosophila

(2013) Joke G. van Bemmel et al.   MOLECULAR CELL

Dynamics extracted from fixed cells reveal feedback linking cell growth to cell cycle

(2013) Ran Kafri et al.   NATURE

Promiscuous RNA binding by Polycomb repressive complex 2

(2013) Chen Davidovich et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcript processing and export kinetics are rate-limiting steps in expressing vertebrate segmentation clock genes

(2013) N. P. Hoyle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A global change in RNA polymerase II pausing during the Drosophila midblastula transition

(2013) Kai Chen et al.   eLife

Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions

(2012) Dev M. Bhatt et al.   CELL

Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation

(2012) M. Sun et al.   GENOME RESEARCH

HP1Swi6 Mediates the Recognition and Destruction of Heterochromatic RNA Transcripts

(2012) Claudia Keller et al.   MOLECULAR CELL

Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels

(2012) Sylvia C Tippmann et al.   Molecular Systems Biology

Systematic discovery of structural elements governing stability of mammalian messenger RNAs

(2012) Hani Goodarzi et al.   NATURE

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

(2012) Cole Trapnell et al.   Nature Protocols

The Oncogene eIF4E Reprograms the Nuclear Pore Complex to Promote mRNA Export and Oncogenic Transformation

(2012) Biljana Culjkovic-Kraljacic et al.   Cell Reports

Identification of Cytoplasmic Capping Targets Reveals a Role for Cap Homeostasis in Translation and mRNA Stability

(2012) Chandrama Mukherjee et al.   Cell Reports

The Function of Introns

(2012) Michal Chorev et al.   Frontiers in Genetics

A powerful and flexible approach to the analysis of RNA sequence count data

(2011) Yi-Hui Zhou et al.   BIOINFORMATICS

Promoter Elements Regulate Cytoplasmic mRNA Decay

(2011) Almog Bregman et al.   CELL

Single-Molecule mRNA Decay Measurements Reveal Promoter- Regulated mRNA Stability in Yeast

(2011) Tatjana Trcek et al.   CELL

Epigenetics in Alternative Pre-mRNA Splicing

(2011) Reini F. Luco et al.   CELL

Cap-binding Protein Complex Links Pre-mRNA Capping to Transcription Elongation and Alternative Splicing through Positive Transcription Elongation Factor b (P-TEFb)

(2011) Tina Lenasi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

(2011) C. Miller et al.   Molecular Systems Biology

A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export

(2011) Ben Montpetit et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

Identification of mRNAs that are spliced but not exported to the cytoplasm in the absence of THOC5 in mouse embryo fibroblasts

(2011) A. Guria et al.   RNA

Major role for mRNA stability in shaping the kinetics of gene induction

(2010) Ran Elkon et al.   BMC GENOMICS

RNA Polymerase II Subunits Link Transcription and mRNA Decay to Translation

(2010) Liat Harel-Sharvit et al.   CELL

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

The transcriptional diversity of 25 Drosophila cell lines

(2010) L. Cherbas et al.   GENOME RESEARCH

Control of mRNA Export and Translation Termination by Inositol Hexakisphosphate Requires Specific Interaction with Gle1

(2010) Abel R. Alcázar-Román et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Drosophila melanogaster Dis3 N-terminal domains are required for ribonuclease activities, nuclear localization and exosome interactions

(2010) Megan Mamolen et al.   NUCLEIC ACIDS RESEARCH

Systematic Analysis of Cis-Elements in Unstable mRNAs Demonstrates that CUGBP1 Is a Key Regulator of mRNA Decay in Muscle Cells

(2010) Jerome E. Lee et al.   PLoS One

Regulation of Alternative Splicing by Histone Modifications

(2010) R. F. Luco et al.   SCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Altered Nuclear Retention of mRNAs Containing Inverted Repeats in Human Embryonic Stem Cells: Functional Role of a Nuclear Noncoding RNA

(2009) Ling-Ling Chen et al.   MOLECULAR CELL

TU-tagging: cell type–specific RNA isolation from intact complex tissues

(2009) Michael R Miller et al.   NATURE METHODS

RNA-binding proteins and post-transcriptional gene regulation

(2008) Tina Glisovic et al.   FEBS LETTERS

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

(2008) L. Dolken et al.   RNA