Increased chromatin accessibility facilitates intron retention in specific cell differentiation states

Intron retention: importance, challenges, and opportunities

(2022) Justin J.-L. Wong et al.   TRENDS IN GENETICS

Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning

(2021) Nadine Körtel et al.   NUCLEIC ACIDS RESEARCH

High frequency of intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAs

(2021) Pinki Dey et al.   Epigenetics & Chromatin

Macrophage development and activation involve coordinated intron retention in key inflammatory regulators

(2020) Immanuel D Green et al.   NUCLEIC ACIDS RESEARCH

Machine learning and clinical epigenetics: a review of challenges for diagnosis and classification

(2020) S. Rauschert et al.   Clinical Epigenetics

Complex landscape of alternative splicing in myeloid neoplasms

(2020) Courtney E. Hershberger et al.   LEUKEMIA

Holding on to junk bonds: intron retention in cancer and therapy

(2020) Geoffray Monteuuis et al.   CANCER RESEARCH

Transcriptome-wide analysis and modelling of prognostic alternative splicing signatures in invasive breast cancer: a prospective clinical study

(2020) Linbang Wang et al.   Scientific Reports

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan et al.   CELL

Combinatorial Genetics Reveals a Scaling Law for the Effects of Mutations on Splicing

(2019) Pablo Baeza-Centurion et al.   CELL

RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing

(2019) Heidi Dvinge et al.   GENOME RESEARCH

Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data

(2019) Karl J V Nordström et al.   NUCLEIC ACIDS RESEARCH

Dynamic changes in intron retention are tightly associated with regulation of splicing factors and proliferative activity during B-cell development

(2019) Sebastian Ullrich et al.   NUCLEIC ACIDS RESEARCH

Position-specific intron retention is mediated by the histone methyltransferase SDG725

(2018) Gang Wei et al.   BMC BIOLOGY

Population-dependent Intron Retention and DNA Methylation in Breast Cancer

(2018) Dongwook Kim et al.   MOLECULAR CANCER RESEARCH

Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing

(2018) Clare Pacini et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys

(2018) Marilyn Parra et al.   RNA

Intron retention is a source of neoepitopes in cancer

(2018) Alicia C Smart et al.   NATURE BIOTECHNOLOGY

TEPIC 2—an extended framework for transcription factor binding prediction and integrative epigenomic analysis

(2018) Florian Schmidt et al.   BIOINFORMATICS

DNA methylation/hydroxymethylation regulate gene expression and alternative splicing during terminal granulopoiesis

(2018) Dadi Gao et al.   Epigenomics

Precision Oncology beyond Targeted Therapy: Combining Omics Data with Machine Learning Matches the Majority of Cancer Cells to Effective Therapeutics

(2017) Michael Q. Ding et al.   MOLECULAR CANCER RESEARCH

RNA Pol II Dynamics Modulate Co-transcriptional Chromatin Modification, CTD Phosphorylation, and Transcriptional Direction

(2017) Nova Fong et al.   MOLECULAR CELL

Intron retention is regulated by altered MeCP2-mediated splicing factor recruitment

(2017) Justin J. -L. Wong et al.   Nature Communications

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells

(2017) Sebastian Pott   eLife

A dynamic intron retention program in the mammalian megakaryocyte and erythrocyte lineages

(2016) C. R. Edwards et al.   BLOOD

DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation

(2016) Matthias Farlik et al.   Cell Stem Cell

Epigenomic Profiling of Human CD4 + T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development

(2016) Pawel Durek et al.   IMMUNITY

Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing

(2016) Tassa Saldi et al.   JOURNAL OF MOLECULAR BIOLOGY

Global intron retention mediated gene regulation during CD4+T cell activation

(2016) Ting Ni et al.   NUCLEIC ACIDS RESEARCH

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Epigenetic dynamics of monocyte-to-macrophage differentiation

(2016) Stefan Wallner et al.   Epigenetics & Chromatin

ATtRACT—a database of RNA-binding proteins and associated motifs

(2016) Girolamo Giudice et al.   Database-The Journal of Biological Databases and Curation

Intron retention in mRNA: No longer nonsense

(2015) Justin J.-L. Wong et al.   BIOESSAYS

The role of DNA methylation in directing the functional organization of the cancer epigenome

(2015) Fides D. Lay et al.   GENOME RESEARCH

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

A diverse epigenetic landscape at human exons with implication for expression

(2015) Meromit Singer et al.   NUCLEIC ACIDS RESEARCH

Defective histone supply causes changes in RNA polymerase II elongation rate and cotranscriptional pre-mRNA splicing

(2015) Silvia Jimeno-González et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functionally distinct patterns of nucleosome remodeling at enhancers in glucocorticoid-treated acute lymphoblastic leukemia

(2015) Jennifer N. Wu et al.   Epigenetics & Chromatin

Building Predictive Models inRUsing thecaretPackage

(2015) Max Kuhn   Journal of Statistical Software

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Deep learning of the tissue-regulated splicing code

(2014) Michael K. K. Leung et al.   BIOINFORMATICS

Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate

(2014) Nova Fong et al.   GENES & DEVELOPMENT

Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer

(2014) Phillippa C. Taberlay et al.   GENOME RESEARCH

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

BS69/ZMYND11 Reads and Connects Histone H3.3 Lysine 36 Trimethylation-Decorated Chromatin to Regulated Pre-mRNA Processing

(2014) Rui Guo et al.   MOLECULAR CELL

The human splicing code reveals new insights into the genetic determinants of disease

(2014) H. Y. Xiong et al.   SCIENCE

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation

(2013) Justin J.-L. Wong et al.   CELL

Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects

(2013) J. M. Simon et al.   GENOME RESEARCH

Regulation of alternative splicing by local histone modifications: potential roles for RNA-guided mechanisms

(2013) H.-L. Zhou et al.   NUCLEIC ACIDS RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Abstract 3968: Exploring cancer datasets in the integrative genomics viewer (IGV)

(2012) James T. Robinson et al.   CANCER RESEARCH

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

(2012) T. K. Kelly et al.   GENOME RESEARCH

Nucleosome-Driven Transcription Factor Binding and Gene Regulation

(2012) Cecilia Ballaré et al.   MOLECULAR CELL

Nucleosome distribution and linker DNA: connecting nuclear function to dynamic chromatin structureThis paper is one of a selection of papers published in a Special Issue entitled 31st Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

(2011) Heather J. Szerlong et al.   Biochemistry and Cell Biology

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes

(2011) J. S. You et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Repitools: an R package for the analysis of enrichment-based epigenomic data

(2010) A. L. Statham et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Deciphering the splicing code

(2010) Yoseph Barash et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Genome-Wide Association between Branch Point Properties and Alternative Splicing

(2010) André Corvelo et al.   PLoS Computational Biology

Nucleosome positioning: How is it established, and why does it matter?

(2009) Marta Radman-Livaja et al.   DEVELOPMENTAL BIOLOGY

Nucleosomes are well positioned in exons and carry characteristic histone modifications

(2009) R. Andersson et al.   GENOME RESEARCH

Nucleosome positioning as a determinant of exon recognition

(2009) Hagen Tilgner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin organization marks exon-intron structure

(2009) Schraga Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Conditional Variable Importance for Random Forests

(2008) Carolin Strobl et al.   BMC BIOINFORMATICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY