Regulation of alternative polyadenylation by the C2H2-zinc-finger protein Sp1

Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing

(2021) Tassa Saldi et al.   MOLECULAR CELL

Functional characterization of RebL1 highlights the evolutionary conservation of oncogenic activities of the RBBP4/7 orthologue in Tetrahymena thermophila

(2021) Syed Nabeel-Shah et al.   NUCLEIC ACIDS RESEARCH

SARS-CoV-2 nucleocapsid protein binds host mRNAs and attenuates stress granules to impair host stress response

(2021) Syed Nabeel-Shah et al.   iScience

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

DNA Methylation Regulates Alternative Polyadenylation via CTCF and the Cohesin Complex

(2020) Vishal Nanavaty et al.   MOLECULAR CELL

How to measure and evaluate binding affinities

(2020) Inga Jarmoskaite et al.   eLife

Activation of the Endonuclease that Defines mRNA 3′ Ends Requires Incorporation into an 8-Subunit Core Cleavage and Polyadenylation Factor Complex

(2019) Chris H. Hill et al.   MOLECULAR CELL

Alternative cleavage and polyadenylation in health and disease

(2019) Andreas J. Gruber et al.   NATURE REVIEWS GENETICS

CDK12 loss in cancer cells affects DNA damage response genes through premature cleavage and polyadenylation

(2019) Malgorzata Krajewska et al.   Nature Communications

RNA Binding Protein CELF2 Regulates Signal-Induced Alternative Polyadenylation by Competing with Enhancers of the Polyadenylation Machinery

(2019) Rakesh Chatrikhi et al.   Cell Reports

Structural Insights into the Human Pre-mRNA 3′-End Processing Machinery

(2019) Yixiao Zhang et al.   MOLECULAR CELL

Specificity Protein Transcription Factors and Cancer: Opportunities for Drug Development

(2018) Stephen Safe et al.   Cancer Prevention Research

Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation

(2018) Yong Zhu et al.   MOLECULAR CELL

3′ UTR shortening represses tumor-suppressor genes in trans by disrupting ceRNA crosstalk

(2018) Hyun Jung Park et al.   NATURE GENETICS

Widespread intronic polyadenylation inactivates tumour suppressor genes in leukaemia

(2018) Shih-Han Lee et al.   NATURE

Transcriptome 3′end organization by PCF11 links alternative polyadenylation to formation and neuronal differentiation of neuroblastoma

(2018) Anton Ogorodnikov et al.   Nature Communications

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms

(2017) Javier Tapial et al.   GENOME RESEARCH

RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins

(2017) Debashish Ray et al.   METHODS

Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors

(2017) Hong Han et al.   MOLECULAR CELL

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens

(2017) Traver Hart et al.   G3-Genes Genomes Genetics

Roles of Rap1 signaling in tumor cell migration and invasion

(2017) Zhang Yi-Lei et al.   Cancer Biology & Medicine

On the Dependency of Cellular Protein Levels on mRNA Abundance

(2016) Yansheng Liu et al.   CELL

Multiparameter functional diversity of human C2H2 zinc finger proteins

(2016) Frank W. Schmitges et al.   GENOME RESEARCH

A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation

(2016) Andreas J. Gruber et al.   GENOME RESEARCH

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

Alternative polyadenylation of mRNA precursors

(2016) Bin Tian et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

3’UTR Shortening Potentiates MicroRNA-Based Repression of Pro-differentiation Genes in Proliferating Human Cells

(2016) Yonit Hoffman et al.   PLoS Genetics

Sp1 and the ‘hallmarks of cancer’

(2015) Kate Beishline et al.   FEBS Journal

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Sp1 transcription factor: A long-standing target in cancer chemotherapy

(2015) Carolina Vizcaíno et al.   PHARMACOLOGY & THERAPEUTICS

Transcription factor trapping by RNA in gene regulatory elements

(2015) A. A. Sigova et al.   SCIENCE

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis

(2014) Guangchuang Yu et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

(2014) Manuel Irimia et al.   CELL

CTCF regulates the human p53 gene through direct interaction with its natural antisense transcript, Wrap53

(2014) R. Saldana-Meyer et al.   GENES & DEVELOPMENT

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

CFIm25 links alternative polyadenylation to glioblastoma tumour suppression

(2014) Chioniso P. Masamha et al.   NATURE

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3′-UTR landscape across seven tumour types

(2014) Zheng Xia et al.   Nature Communications

Human-Chromatin-Related Protein Interactions Identify a Demethylase Complex Required for Chromosome Segregation

(2014) Edyta Marcon et al.   Cell Reports

Systematic Analysis of the Role of RNA-Binding Proteins in the Regulation of RNA Stability

(2014) Ayesha Hasan et al.   PLoS Genetics

Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression

(2013) S. Lianoglou et al.   GENES & DEVELOPMENT

SAINTexpress: Improvements and additional features in Significance Analysis of INTeractome software

(2013) Guoci Teo et al.   Journal of Proteomics

iCLIP: Protein–RNA interactions at nucleotide resolution

(2013) Ina Huppertz et al.   METHODS

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Alternative cleavage and polyadenylation: extent, regulation and function

(2013) Ran Elkon et al.   NATURE REVIEWS GENETICS

Structure, function and regulation of Transcription Factor IIIA: From Xenopus to Arabidopsis

(2012) Elodie Layat et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Site identification in high-throughput RNA–protein interaction data

(2012) Philip J. Uren et al.   BIOINFORMATICS

A quantitative atlas of polyadenylation in five mammals

(2012) Adnan Derti et al.   GENOME RESEARCH

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

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

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

Alternative polyadenylation: New insights from global analyses

(2012) Y. Shi   RNA

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

E2F mediates enhanced alternative polyadenylation in proliferation

(2012) Ran Elkon et al.   GENOME BIOLOGY

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

YY1 Tethers Xist RNA to the Inactive X Nucleation Center

(2011) Yesu Jeon et al.   CELL

Ending the message: poly(A) signals then and now

(2011) N. J. Proudfoot   GENES & DEVELOPMENT

Mechanisms and Consequences of Alternative Polyadenylation

(2011) Dafne Campigli Di Giammartino et al.   MOLECULAR CELL

A germline variant in the TP53 polyadenylation signal confers cancer susceptibility

(2011) Simon N Stacey et al.   NATURE GENETICS

Sp1 expression regulates lung tumor progression

(2011) T-I Hsu et al.   ONCOGENE

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

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

(2010) Markus Hafner et al.   CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Structural basis of UGUA recognition by the Nudix protein CFIm25 and implications for a regulatory role in mRNA 3' processing

(2010) Q. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

(2009) Christine Mayr et al.   CELL

Sp1 Phosphorylation and Its Regulation of Gene Transcription

(2009) N. Y. Tan et al.   MOLECULAR AND CELLULAR BIOLOGY

Molecular Architecture of the Human Pre-mRNA 3′ Processing Complex

(2009) Yongsheng Shi et al.   MOLECULAR CELL

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

(2009) Debashish Ray et al.   NATURE BIOTECHNOLOGY

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

(2008) R. Sandberg et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY