Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing

LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival

(2021) Raeann Goering et al.   BMC GENOMICS

Transcriptome-wide profiling of multiple RNA modifications simultaneously at single-base resolution

(2019) Vahid Khoddami et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

mRNA structure determines modification by pseudouridine synthase 1

(2019) Thomas M. Carlile et al.   Nature Chemical Biology

Most human introns are recognized via multiple and tissue-specific branchpoints

(2018) Jose Mario Bello Pineda et al.   GENES & DEVELOPMENT

Systematic Discovery of RNA Binding Proteins that Regulate MicroRNA Levels

(2018) Julia K. Nussbacher et al.   MOLECULAR CELL

Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing

(2018) Jan Attig et al.   CELL

Landscape of the complete RNA chemical modifications in the human 80S ribosome

(2018) Masato Taoka et al.   NUCLEIC ACIDS RESEARCH

Variants in PUS7 Cause Intellectual Disability with Speech Delay, Microcephaly, Short Stature, and Aggressive Behavior

(2018) Arjan P.M. de Brouwer et al.   AMERICAN JOURNAL OF HUMAN GENETICS

m 6 A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover

(2017) Shengdong Ke et al.   GENES & DEVELOPMENT

Large-scale analysis of branchpoint usage across species and cell lines

(2017) Allison J. Taggart et al.   GENOME RESEARCH

TRUB1 is the predominant pseudouridine synthase acting on mammalian mRNA via a predictable and conserved code

(2017) Modi Safra et al.   GENOME RESEARCH

Pseudouridine Modification Inhibits Muscleblind-like 1 (MBNL1) Binding to CCUG Repeats and Minimally Structured RNA through Reduced RNA Flexibility

(2017) Elaine deLorimier et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dual nature of pseudouridylation in U2 snRNA: Pus1p-dependent and Pus1p-independent activities in yeasts and higher eukaryotes

(2017) Svetlana Deryusheva et al.   RNA

Pseudouridine and N 6 -methyladenosine modifications weaken PUF protein/RNA interactions

(2017) Pavanapuresan P. Vaidyanathan et al.   RNA

Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries

(2016) Elena Grassi et al.   BMC BIOINFORMATICS

Pseudouridylation of 7SK snRNA promotes 7SK snRNP formation to suppress HIV‐1 transcription and escape from latency

(2016) Yang Zhao et al.   EMBO REPORTS

A homozygous truncating mutation in PUS3 expands the role of tRNA modification in normal cognition

(2016) Ranad Shaheen et al.   HUMAN GENETICS

eQTL analysis links inflammatory bowel disease associated 1q21 locus to ECM1 gene

(2016) Katja Repnik et al.   JOURNAL OF APPLIED GENETICS

Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens

(2016) Caleb D. Marceau et al.   NATURE

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

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

Messenger RNA modifications: Form, distribution, and function

(2016) W. V. Gilbert et al.   SCIENCE

Genome-wide discovery of human splicing branchpoints

(2015) Tim R. Mercer et al.   GENOME RESEARCH

Global estimation of the 3′ untranslated region landscape using RNA sequencing

(2015) MinHyeok Kim et al.   METHODS

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

(2015) Nian Liu et al.   NATURE

Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome

(2015) Xiaoyu Li et al.   Nature Chemical Biology

The MEME Suite

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

Chromatin proteomic profiling reveals novel proteins associated with histone-marked genomic regions

(2015) Xiong Ji et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA

(2014) Schraga Schwartz et al.   CELL

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

Context-dependent control of alternative splicing by RNA-binding proteins

(2014) Xiang-Dong Fu et al.   NATURE REVIEWS GENETICS

Transcriptome-Wide Mapping of Pseudouridines: Pseudouridine Synthases Modify Specific mRNAs in S. cerevisiae

(2014) Alexander F. Lovejoy et al.   PLoS One

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

Small nucleolar RNAs functioning and potential roles in cancer

(2014) Nithyananda Thorenoor et al.   TUMOR BIOLOGY

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

(2014) Zheng Xia et al.   Nature Communications

The RNA-Binding Protein QKI Suppresses Cancer-Associated Aberrant Splicing

(2014) Feng-Yang Zong et al.   PLoS Genetics

Small RNAs with big implications: new insights into H/ACA snoRNA function and their role in human disease

(2014) Mary McMahon et al.   Wiley Interdisciplinary Reviews-RNA

In Human Pseudouridine Synthase 1 (hPus1), a C-Terminal Helical Insert Blocks tRNA from Binding in the Same Orientation as in the Pus1 Bacterial Homologue TruA, Consistent with Their Different Target Selectivities

(2013) Nadine Czudnochowski et al.   JOURNAL OF MOLECULAR BIOLOGY

Identification of direct targets and modified bases of RNA cytosine methyltransferases

(2013) Vahid Khoddami et al.   NATURE BIOTECHNOLOGY

Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells

(2013) Charlotte Stadler et al.   NATURE METHODS

The contribution of pseudouridine to stabilities and structure of RNAs

(2013) Elzbieta Kierzek et al.   NUCLEIC ACIDS RESEARCH

Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression

(2013) A. Pandya-Jones et al.   RNA

Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides

(2013) G. A. Hudson et al.   RNA

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) Dev M. Bhatt et al.   CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila

(2011) Y. L. Khodor et al.   GENES & DEVELOPMENT

A Meta-Analysis of Genome-Wide Association Scans Identifies IL18RAP, PTPN2, TAGAP, and PUS10 As Shared Risk Loci for Crohn's Disease and Celiac Disease

(2011) Eleonora A. M. Festen et al.   PLoS Genetics

Functions and mechanisms of spliceosomal small nuclear RNA pseudouridylation

(2011) Guowei Wu et al.   Wiley Interdisciplinary Reviews-RNA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A Flexible RNA Backbone within the Polypyrimidine Tract Is Required for U2AF65 Binding and Pre-mRNA Splicing In Vivo

(2010) C. Chen et al.   MOLECULAR AND CELLULAR BIOLOGY

Yeast Pre-rRNA Processing and Modification Occur Cotranscriptionally

(2010) Martin Koš et al.   MOLECULAR CELL

Multiple common variants for celiac disease influencing immune gene expression

(2010) Patrick C A Dubois et al.   NATURE GENETICS

Genome-wide association identifies multiple ulcerative colitis susceptibility loci

(2010) Dermot P B McGovern et al.   NATURE GENETICS

Spliceosomal snRNA modifications and their function

(2010) John Karijolich et al.   RNA Biology

Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease

(2008) Jeffrey C Barrett et al.   NATURE GENETICS