Regulation of alternative splicing by histone modifications.

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CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature (2011) 5.50

Histone methylation: a dynamic mark in health, disease and inheritance. Nat Rev Genet (2012) 5.42

Relationship between nucleosome positioning and DNA methylation. Nature (2010) 5.27

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Epigenetics in alternative pre-mRNA splicing. Cell (2011) 4.74

Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet (2010) 4.30

Mechanisms and consequences of alternative polyadenylation. Mol Cell (2011) 3.96

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res (2012) 3.83

Understanding the language of Lys36 methylation at histone H3. Nat Rev Mol Cell Biol (2012) 3.52

The honey bee epigenomes: differential methylation of brain DNA in queens and workers. PLoS Biol (2010) 3.42

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Functional consequences of developmentally regulated alternative splicing. Nat Rev Genet (2011) 3.27

Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet (2010) 3.19

Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J (2011) 3.16

The rise of regulatory RNA. Nat Rev Genet (2014) 3.02

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Complexity of the alternative splicing landscape in plants. Plant Cell (2013) 2.62

The RNA polymerase II CTD coordinates transcription and RNA processing. Genes Dev (2012) 2.55

Readers of histone modifications. Cell Res (2011) 2.40

Epigenetic mechanisms in cognition. Neuron (2011) 2.31

The histone H3K36 methyltransferase MES-4 acts epigenetically to transmit the memory of germline gene expression to progeny. PLoS Genet (2010) 2.30

Dynamic integration of splicing within gene regulatory pathways. Cell (2013) 2.25

Reciprocal intronic and exonic histone modification regions in humans. Nat Struct Mol Biol (2010) 2.20

Understanding splicing regulation through RNA splicing maps. Trends Genet (2011) 2.12

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Res (2012) 2.09

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Function of alternative splicing. Gene (2012) 2.00

Alternative splicing in plants--coming of age. Trends Plant Sci (2012) 1.93

Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens. Genome Biol (2014) 1.88

Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36. Nat Struct Mol Biol (2011) 1.85

Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing. PLoS Genet (2012) 1.82

Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. Genome Res (2010) 1.80

Argonaute proteins couple chromatin silencing to alternative splicing. Nat Struct Mol Biol (2012) 1.80

5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary. Nat Struct Mol Biol (2012) 1.74

Mechanisms of the androgen receptor splicing in prostate cancer cells. Oncogene (2013) 1.67

Pre-mRNA splicing is a determinant of histone H3K36 methylation. Proc Natl Acad Sci U S A (2011) 1.66

Phosphoproteomics screen reveals akt isoform-specific signals linking RNA processing to lung cancer. Mol Cell (2014) 1.61

Mechanisms and Regulation of Alternative Pre-mRNA Splicing. Annu Rev Biochem (2015) 1.59

Epigenetics and bacterial infections. Cold Spring Harb Perspect Med (2012) 1.56

Chromatin density and splicing destiny: on the cross-talk between chromatin structure and splicing. EMBO J (2010) 1.53

RBFOX1 regulates both splicing and transcriptional networks in human neuronal development. Hum Mol Genet (2012) 1.51

rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc Natl Acad Sci U S A (2014) 1.47

Epigenome mapping in normal and disease States. Circ Res (2010) 1.47

Exon junction complex subunits are required to splice Drosophila MAP kinase, a large heterochromatic gene. Cell (2010) 1.46

Promoter-like epigenetic signatures in exons displaying cell type-specific splicing. Genome Biol (2015) 1.46

Transcriptional activity regulates alternative cleavage and polyadenylation. Mol Syst Biol (2011) 1.41

Mediator complex regulates alternative mRNA processing via the MED23 subunit. Mol Cell (2012) 1.41

DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. Nat Genet (2013) 1.40

Cell-to-cell variability of alternative RNA splicing. Mol Syst Biol (2011) 1.38

Genome-wide control of RNA polymerase II activity by cohesin. PLoS Genet (2013) 1.38

Histone deacetylase activity modulates alternative splicing. PLoS One (2011) 1.37

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets. Genome Biol (2011) 1.36

Arginine methylation mediated by the Arabidopsis homolog of PRMT5 is essential for proper pre-mRNA splicing. Proc Natl Acad Sci U S A (2010) 1.36

Type II protein arginine methyltransferase 5 (PRMT5) is required for circadian period determination in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2010) 1.33

Quantitative evaluation of all hexamers as exonic splicing elements. Genome Res (2011) 1.32

Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects. Genome Res (2013) 1.31

Hu proteins regulate alternative splicing by inducing localized histone hyperacetylation in an RNA-dependent manner. Proc Natl Acad Sci U S A (2011) 1.30

Gene body methylation is conserved between plant orthologs and is of evolutionary consequence. Proc Natl Acad Sci U S A (2013) 1.28

KDM5B regulates embryonic stem cell self-renewal and represses cryptic intragenic transcription. EMBO J (2011) 1.27

Myeloid malignancies: mutations, models and management. BMC Cancer (2012) 1.24

A selective inhibitor and probe of the cellular functions of Jumonji C domain-containing histone demethylases. J Am Chem Soc (2011) 1.22

SET for life: biochemical activities and biological functions of SET domain-containing proteins. Trends Biochem Sci (2013) 1.22

The splicing regulator PTBP2 interacts with the cytidine deaminase AID and promotes binding of AID to switch-region DNA. Nat Immunol (2010) 1.20

Neuronal regulation of pre-mRNA splicing by polypyrimidine tract binding proteins, PTBP1 and PTBP2. Crit Rev Biochem Mol Biol (2012) 1.20

Potential in vivo roles of nucleic acid triple-helices. RNA Biol (2011) 1.20

Mutation of Arabidopsis spliceosomal timekeeper locus1 causes circadian clock defects. Plant Cell (2012) 1.17

Dynamic histone acetylation is critical for cotranscriptional spliceosome assembly and spliceosomal rearrangements. Proc Natl Acad Sci U S A (2011) 1.16

Pharmacogenomics of the RNA world: structural RNA polymorphisms in drug therapy. Clin Pharmacol Ther (2011) 1.15

Global dissection of alternative splicing in paleopolyploid soybean. Plant Cell (2014) 1.15

Activation of DNA damage response signaling by condensed chromatin. Cell Rep (2014) 1.14

Networking in a global world: establishing functional connections between neural splicing regulators and their target transcripts. RNA (2011) 1.14

Histone methyltransferase SETD2 coordinates FACT recruitment with nucleosome dynamics during transcription. Nucleic Acids Res (2013) 1.12

Epigenetic features are significantly associated with alternative splicing. BMC Genomics (2012) 1.11

Spliceosome mutations exhibit specific associations with epigenetic modifiers and proto-oncogenes mutated in myelodysplastic syndrome. Haematologica (2013) 1.11

Two new and distinct roles for Drosophila Argonaute-2 in the nucleus: alternative pre-mRNA splicing and transcriptional repression. Genes Dev (2013) 1.10

Regulation of alternative splicing by local histone modifications: potential roles for RNA-guided mechanisms. Nucleic Acids Res (2013) 1.10

Chromatin and epigenetic regulation of pre-mRNA processing. Hum Mol Genet (2012) 1.10

Complex exon-intron marking by histone modifications is not determined solely by nucleosome distribution. PLoS One (2010) 1.09

Histone lysine methyltransferase Wolf-Hirschhorn syndrome candidate 1 is involved in human carcinogenesis through regulation of the Wnt pathway. Neoplasia (2011) 1.08

An RNA polymerase II-coupled function for histone H3K36 methylation in checkpoint activation and DSB repair. Nat Commun (2014) 1.08

Co-transcriptional regulation of alternative pre-mRNA splicing. Biochim Biophys Acta (2012) 1.08

Interrogating the function of metazoan histones using engineered gene clusters. Dev Cell (2015) 1.07

A conserved role for intragenic DNA methylation in alternative pre-mRNA splicing. Transcription (2012) 1.07

Updating the CTD Story: From Tail to Epic. Genet Res Int (2011) 1.06

Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer. Nucleic Acids Res (2015) 1.06

Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells. Proc Natl Acad Sci U S A (2014) 1.05

Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells. Mol Cell (2012) 1.05

3' end formation of pre-mRNA and phosphorylation of Ser2 on the RNA polymerase II CTD are reciprocally coupled in human cells. Genes Dev (2014) 1.05

Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus. Nucleic Acids Res (2012) 1.04

BS69/ZMYND11 reads and connects histone H3.3 lysine 36 trimethylation-decorated chromatin to regulated pre-mRNA processing. Mol Cell (2014) 1.04

Buffering and the evolution of chromosome-wide gene regulation. Chromosoma (2011) 1.04

Genome-wide detection of condition-sensitive alternative splicing in Arabidopsis roots. Plant Physiol (2013) 1.03

Epigenetic virtues of chromodomains. Crit Rev Biochem Mol Biol (2011) 1.03

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet (2008) 24.51

Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol (2005) 13.21

Alternative splicing: new insights from global analyses. Cell (2006) 10.31

Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet (2009) 8.11

Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet (2007) 7.42

Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell (2004) 7.32

The human SWI/SNF subunit Brm is a regulator of alternative splicing. Nat Struct Mol Biol (2005) 6.60

Chromatin organization marks exon-intron structure. Nat Struct Mol Biol (2009) 5.90

A slow RNA polymerase II affects alternative splicing in vivo. Mol Cell (2003) 5.82

Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing. Mol Cell (2007) 5.78

Nucleosome positioning as a determinant of exon recognition. Nat Struct Mol Biol (2009) 5.14

ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicing. Mol Cell (2009) 5.03

Multiple links between transcription and splicing. RNA (2004) 4.90

Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res (2009) 3.95

Biased chromatin signatures around polyadenylation sites and exons. Mol Cell (2009) 3.74

DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation. Cell (2009) 3.66

Control of alternative splicing through siRNA-mediated transcriptional gene silencing. Nat Struct Mol Biol (2009) 3.47

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nat Biotechnol (2009) 3.44

Crossregulation and functional redundancy between the splicing regulator PTB and its paralogs nPTB and ROD1. Mol Cell (2007) 3.22

Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing. Proc Natl Acad Sci U S A (2009) 2.94

Transcriptional activators differ in their abilities to control alternative splicing. J Biol Chem (2002) 2.56

RNAi-mediated PTB depletion leads to enhanced exon definition. Mol Cell (2002) 2.34

Chromatin binding of SRp20 and ASF/SF2 and dissociation from mitotic chromosomes is modulated by histone H3 serine 10 phosphorylation. Mol Cell (2009) 2.10

Structure of human MRG15 chromo domain and its binding to Lys36-methylated histone H3. Nucleic Acids Res (2006) 2.09

An intronic splicing silencer causes skipping of the IIIb exon of fibroblast growth factor receptor 2 through involvement of polypyrimidine tract binding protein. Mol Cell Biol (2000) 2.08

RBP2 is an MRG15 complex component and down-regulates intragenic histone H3 lysine 4 methylation. Genes Cells (2007) 1.71

MAZ elements alter transcription elongation and silencing of the fibroblast growth factor receptor 2 exon IIIb. J Biol Chem (2004) 1.52

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet (2008) 24.51

Release of chromatin protein HMGB1 by necrotic cells triggers inflammation. Nature (2002) 19.77

RAF inhibitor resistance is mediated by dimerization of aberrantly spliced BRAF(V600E). Nature (2011) 10.77

Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature (2011) 10.16

The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell (2010) 8.66

Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. Dev Cell (2006) 8.53

An RNA map predicting Nova-dependent splicing regulation. Nature (2006) 7.63

Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell (2004) 7.32

Lamin A-dependent nuclear defects in human aging. Science (2006) 6.71

Most "dark matter" transcripts are associated with known genes. PLoS Biol (2010) 6.60

Deciphering the splicing code. Nature (2010) 6.27

Global transcription in pluripotent embryonic stem cells. Cell Stem Cell (2008) 5.81

Ubiquitination regulates PTEN nuclear import and tumor suppression. Cell (2007) 5.62

The double bromodomain protein Brd4 binds to acetylated chromatin during interphase and mitosis. Proc Natl Acad Sci U S A (2003) 5.59

Chromatin in pluripotent embryonic stem cells and differentiation. Nat Rev Mol Cell Biol (2006) 5.18

Reversal of the cellular phenotype in the premature aging disease Hutchinson-Gilford progeria syndrome. Nat Med (2005) 5.01

Probing microRNAs with microarrays: tissue specificity and functional inference. RNA (2004) 4.91

A compendium of RNA-binding motifs for decoding gene regulation. Nature (2013) 4.91

The evolutionary landscape of alternative splicing in vertebrate species. Science (2012) 4.78

Epigenetics in alternative pre-mRNA splicing. Cell (2011) 4.74

Maintenance of stable heterochromatin domains by dynamic HP1 binding. Science (2003) 4.74

A kinetic framework for a mammalian RNA polymerase in vivo. Science (2002) 4.42

Global nature of dynamic protein-chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins. Mol Cell Biol (2004) 4.41

Positional stability of single double-strand breaks in mammalian cells. Nat Cell Biol (2007) 4.35

Activation of innate immune antiviral responses by Nod2. Nat Immunol (2009) 4.19

Transcription dynamics. Mol Cell (2009) 4.15

Spatial proximity of translocation-prone gene loci in human lymphomas. Nat Genet (2003) 3.91

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nat Biotechnol (2009) 3.44

Using expression profiling data to identify human microRNA targets. Nat Methods (2007) 3.37

Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. Genes Dev (2006) 3.18

Activation of the cellular DNA damage response in the absence of DNA lesions. Science (2008) 3.17

Measurement of dynamic protein binding to chromatin in vivo, using photobleaching microscopy. Methods Enzymol (2004) 3.02

Lamin A-dependent misregulation of adult stem cells associated with accelerated ageing. Nat Cell Biol (2008) 2.93

An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming. Cell (2011) 2.89

SRm160 splicing coactivator promotes transcript 3'-end cleavage. Mol Cell Biol (2002) 2.73

TDP-43 regulates retinoblastoma protein phosphorylation through the repression of cyclin-dependent kinase 6 expression. Proc Natl Acad Sci U S A (2008) 2.58

Tissue-specific spatial organization of genomes. Genome Biol (2004) 2.57

Distinct structural and mechanical properties of the nuclear lamina in Hutchinson-Gilford progeria syndrome. Proc Natl Acad Sci U S A (2006) 2.53

DNA end joining becomes less efficient and more error-prone during cellular senescence. Proc Natl Acad Sci U S A (2004) 2.51

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming. Nature (2013) 2.49

Cell biology: chromosome territories. Nature (2007) 2.47

Ageing-related chromatin defects through loss of the NURD complex. Nat Cell Biol (2009) 2.40

Neural induction promotes large-scale chromatin reorganisation of the Mash1 locus. J Cell Sci (2006) 2.37

Network of dynamic interactions between histone H1 and high-mobility-group proteins in chromatin. Mol Cell Biol (2004) 2.33

Chromosome positioning in the interphase nucleus. Trends Cell Biol (2002) 2.32

The ATM repair pathway inhibits RNA polymerase I transcription in response to chromosome breaks. Nature (2007) 2.30

Alternative splicing of conserved exons is frequently species-specific in human and mouse. Trends Genet (2005) 2.26

Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay. Mol Cell Biol (2008) 2.25

Dynamic integration of splicing within gene regulatory pathways. Cell (2013) 2.25

The meaning of gene positioning. Cell (2008) 2.16

Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs. Nat Genet (2005) 2.15

Functional implications of genome topology. Nat Struct Mol Biol (2013) 2.13

Spatial genome organization in the formation of chromosomal translocations. Semin Cancer Biol (2006) 2.12

Global analysis of alternative splicing during T-cell activation. RNA (2007) 2.11

Tissue-specific alternative splicing remodels protein-protein interaction networks. Mol Cell (2012) 2.08

Global analysis of alternative splicing differences between humans and chimpanzees. Genes Dev (2007) 2.00

Regulation of vertebrate nervous system alternative splicing and development by an SR-related protein. Cell (2009) 1.98

HTLV-1-encoded p30II is a post-transcriptional negative regulator of viral replication. Nat Med (2004) 1.97

Spatial dynamics of chromosome translocations in living cells. Science (2013) 1.95

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In vivo kinetics of Cajal body components. J Cell Biol (2004) 1.91

Condensed mitotic chromatin is accessible to transcription factors and chromatin structural proteins. J Cell Biol (2004) 1.86

The lamin protein family. Genome Biol (2011) 1.85

Functional association of Sun1 with nuclear pore complexes. J Cell Biol (2007) 1.81

Human chromokinesin KIF4A functions in chromosome condensation and segregation. J Cell Biol (2004) 1.81

Functional coordination of alternative splicing in the mammalian central nervous system. Genome Biol (2007) 1.80

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5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary. Nat Struct Mol Biol (2012) 1.74

Competition between histone H1 and HMGN proteins for chromatin binding sites. EMBO Rep (2002) 1.74

Inferring global levels of alternative splicing isoforms using a generative model of microarray data. Bioinformatics (2006) 1.72

Splicing and transcription-associated proteins PSF and p54nrb/nonO bind to the RNA polymerase II CTD. RNA (2002) 1.71

Biogenesis of nuclear bodies. Cold Spring Harb Perspect Biol (2010) 1.69

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Allele-specific nuclear positioning of the monoallelically expressed astrocyte marker GFAP. Genes Dev (2008) 1.62

In vitro generation of human cells with cancer stem cell properties. Nat Cell Biol (2011) 1.61

Regulation of alternative splicing by the core spliceosomal machinery. Genes Dev (2011) 1.60

Quantitation of GFP-fusion proteins in single living cells. J Struct Biol (2002) 1.59

Smg1 is required for embryogenesis and regulates diverse genes via alternative splicing coupled to nonsense-mediated mRNA decay. Proc Natl Acad Sci U S A (2010) 1.59

Conservation of relative chromosome positioning in normal and cancer cells. Curr Biol (2002) 1.58

Locus-specific and activity-independent gene repositioning during early tumorigenesis. J Cell Biol (2008) 1.56

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Global profiling and molecular characterization of alternative splicing events misregulated in lung cancer. Mol Cell Biol (2010) 1.53

The road much traveled: trafficking in the cell nucleus. Curr Opin Cell Biol (2006) 1.52

Expression of human telomerase (hTERT) does not prevent stress-induced senescence in normal human fibroblasts but protects the cells from stress-induced apoptosis and necrosis. J Biol Chem (2002) 1.50

A cyclophilin functions in pre-mRNA splicing. EMBO J (2002) 1.49