CD44 alternative splicing senses intragenic DNA methylation in tumors via direct and indirect mechanisms

The RNA-binding protein AKAP8 suppresses tumor metastasis by antagonizing EMT-associated alternative splicing

(2020) Xiaohui Hu et al.   Nature Communications

Sam68 promotes aerobic glycolysis in colorectal cancer by regulating PKM2 alternative splicing

(2020) Jing Zhao et al.   Annals of Translational Medicine

CD44 splice isoform switching determines breast cancer stem cell state

(2019) Honghong Zhang et al.   GENES & DEVELOPMENT

We skip to work: alternative splicing in normal and malignant myelopoiesis

(2018) Alex C. H. Wong et al.   LEUKEMIA

The Importance of DNA Methylation of Exons on Alternative Splicing

(2018) Ronna Shayevitch et al.   RNA

Alternative-splicing defects in cancer: Splicing regulators and their downstream targets, guiding the way to novel cancer therapeutics

(2018) Laura M. Urbanski et al.   Wiley Interdisciplinary Reviews-RNA

Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases

(2018) Lin Lin et al.   GigaScience

Mammalian DNA methyltransferases: new discoveries and open questions

(2018) Humaira Gowher et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The long non-coding RNA MALAT1 promotes ovarian cancer progression by regulating RBFOX2-mediated alternative splicing

(2018) Michael A. Gordon et al.   MOLECULAR CARCINOGENESIS

RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing

(2018) Takayuki Nojima et al.   MOLECULAR CELL

Cell-adhesion molecules and their soluble forms: Promising predictors of “tumor progression” and relapse in leukemia

(2018) Ieda Cristina Cunha Ferreira e Fonseca et al.   TUMOR BIOLOGY

EMT and stemness: flexible processes tuned by alternative splicing in development and cancer progression

(2017) Davide Pradella et al.   Molecular Cancer

Intragenic DNA methylation prevents spurious transcription initiation

(2017) Francesco Neri et al.   NATURE

Independence between pre-mRNA splicing and DNA methylation in an isogenic minigene resource

(2017) Kyster K. Nanan et al.   NUCLEIC ACIDS RESEARCH

DNA methylation variations are required for epithelial-to-mesenchymal transition induced by cancer-associated fibroblasts in prostate cancer cells

(2017) C Pistore et al.   ONCOGENE

Intragenic DNA methylation and BORIS-mediated cancer-specific splicing contribute to the Warburg effect

(2017) Smriti Singh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A CD44v+ subpopulation of breast cancer stem-like cells with enhanced lung metastasis capacity

(2017) Jing Hu et al.   Cell Death & Disease

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

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

MeCP2 regulates Tet1-catalyzed demethylation, CTCF binding, and learning-dependent alternative splicing of the BDNF gene in Turtle

(2017) Zhaoqing Zheng et al.   eLife

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Repurposing the CRISPR-Cas9 system for targeted DNA methylation

(2016) Aleksandar Vojta et al.   NUCLEIC ACIDS RESEARCH

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Dlx-2 and glutaminase upregulate epithelial-mesenchymal transition and glycolytic switch

(2016) Su Yeon Lee et al.   Oncotarget

Alternative Splicing of G9a Regulates Neuronal Differentiation

(2016) Ana Fiszbein et al.   Cell Reports

A Broad Set of Chromatin Factors Influences Splicing

(2016) Eric Allemand et al.   PLoS Genetics

Genome-wide DNA methylation analysis of pseudohypoparathyroidism patients with GNAS imprinting defects

(2016) Anne Rochtus et al.   Clinical Epigenetics

A new view of transcriptome complexity and regulation through the lens of local splicing variations

(2016) Jorge Vaquero-Garcia et al.   eLife

Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation

(2016) James I. McDonald et al.   Biology Open

DNMT1 Regulates Epithelial-Mesenchymal Transition and Cancer Stem Cells, Which Promotes Prostate Cancer Metastasis

(2016) Eunsohl Lee et al.   NEOPLASIA

Regulation of Alternative Splicing Through Coupling with Transcription and Chromatin Structure

(2015) Shiran Naftelberg et al.   Annual Review of Biochemistry

hnRNP L inhibits CD44 V10 exon splicing through interacting with its upstream intron

(2015) Tiing Jen Loh et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

TET-catalyzed oxidation of intragenic 5-methylcytosine regulates CTCF-dependent alternative splicing

(2015) R. J. Marina et al.   EMBO JOURNAL

Integrated methylome and transcriptome analysis reveals novel regulatory elements in pediatric acute lymphoblastic leukemia

(2015) Md Almamun et al.   Epigenetics

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

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

SRSF1-Regulated Alternative Splicing in Breast Cancer

(2015) Olga Anczuków et al.   MOLECULAR CELL

Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation

(2015) Tuncay Baubec et al.   NATURE

Highly efficient Cas9-mediated transcriptional programming

(2015) Alejandro Chavez et al.   NATURE METHODS

Alternative splicing regulates the expression of G9A and SUV39H2 methyltransferases, and dramatically changes SUV39H2 functions

(2015) Oriane Mauger et al.   NUCLEIC ACIDS RESEARCH

CD44 alternative splicing and hnRNP A1 expression are associated with the metastasis of breast cancer

(2015) TIING JEN LOH et al.   ONCOLOGY REPORTS

Transcriptional control of alternative splicing along time: Ideas change, experiments remain

(2015) Alberto R. Kornblihtt   RNA

Methyl-CpG-binding domain proteins: readers of the epigenome

(2015) Qian Du et al.   Epigenomics

Role of DNA Methylation in Modulating Transcription Factor Occupancy

(2015) Matthew T. Maurano et al.   Cell Reports

HP1 Is Involved in Regulating the Global Impact of DNA Methylation on Alternative Splicing

(2015) Ahuvi Yearim et al.   Cell Reports

An integrative analysis of colon cancer identifies an essential function for PRPF6 in tumor growth

(2014) A. S. Adler et al.   GENES & DEVELOPMENT

Cell type-restricted activity of hnRNPM promotes breast cancer metastasis via regulating alternative splicing

(2014) Y. Xu et al.   GENES & DEVELOPMENT

How Slow RNA Polymerase II Elongation Favors Alternative Exon Skipping

(2014) Gwendal Dujardin et al.   MOLECULAR CELL

Genome-Wide Binding of MBD2 Reveals Strong Preference for Highly Methylated Loci

(2014) Roberta Menafra et al.   PLoS One

BCLAF1 and its splicing regulator SRSF10 regulate the tumorigenic potential of colon cancer cells

(2014) Xuexia Zhou et al.   Nature Communications

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments

(2013) Matthias Lienhard et al.   BIOINFORMATICS

Dynamic Integration of Splicing within Gene Regulatory Pathways

(2013) Ulrich Braunschweig et al.   CELL

Methylation-Dependent and -Independent Genomic Targeting Principles of the MBD Protein Family

(2013) Tuncay Baubec et al.   CELL

Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition

(2013) Alika K Maunakea et al.   CELL RESEARCH

Endothelial, epithelial, and fibroblast cells exhibit specific splicing programs independently of their tissue of origin

(2013) P. Mallinjoud et al.   GENOME RESEARCH

DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure

(2013) S. Gelfman et al.   GENOME RESEARCH

DNA methylation dynamics in health and disease

(2013) Yehudit Bergman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Differential roles for MBD2 and MBD3 at methylated CpG islands, active promoters and binding to exon sequences

(2013) Katharina Günther et al.   NUCLEIC ACIDS RESEARCH

The RNA-binding protein Rbfox2: an essential regulator of EMT-driven alternative splicing and a mediator of cellular invasion

(2013) C Braeutigam et al.   ONCOGENE

Programming of DNA Methylation Patterns

(2012) Howard Cedar et al.   Annual Review of Biochemistry

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Maintenance of DNA methylation: Dnmt3b joins the dance

(2012) Emma L. Walton et al.   Epigenetics

Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues

(2012) Femke Simmer et al.   Epigenetics

G9a interacts with Snail and is critical for Snail-mediated E-cadherin repression in human breast cancer

(2012) Chenfang Dong et al.   JOURNAL OF CLINICAL INVESTIGATION

The splicing factor SRSF6 is amplified and is an oncoprotein in lung and colon cancers

(2012) Michal Cohen-Eliav et al.   JOURNAL OF PATHOLOGY

RBFOX2 Is an Important Regulator of Mesenchymal Tissue-Specific Splicing in both Normal and Cancer Tissues

(2012) J. P. Venables et al.   MOLECULAR AND CELLULAR BIOLOGY

Argonaute proteins couple chromatin silencing to alternative splicing

(2012) Maya Ameyar-Zazoua et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Alternative splicing of CD44 mRNA by ESRP1 enhances lung colonization of metastatic cancer cell

(2012) Toshifumi Yae et al.   Nature Communications

Psip1/Ledgf p52 Binds Methylated Histone H3K36 and Splicing Factors and Contributes to the Regulation of Alternative Splicing

(2012) Madapura M. Pradeepa et al.   PLoS Genetics

KDM5B regulates embryonic stem cell self-renewal and represses cryptic intragenic transcription

(2011) Liangqi Xie et al.   EMBO JOURNAL

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

(2011) G. C. Hon et al.   GENOME RESEARCH

Understanding the Dual Nature of CD44 in Breast Cancer Progression

(2011) J. M. V. Louderbough et al.   MOLECULAR CANCER RESEARCH

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons

(2011) Violaine Saint-André et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36

(2011) Sérgio Fernandes de Almeida et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

NSrp70 is a novel nuclear speckle-related protein that modulates alternative pre-mRNA splicing in vivo

(2011) Young-Dae Kim et al.   NUCLEIC ACIDS RESEARCH

Relationship between Gene Body DNA Methylation and Intragenic H3K9me3 and H3K36me3 Chromatin Marks

(2011) Maria A. Hahn et al.   PLoS One

Pre-mRNA splicing is a determinant of histone H3K36 methylation

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

Sam68 regulates EMT through alternative splicing–activated nonsense-mediated mRNA decay of the SF2/ASF proto-oncogene

(2010) Cristina Valacca et al.   JOURNAL OF CELL BIOLOGY

The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate diverse types of alternative splicing events

(2010) Claude C. Warzecha et al.   RNA Biology

Regulation of Alternative Splicing by Histone Modifications

(2010) R. F. Luco et al.   SCIENCE

The Honey Bee Epigenomes: Differential Methylation of Brain DNA in Queens and Workers

(2010) Frank Lyko et al.   PLOS BIOLOGY

Contrasting chromatin organization of CpG islands and exons in the human genome

(2010) Jung Kyoon Choi   GENOME BIOLOGY

Oxidative stress-induced alternative splicing of transformer 2β (SFRS10) and CD44 pre-mRNAs in gastric epithelial cells

(2009) Keiko Takeo et al.   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY

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

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

Alternative Splicing of the Cyclin D1 Proto-Oncogene Is Regulated by the RNA-Binding Protein Sam68

(2009) M. P. Paronetto et al.   CANCER RESEARCH

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Differential chromatin marking of introns and expressed exons by H3K36me3

(2009) Paulina Kolasinska-Zwierz et al.   NATURE GENETICS

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY