Regulation of alternative polyadenylation in the yeast Saccharomyces cerevisiae by histone H3K4 and H3K36 methyltransferases

Regulation of the Ysh1 endonuclease of the mRNA cleavage/polyadenylation complex by ubiquitin-mediated degradation

(2020) Susan D. Lee et al.   RNA Biology

Differential Alternative Polyadenylation Landscapes Mediate Hematopoietic Stem Cell Activation and Regulate Glutamine Metabolism

(2020) Pia Sommerkamp et al.   Cell Stem Cell

Choice of Alternative Polyadenylation Sites, Mediated by the RNA-Binding Protein Elavl3, Plays a Role in Differentiation of Inhibitory Neuronal Progenitors

(2019) Elena Grassi et al.   Frontiers in Cellular Neuroscience

Ipa1 Is an RNA Polymerase II Elongation Factor that Facilitates Termination by Maintaining Levels of the Poly(A) Site Endonuclease Ysh1

(2019) Erika L. Pearson et al.   Cell Reports

Role of alternative polyadenylation dynamics in acute myeloid leukaemia at single-cell resolution

(2019) Congting Ye et al.   RNA Biology

A conserved genetic interaction between Spt6 and Set2 regulates H3K36 methylation

(2019) Rajaraman Gopalakrishnan et al.   NUCLEIC ACIDS RESEARCH

Alternative polyadenylation dependent function of splicing factor SRSF3 contributes to cellular senescence

(2019) Ting Shen et al.   Aging-US

Alternative cleavage and polyadenylation of genes associated with protein turnover and mitochondrial function are deregulated in Parkinson’s, Alzheimer’s and ALS disease

(2019) Radhika Patel et al.   BMC Medical Genomics

Cleavage factor 25 deregulation contributes to pulmonary fibrosis through alternative polyadenylation

(2019) Tingting Weng et al.   JOURNAL OF CLINICAL INVESTIGATION

Contribution of H3K4 demethylase KDM5B to nucleosome organization in embryonic stem cells revealed by micrococcal nuclease sequencing

(2019) Jiji T. Kurup et al.   Epigenetics & Chromatin

Histone Methylation and Memory of Environmental Stress

(2019) Paola Fabrizio et al.   Cells

Alternative cleavage and polyadenylation in health and disease

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

Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data

(2019) Eldad David Shulman et al.   NUCLEIC ACIDS RESEARCH

Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast

(2019) Wu Wei et al.   GENOME RESEARCH

Mechanistic insights into mRNA 3′-end processing

(2019) Ananthanarayanan Kumar et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling

(2018) Justin Brumbaugh et al.   CELL

Mechanisms for the epigenetic inheritance of stress response in single cells

(2018) Yuan Xue et al.   CURRENT GENETICS

3′ UTR lengthening as a novel mechanism in regulating cellular senescence

(2018) Meng Chen et al.   GENOME RESEARCH

Mapping diet-induced alternative polyadenylation of hypothalamic transcripts in the obese rat

(2018) Julianna N. Brutman et al.   PHYSIOLOGY & BEHAVIOR

Epigenetic Regulation in Neurodegenerative Diseases

(2018) Amit Berson et al.   TRENDS IN NEUROSCIENCES

Widespread intronic polyadenylation diversifies immune cell transcriptomes

(2018) Irtisha Singh et al.   Nature Communications

Cellular stress alters 3′UTR landscape through alternative polyadenylation and isoform-specific degradation

(2018) Dinghai Zheng et al.   Nature Communications

Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo

(2018) Ralf Gilsbach et al.   Nature Communications

H3K4 Methylation Dependent and Independent Chromatin Regulation by JHD2 and SET1 in Budding Yeast

(2018) Kwan Yin Lee et al.   G3-Genes Genomes Genetics

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

(2018) Anton Ogorodnikov et al.   Nature Communications

Histone H3K4 and H3K36 Methylation Independently Recruit the NuA3 Histone Acetyltransferase in Saccharomyces cerevisiae

(2017) Benjamin J. E. Martin et al.   GENETICS

Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe

(2017) Xiaochuan Liu et al.   GENOME RESEARCH

Small Nuclear Ribonucleoprotein Polypeptide A–Mediated Alternative Polyadenylation of STAT5B during Th1 Cell Differentiation

(2017) Feifei Qiu et al.   JOURNAL OF IMMUNOLOGY

RNA Binding by Histone Methyltransferases Set1 and Set2

(2017) Camille Sayou et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2017) Nova Fong et al.   MOLECULAR CELL

Noncanonical Alternative Polyadenylation Contributes to Gene Regulation in Response to Hypoxia

(2017) Laura de Lorenzo et al.   PLANT CELL

The role of alternative polyadenylation in the antiviral innate immune response

(2017) Xin Jia et al.   Nature Communications

H3K36 Methylation Regulates Nutrient Stress Response in Saccharomyces cerevisiae by Enforcing Transcriptional Fidelity

(2017) Stephen L. McDaniel et al.   Cell Reports

RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases

(2017) Sofia Battaglia et al.   eLife

Histone H3K4 and H3K36 Methylation Independently Recruit the NuA3 Histone Acetyltransferase in Saccharomyces cerevisiae

(2017) Benjamin J. E. Martin et al.   GENETICS

Binding to RNA regulates Set1 function

(2017) Pierre Luciano et al.   Cell Discovery

Alternative Polyadenylation in Triple-Negative Breast Tumors Allows NRAS and c-JUN to Bypass PUMILIO Posttranscriptional Regulation

(2016) Wayne O. Miles et al.   CANCER RESEARCH

Epigenetic Mechanisms of Longevity and Aging

(2016) Payel Sen et al.   CELL

Common genomic elements promote transcriptional and DNA replication roadblocks

(2016) Kevin Roy et al.   GENOME RESEARCH

Epigenetic regulation of alternative promoters and enhancers in progenitor, immature, and mature gonadotrope cell lines

(2016) Jean-Noël Laverrière et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Interplay between Metabolism and Epigenetics: A Nuclear Adaptation to Environmental Changes

(2016) Jean-Pierre Etchegaray et al.   MOLECULAR CELL

The molecular hallmarks of epigenetic control

(2016) C. David Allis et al.   NATURE REVIEWS GENETICS

Alternative polyadenylation of mRNA precursors

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

The differential expression of alternatively polyadenylated transcripts is a common stress-induced response mechanism that modulates mammalian mRNA expression in a quantitative and qualitative fashion

(2016) Ina Hollerer et al.   RNA

A global genetic interaction network maps a wiring diagram of cellular function

(2016) M. Costanzo et al.   SCIENCE

Counteracting H3K4 methylation modulators Set1 and Jhd2 co-regulate chromatin dynamics and gene transcription

(2016) Saravanan Ramakrishnan et al.   Nature Communications

Selective suppression of antisense transcription by Set2-mediated H3K36 methylation

(2016) Swaminathan Venkatesh et al.   Nature Communications

Modulation of mRNA and lncRNA expression dynamics by the Set2–Rpd3S pathway

(2016) Ji Hyun Kim et al.   Nature Communications

Premature polyadenylation of MAGI3 produces a dominantly-acting oncogene in human breast cancer

(2016) Thomas K Ni et al.   eLife

KDM5 lysine demethylases are involved in maintenance of 3'UTR length

(2016) L. P. Blair et al.   Science Advances

Intronic cleavage and polyadenylation regulates gene expression during DNA damage response through U1 snRNA

(2016) Emral Devany et al.   Cell Discovery

How eukaryotic genes are transcribed

(2016) Bryan J. Venters et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Genome-wide mapping of nucleosome positions in Saccharomyces cerevisiae in response to different nitrogen conditions

(2016) Peng Zhang et al.   Scientific Reports

The stress-induced heat shock protein 70.3 expression is regulated by a dual-component mechanism involving alternative polyadenylation and HuR

(2015) Stephen M. Kraynik et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing

(2015) Takayuki Nojima et al.   CELL

Genome-Wide Polyadenylation Maps Reveal Dynamic mRNA 3′-End Formation in the Failing Human HeartNovelty and Significance

(2015) Esther E. Creemers et al.   CIRCULATION RESEARCH

H3K36 methylation promotes longevity by enhancing transcriptional fidelity

(2015) Payel Sen et al.   GENES & DEVELOPMENT

Combined Interactions of Plant Homeodomain and Chromodomain Regulate NuA4 Activity at DNA Double-Strand Breaks

(2015) W.-P. Su et al.   GENETICS

H3K4 monomethylation dictates nucleosome dynamics and chromatin remodeling at stress-responsive genes

(2015) Mariona Nadal-Ribelles et al.   NUCLEIC ACIDS RESEARCH

Global insights into alternative polyadenylation regulation

(2015) Ranjan Batra et al.   RNA Biology

Epigenetics of idiopathic pulmonary fibrosis

(2015) Ivana V. Yang et al.   Translational Research

mRNA 3′-UTR shortening is a molecular signature of mTORC1 activation

(2015) Jae-Woong Chang et al.   Nature Communications

Loss of the Set2 histone methyltransferase increases cellular lifespan in yeast cells

(2014) Hong-Yeoul Ryu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

RNA polymerase II termination involves C-terminal-domain tyrosine dephosphorylation by CPF subunit Glc7

(2014) Amelie Schreieck et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

An RNA polymerase II-coupled function for histone H3K36 methylation in checkpoint activation and DSB repair

(2014) Deepak Kumar Jha et al.   Nature Communications

The Evolutionarily Conserved Pol II Flap Loop Contributes to Proper Transcription Termination on Short Yeast Genes

(2014) Erika Pearson et al.   Cell Reports

Heterochromatin assembly and transcriptome repression by Set1 in coordination with a class II histone deacetylase

(2014) David R Lorenz et al.   eLife

SETD2 is required for DNA double-strand break repair and activation of the p53-mediated checkpoint

(2014) Sílvia Carvalho et al.   eLife

Alternative polyadenylation sites reveal distinct chromatin accessibility and histone modification in human cell lines

(2013) C.-y. Lee et al.   BIOINFORMATICS

The Histone Mark H3K36me3 Regulates Human DNA Mismatch Repair through Its Interaction with MutSα

(2013) Feng Li et al.   CELL

All's well that ends well: alternative polyadenylation and its implications for stem cell biology

(2013) Alisa A Mueller et al.   CURRENT OPINION IN CELL BIOLOGY

DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast

(2013) J. H. Graber et al.   GENOME RESEARCH

UV damage regulates alternative polyadenylation of the RPB2 gene in yeast

(2013) Lijian Yu et al.   NUCLEIC ACIDS RESEARCH

Histone methyltransferase SETD2 coordinates FACT recruitment with nucleosome dynamics during transcription

(2013) Sílvia Carvalho et al.   NUCLEIC ACIDS RESEARCH

Role of Alternative Polyadenylation during Adipogenic Differentiation: An In Silico Approach

(2013) Lucía Spangenberg et al.   PLoS One

Cold-induced RNA-binding proteins regulate circadian gene expression by controlling alternative polyadenylation

(2013) Yuting Liu et al.   Scientific Reports

Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors

(2013) Andreas R. Gruber et al.   Wiley Interdisciplinary Reviews-RNA

The RNA polymerase II CTD coordinates transcription and RNA processing

(2012) J.-P. Hsin et al.   GENES & DEVELOPMENT

Yeast Swd2 Is Essential Because of Antagonism between Set1 Histone Methyltransferase Complex and APT (Associated with Pta1) Termination Factor

(2012) Luis M. Soares et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Spt5 C-Terminal Region Recruits Yeast 3' RNA Cleavage Factor I

(2012) A. Mayer et al.   MOLECULAR AND CELLULAR BIOLOGY

Set2 methylation of histone H3 lysine 36 suppresses histone exchange on transcribed genes

(2012) Swaminathan Venkatesh et al.   NATURE

Estrogen-induced upregulation and 3′-UTR shortening of CDC6

(2012) Begum H. Akman et al.   NUCLEIC ACIDS RESEARCH

CTD Tyrosine Phosphorylation Impairs Termination Factor Recruitment to RNA Polymerase II

(2012) A. Mayer et al.   SCIENCE

Epigenetics in Alternative Pre-mRNA Splicing

(2011) Reini F. Luco et al.   CELL

Coordinated Post-transcriptional Regulation of Hsp70.3 Gene Expression by MicroRNA and Alternative Polyadenylation

(2011) Michael Tranter et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

RNA Polymerase II Carboxyl-terminal Domain Phosphorylation Regulates Protein Stability of the Set2 Methyltransferase and Histone H3 Di- and Trimethylation at Lysine 36

(2011) Stephen M. Fuchs et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification of Histone Mutants That Are Defective for Transcription-Coupled Nucleosome Occupancy

(2011) S. J. Hainer et al.   MOLECULAR AND CELLULAR BIOLOGY

Histone H3 Lysine 4 Hypermethylation Prevents Aberrant Nucleosome Remodeling at the PHO5 Promoter

(2011) S.-S. Wang et al.   MOLECULAR AND CELLULAR BIOLOGY

H3K4 Trimethylation by Set1 Promotes Efficient Termination by the Nrd1-Nab3-Sen1 Pathway

(2011) N. Terzi et al.   MOLECULAR AND CELLULAR BIOLOGY

Transcriptional activity regulates alternative cleavage and polyadenylation

(2011) Z. Ji et al.   Molecular Systems Biology

Epigenomic and RNA structural correlates of polyadenylation

(2011) Mugdha Khaladkar et al.   RNA Biology

A Nucleosome Surface Formed by Histone H4, H2A, and H3 Residues Is Needed for Proper Histone H3 Lys36Methylation, Histone Acetylation, and Repression of Cryptic Transcription

(2010) Hai-Ning Du et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation

(2010) X. Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Landscape of C. elegans 3'UTRs

(2010) M. Mangone et al.   SCIENCE

Rewiring of Genetic Networks in Response to DNA Damage

(2010) S. Bandyopadhyay et al.   SCIENCE

Regulation of Alternative Splicing by Histone Modifications

(2010) R. F. Luco et al.   SCIENCE

Methylated H3K4, a Transcription-Associated Histone Modification, Is Involved in the DNA Damage Response Pathway

(2010) David Faucher et al.   PLoS Genetics

Dimethylation of H3K4 by Set1 Recruits the Set3 Histone Deacetylase Complex to 5′ Transcribed Regions

(2009) TaeSoo Kim et al.   CELL

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

(2009) Christine Mayr et al.   CELL

H3 lysine 4 di- and tri-methylation deposited by cryptic transcription attenuates promoter activation

(2009) Marina Pinskaya et al.   EMBO JOURNAL

Histone H3 Lysine 36 Dimethylation (H3K36me2) Is Sufficient to Recruit the Rpd3s Histone Deacetylase Complex and to Repress Spurious Transcription

(2009) Bing Li et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Rtr1 Is a CTD Phosphatase that Regulates RNA Polymerase II during the Transition from Serine 5 to Serine 2 Phosphorylation

(2009) Amber L. Mosley et al.   MOLECULAR CELL

Phosphorylation of the Pol II CTD by KIN28 Enhances BUR1/BUR2 Recruitment and Ser2 CTD Phosphorylation Near Promoters

(2009) Hongfang Qiu et al.   MOLECULAR CELL

Histone H3 K36 methylation is mediated by a trans-histone methylation pathway involving an interaction between Set2 and histone H4

(2008) H.-N. Du et al.   GENES & DEVELOPMENT

A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation

(2008) Z. Lian et al.   GENOME RESEARCH

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

(2008) T. N. Mavrich et al.   GENOME RESEARCH

Stress-Dependent Dynamics of Global Chromatin Remodeling in Yeast: Dual Role for SWI/SNF in the Heat Shock Stress Response

(2008) S. Shivaswamy et al.   MOLECULAR AND CELLULAR BIOLOGY

Roles for Ctk1 and Spt6 in Regulating the Different Methylation States of Histone H3 Lysine 36

(2008) M. L. Youdell et al.   MOLECULAR AND CELLULAR BIOLOGY