CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis

Paraspeckles are constructed as block copolymer micelles

(2021) Tomohiro Yamazaki et al.   EMBO JOURNAL

Pancancer survival analysis of cancer hallmark genes

(2021) Ádám Nagy et al.   Scientific Reports

Targeting MAPK Signaling in Cancer: Mechanisms of Drug Resistance and Sensitivity

(2020) Shannon Lee et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A Cancer-Specific Ubiquitin Ligase Drives mRNA Alternative Polyadenylation by Ubiquitinating the mRNA 3′ End Processing Complex

(2020) Seung Wook Yang et al.   MOLECULAR CELL

Profiles of prognostic alternative splicing signature in hepatocellular carcinoma

(2020) Fangming Wu et al.   Cancer Medicine

Differential Alternative Polyadenylation Landscapes Mediate Hematopoietic Stem Cell Activation and Regulate Glutamine Metabolism

(2020) Pia Sommerkamp et al.   Cell Stem Cell

Protein Kinase CK2 in Cancer Energetics

(2020) Eduardo Silva-Pavez et al.   Frontiers in Oncology

Prevention of dsRNA‐induced interferon signaling by AGO1x is linked to breast cancer cell proliferation

(2020) Souvik Ghosh et al.   EMBO JOURNAL

Role of protein kinase CK2 in antitumor drug resistance

(2019) Christian Borgo et al.   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

CFIm25 and alternative polyadenylation: Conflicting roles in cancer

(2019) Mohammad Hassan Jafari Najaf Abadi et al.   CANCER LETTERS

JAZF1 Suppresses Papillary Thyroid Carcinoma Cell Proliferation and Facilitates Apoptosis via Regulating TAK1/NF-κB Pathways

(2019) Liangliang Huang et al.   OncoTargets and Therapy

Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling

(2018) Justin Brumbaugh et al.   CELL

p38δ MAPK regulates aggresome biogenesis by phosphorylating SQSTM1 in response to proteasomal stress

(2018) Chenliang Zhang et al.   JOURNAL OF CELL SCIENCE

Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation

(2018) Yong Zhu et al.   MOLECULAR CELL

Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation

(2018) Tomohiro Yamazaki et al.   MOLECULAR CELL

NUDT21 negatively regulates PSMB2 and CXXC5 by alternative polyadenylation and contributes to hepatocellular carcinoma suppression

(2018) Sheng Tan et al.   ONCOGENE

ERK Inhibition: A New Front in the War against MAPK Pathway–Driven Cancers?

(2018) Inna Smalley et al.   Cancer Discovery

Quantifying intracellular rates of glycolytic and oxidative ATP production and consumption using extracellular flux measurements

(2018) Shona A. Mookerjee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2019

(2018) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

The ERK and JNK pathways in the regulation of metabolic reprogramming

(2018) Salvatore Papa et al.   ONCOGENE

Knockdown of NUDT21 inhibits proliferation and promotes apoptosis of human K562 leukemia cells through ERK pathway

(2018) Lan Zhang et al.   Cancer Management and Research

Hyper-phosphorylation of Sequestosome-1 Distinguishes Resistance to Cisplatin in Patient Derived High Grade Serous Ovarian Cancer Cells

(2017) Elizabeth V. Nguyen et al.   MOLECULAR & CELLULAR PROTEOMICS

NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing

(2017) Li Jiang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues

(2017) Alejandro Reyes et al.   NUCLEIC ACIDS RESEARCH

P38 delta MAPK promotes breast cancer progression and lung metastasis by enhancing cell proliferation and cell detachment

(2017) M Wada et al.   ONCOGENE

Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments

(2017) Yuval Malka et al.   Nature Communications

NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing

(2017) Li Jiang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Discovery of (S)-1-(1-(4-Chloro-3-fluorophenyl)-2-hydroxyethyl)-4-(2-((1-methyl-1H-pyrazol-5-yl)amino)pyrimidin-4-yl)pyridin-2(1H)-one (GDC-0994), an Extracellular Signal-Regulated Kinase 1/2 (ERK1/2) Inhibitor in Early Clinical Development

(2016) James F. Blake et al.   JOURNAL OF MEDICINAL CHEMISTRY

Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments

(2016) Erik Ahrné et al.   JOURNAL OF PROTEOME RESEARCH

Robust, Sensitive, and Automated Phosphopeptide Enrichment Optimized for Low Sample Amounts Applied to Primary Hippocampal Neurons

(2016) Harm Post et al.   JOURNAL OF PROTEOME RESEARCH

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A) Site Usage

(2016) Hun-Way Hwang et al.   Cell Reports

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

(2015) Henry Heberle et al.   BMC BIOINFORMATICS

Polysome arrest restricts miRNA turnover by preventing exosomal export of miRNA in growth-retarded mammalian cells

(2015) Souvik Ghosh et al.   MOLECULAR BIOLOGY OF THE CELL

Efficient Test and Visualization of Multi-Set Intersections

(2015) Minghui Wang et al.   Scientific Reports

Systematic Profiling of Poly(A)+ Transcripts Modulated by Core 3’ End Processing and Splicing Factors Reveals Regulatory Rules of Alternative Cleavage and Polyadenylation

(2015) Wencheng Li et al.   PLoS Genetics

The role of MAPK signalling pathways in the response to endoplasmic reticulum stress

(2014) Nicola J. Darling et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Driving glioblastoma growth by alternative polyadenylation

(2014) Ting Han et al.   CELL RESEARCH

CFIm25 links alternative polyadenylation to glioblastoma tumour suppression

(2014) Chioniso P. Masamha et al.   NATURE

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Global 3′ UTR shortening has a limited effect on protein abundance in proliferating T cells

(2014) Andreas R. Gruber et al.   Nature Communications

3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts

(2013) N. Spies et al.   GENOME RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

U1 snRNP Determines mRNA Length and Regulates Isoform Expression

(2012) Michael G. Berg et al.   CELL

mRNA 3′ End Processing Factors: A Phylogenetic Comparison

(2012) Sarah K. Darmon et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

Alternative 3′-end processing of long noncoding RNA initiates construction of nuclear paraspeckles

(2012) Takao Naganuma et al.   EMBO JOURNAL

Inhibition of MKK7–JNK by the TOR Signaling Pathway Regulator-Like Protein Contributes to Resistance of HCC Cells to TRAIL-Induced Apoptosis

(2012) In Sung Song et al.   GASTROENTEROLOGY

A quantitative atlas of polyadenylation in five mammals

(2012) Adnan Derti et al.   GENOME RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Cleavage factor Imis a key regulator of 3′ UTR length

(2012) Andreas R. Gruber et al.   RNA Biology

Genome-wide Analysis of Pre-mRNA 3′ End Processing Reveals a Decisive Role of Human Cleavage Factor I in the Regulation of 3′ UTR Length

(2012) Georges Martin et al.   Cell Reports

Erk regulation of pyruvate dehydrogenase flux through PDK4 modulates cell proliferation

(2011) A. R. Grassian et al.   GENES & DEVELOPMENT

Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells

(2011) Yuexi Wang et al.   PROTEOMICS

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

(2011) P. J. Shepard et al.   RNA

Crystal Structure of a Human Cleavage Factor CFIm25/CFIm68/RNA Complex Provides an Insight into Poly(A) Site Recognition and RNA Looping

(2011) Qin Yang et al.   STRUCTURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Evidence that cleavage factor Im is a heterotetrameric protein complex controlling alternative polyadenylation

(2010) Sol Kim et al.   GENES TO CELLS

Regulation of PTEN/Akt and MAP kinase signaling pathways by the ubiquitin ligase activators Ndfip1 and Ndfip2

(2010) T. Mund et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Addiction to protein kinase CK2: A common denominator of diverse cancer cells?

(2009) Maria Ruzzene et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

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

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

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr et al.   CELL

Quantitative cell signalling analysis reveals down-regulation of MAPK pathway activation in colorectal cancer

(2009) Christian Gulmann et al.   JOURNAL OF PATHOLOGY

Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation

(2009) M. G. Vander Heiden et al.   SCIENCE

Pyruvate Dehydrogenase Complex Activity Controls Metabolic and Malignant Phenotype in Cancer Cells

(2008) Thomas McFate et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites

(2008) R. Sandberg et al.   SCIENCE