Anything but Ordinary – Emerging Splicing Mechanisms in Eukaryotic Gene Regulation

METTL4 is an snRNA m6Am methyltransferase that regulates RNA splicing

(2020) Hao Chen et al.   CELL RESEARCH

LARP7-Mediated U6 snRNA Modification Ensures Splicing Fidelity and Spermatogenesis in Mice

(2020) Xin Wang et al.   MOLECULAR CELL

The Alazami Syndrome-Associated Protein LARP7 Guides U6 Small Nuclear RNA Modification and Contributes to Splicing Robustness

(2020) Daniele Hasler et al.   MOLECULAR CELL

The Interlocking Lives of LARP7: Fine-Tuning Transcription, RNA Modification, and Splicing through Multiple Non-coding RNAs

(2020) Mikko J. Frilander et al.   MOLECULAR CELL

N6-Deoxyadenosine Methylation in Mammalian Mitochondrial DNA

(2020) Ziyang Hao et al.   MOLECULAR CELL

Roles and mechanisms of alternative splicing in cancer — implications for care

(2020) Sophie C. Bonnal et al.   Nature Reviews Clinical Oncology

Modulation of circRNA Metabolism by m6A Modification

(2020) Gaia Di Timoteo et al.   Cell Reports

Cryo-EM snapshots of the human spliceosome reveal structural adaptions for splicing regulation

(2020) Sebastian M Fica   CURRENT OPINION IN STRUCTURAL BIOLOGY

Molecular Mechanisms of pre-mRNA Splicing through Structural Biology of the Spliceosome

(2019) Chuangye Yan et al.   Cold Spring Harbor Perspectives in Biology

RNAs in the spliceosome: Insight from cryoEM structures

(2019) Lingdi Zhang et al.   Wiley Interdisciplinary Reviews-RNA

Insights into the biogenesis and potential functions of exonic circular RNA

(2019) Chikako Ragan et al.   Scientific Reports

Promoter-proximal pausing mediated by the exon junction complex regulates splicing

(2019) Junaid Akhtar et al.   Nature Communications

Structural Insights into Nuclear pre-mRNA Splicing in Higher Eukaryotes

(2019) Berthold Kastner et al.   Cold Spring Harbor Perspectives in Biology

FTO controls reversible m6Am RNA methylation during snRNA biogenesis

(2019) Jan Mauer et al.   Nature Chemical Biology

Histone H3 trimethylation at lysine 36 guides m6A RNA modification co-transcriptionally

(2019) Huilin Huang et al.   NATURE

Mettl3 Regulates Osteogenic Differentiation and Alternative Splicing of Vegfa in Bone Marrow Mesenchymal Stem Cells

(2019) Cheng Tian et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons

(2019) Antonio Torres-Méndez et al.   Nature Ecology & Evolution

An Adversarial DNA N6-Methyladenine-Sensor Network Preserves Polycomb Silencing

(2019) Soo-Mi Kweon et al.   MOLECULAR CELL

Where, When, and How: Context-Dependent Functions of RNA Methylation Writers, Readers, and Erasers

(2019) Hailing Shi et al.   MOLECULAR CELL

Nonsense‐mediated mRNA decay: The challenge of telling right from wrong in a complex transcriptome

(2019) Aparna Kishor et al.   Wiley Interdisciplinary Reviews-RNA

Past, present, and future of circ RNA s

(2019) Ines Lucia Patop et al.   EMBO JOURNAL

Nuclear TARBP2 Drives Oncogenic Dysregulation of RNA Splicing and Decay

(2019) Lisa Fish et al.   MOLECULAR CELL

RNA sequencing: the teenage years

(2019) Rory Stark et al.   NATURE REVIEWS GENETICS

N6-methyladenosine Modulates Nonsense-mediated mRNA Decay in Human Glioblastoma

(2019) Fuxi Li et al.   CANCER RESEARCH

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

(2019) Yang Eric Guo et al.   NATURE

Reading, writing and erasing mRNA methylation

(2019) Sara Zaccara et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Nascent RNA and the Coordination of Splicing with Transcription

(2019) Karla M. Neugebauer   Cold Spring Harbor Perspectives in Biology

Identification of FUBP1 as a Long Tail Cancer Driver and Widespread Regulator of Tumor Suppressor and Oncogene Alternative Splicing

(2019) Jessica S. Elman et al.   Cell Reports

Regulation of Co-transcriptional Pre-mRNA Splicing by m6A through the Low-Complexity Protein hnRNPG

(2019) Katherine I. Zhou et al.   MOLECULAR CELL

Landscape and Regulation of m6A and m6Am Methylome across Human and Mouse Tissues

(2019) Jun’e Liu et al.   MOLECULAR CELL

RNA Splicing by the Spliceosome

(2019) Max E. Wilkinson et al.   Annual Review of Biochemistry

Splicing Kinetics and Coordination Revealed by Direct Nascent RNA Sequencing through Nanopores

(2019) Heather L. Drexler et al.   MOLECULAR CELL

Altered m6A Modification of Specific Cellular Transcripts Affects Flaviviridae Infection

(2019) Nandan S. Gokhale et al.   MOLECULAR CELL

m6A mRNA Methylation Is Essential for Oligodendrocyte Maturation and CNS Myelination

(2019) Huan Xu et al.   NEURON

Integrative network analysis identifies cell-specific trans regulators of m6A

(2019) Sanqi An et al.   NUCLEIC ACIDS RESEARCH

Atlas of quantitative single-base-resolution N6-methyl-adenine methylomes

(2019) Casslynn W. Q. Koh et al.   Nature Communications

Modifications in small nuclear RNAs and their roles in spliceosome assembly and function

(2018) Markus T. Bohnsack et al.   BIOLOGICAL CHEMISTRY

Long-read sequencing of nascent RNA reveals coupling among RNA processing events

(2018) Lydia Herzel et al.   GENOME RESEARCH

Splicing mutations in human genetic disorders: examples, detection, and confirmation

(2018) Abramowicz Anna et al.   JOURNAL OF APPLIED GENETICS

METTL3 regulates alternative splicing of MyD88 upon the lipopolysaccharide-induced inflammatory response in human dental pulp cells

(2018) Zhihui Feng et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Short cryptic exons mediate recursive splicing in Drosophila

(2018) Brian Joseph et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Engineering circular RNA for potent and stable translation in eukaryotic cells

(2018) R. Alexander Wesselhoeft et al.   Nature Communications

Short cryptic exons mediate recursive splicing in Drosophila

(2018) Brian Joseph et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transient N-6-Methyladenosine Transcriptome Sequencing Reveals a Regulatory Role of m6A in Splicing Efficiency

(2018) Annita Louloupi et al.   Cell Reports

METTL3-mediated m6A modification is required for cerebellar development

(2018) Chen-Xin Wang et al.   PLOS BIOLOGY

Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development

(2018) Seth D. Kasowitz et al.   PLoS Genetics

Methylation of Structured RNA by the m6A Writer METTL16 Is Essential for Mouse Embryonic Development

(2018) Mateusz Mendel et al.   MOLECULAR CELL

Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II

(2018) Huasong Lu et al.   NATURE

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing

(2018) Lorea Blazquez et al.   MOLECULAR CELL

Exon Junction Complexes Suppress Spurious Splice Sites to Safeguard Transcriptome Integrity

(2018) Volker Boehm et al.   MOLECULAR CELL

Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons

(2018) Thomas Gonatopoulos-Pournatzis et al.   MOLECULAR CELL

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

(2018) Takayuki Nojima et al.   MOLECULAR CELL

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

Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast

(2017) Vahid Aslanzadeh et al.   GENOME RESEARCH

Translation of CircRNAs

(2017) Nagarjuna Reddy Pamudurti et al.   MOLECULAR CELL

Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis

(2017) Ivano Legnini et al.   MOLECULAR CELL

The Output of Protein-Coding Genes Shifts to Circular RNAs When the Pre-mRNA Processing Machinery Is Limiting

(2017) Dongming Liang et al.   MOLECULAR CELL

Mechanistic insights into precursor messenger RNA splicing by the spliceosome

(2017) Yigong Shi   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNA fate determination through cotranscriptional adenosine methylation and microprocessor binding

(2017) Philip Knuckles et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3′-end processing

(2017) Marek Bartosovic et al.   NUCLEIC ACIDS RESEARCH

N 6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein

(2017) Nian Liu et al.   NUCLEIC ACIDS RESEARCH

Substoichiometric ribose methylations in spliceosomal snRNAs

(2017) Nicolai Krogh et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

ALKBH5-dependent m6A demethylation controls splicing and stability of long 3′-UTR mRNAs in male germ cells

(2017) Chong Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pre-mRNA processing includes N 6 methylation of adenosine residues that are retained in mRNA exons and the fallacy of “RNA epigenetics”

(2017) Robert B. Darnell et al.   RNA

Our views of dynamic N 6 -methyladenosine RNA methylation

(2017) Boxuan Simen Zhao et al.   RNA

m 6 A in mRNA: An Ancient Mechanism for Fine-Tuning Gene Expression

(2017) Jean-Yves Roignant et al.   TRENDS IN GENETICS

The m6A pathway facilitates sex determination in Drosophila

(2017) Lijuan Kan et al.   Nature Communications

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

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

RNA fate determination through cotranscriptional adenosine methylation and microprocessor binding

(2017) Philip Knuckles et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Impact of Alternative Splicing on the Human Proteome

(2017) Yansheng Liu et al.   Cell Reports

Microexons: discovery, regulation, and function

(2017) Dmytro Ustianenko et al.   Wiley Interdisciplinary Reviews-RNA

Splicing factor gene mutations in hematologic malignancies

(2016) Borja Saez et al.   BLOOD

Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II

(2016) Fernando Carrillo Oesterreich et al.   CELL

Nuclear m 6 A Reader YTHDC1 Regulates mRNA Splicing

(2016) Wen Xiao et al.   MOLECULAR CELL

m6A potentiates Sxl alternative pre-mRNA splicing for robust Drosophila sex determination

(2016) Irmgard U. Haussmann et al.   NATURE

m6A modulates neuronal functions and sex determination in Drosophila

(2016) Tina Lence et al.   NATURE

Mechanism and regulation of the nonsense-mediated decay pathway

(2016) Nele Hug et al.   NUCLEIC ACIDS RESEARCH

m6A: Signaling for mRNA splicing

(2016) Samir Adhikari et al.   RNA Biology

Splicing-factor alterations in cancers

(2016) Olga Anczuków et al.   RNA

Nuclear m 6 A Reader YTHDC1 Regulates mRNA Splicing

(2016) Ian A. Roundtree et al.   TRENDS IN GENETICS

RNA-Seq methods for transcriptome analysis

(2016) Radmila Hrdlickova et al.   Wiley Interdisciplinary Reviews-RNA

Mechanisms and Regulation of Alternative Pre-mRNA Splicing

(2015) Yeon Lee et al.   Annual Review of Biochemistry

Nonsense-Mediated mRNA Decay: Degradation of Defective Transcripts Is Only Part of the Story

(2015) Feng He et al.   Annual Review of Genetics

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

(2015) Andreas Mayer et al.   CELL

The RNA Binding Protein Quaking Regulates Formation of circRNAs

(2015) Simon J. Conn et al.   CELL

HNRNPA2B1 Is a Mediator of m6A-Dependent Nuclear RNA Processing Events

(2015) Claudio R. Alarcón et al.   CELL

A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation

(2015) Shengdong Ke et al.   GENES & DEVELOPMENT

Mammalian Introns: When the Junk Generates Molecular Diversity

(2015) Florent Hubé et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed

(2015) Agnieszka Rybak-Wolf et al.   MOLECULAR CELL

Recursive splicing in long vertebrate genes

(2015) Christopher R. Sibley et al.   NATURE

Genome-wide identification of zero nucleotide recursive splicing in Drosophila

(2015) Michael O. Duff et al.   NATURE

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

(2015) Nian Liu et al.   NATURE

RNA mis-splicing in disease

(2015) Marina M. Scotti et al.   NATURE REVIEWS GENETICS

Splicing of many human genes involves sites embedded within introns

(2015) Steven Kelly et al.   NUCLEIC ACIDS RESEARCH

Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes

(2015) A Sveen et al.   ONCOGENE

Regulation of circRNA biogenesis

(2015) Ling-Ling Chen et al.   RNA Biology

Exon Circularization Requires Canonical Splice Signals

(2015) Stefan Starke et al.   Cell Reports

Analysis of Intron Sequences Reveals Hallmarks of Circular RNA Biogenesis in Animals

(2015) Andranik Ivanov et al.   Cell Reports

Dynamic m 6 A modification and its emerging regulatory role in mRNA splicing

(2015) Ying Yang et al.   Science Bulletin

Correlation of circular RNA abundance with proliferation – exemplified with colorectal and ovarian cancer, idiopathic lung fibrosis and normal human tissues

(2015) Anna Bachmayr-Heyda et al.   Scientific Reports

A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

(2014) Manuel Irimia et al.   CELL

Complementary Sequence-Mediated Exon Circularization

(2014) Xiao-Ou Zhang et al.   CELL

FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis

(2014) Xu Zhao et al.   CELL RESEARCH

Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase

(2014) Xiao-Li Ping et al.   CELL RESEARCH

Short intronic repeat sequences facilitate circular RNA production

(2014) Dongming Liang et al.   GENES & DEVELOPMENT

How Slow RNA Polymerase II Elongation Favors Alternative Exon Skipping

(2014) Gwendal Dujardin et al.   MOLECULAR CELL

circRNA Biogenesis Competes with Pre-mRNA Splicing

(2014) Reut Ashwal-Fluss et al.   MOLECULAR CELL

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

Detecting and characterizing circular RNAs

(2014) William R Jeck et al.   NATURE BIOTECHNOLOGY

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

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

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

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

(2014) H. Y. Xiong et al.   SCIENCE

A Pseudouridine Residue in the Spliceosome Core Is Part of the Filamentous Growth Program in Yeast

(2014) Anindita Basak et al.   Cell Reports

Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation

(2014) Jakub O. Westholm et al.   Cell Reports

Kinetic competition during the transcription cycle results in stochastic RNA processing

(2014) Antoine Coulon et al.   eLife

Exon identity crisis: disease-causing mutations that disrupt the splicing code

(2014) Timothy Sterne-Weiler et al.   GENOME BIOLOGY

SR Proteins Collaborate with 7SK and Promoter-Associated Nascent RNA to Release Paused Polymerase

(2013) Xiong Ji et al.   CELL

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

(2013) Alika K Maunakea et al.   CELL RESEARCH

Pick one, but be quick: 5' splice sites and the problems of too many choices

(2013) X. Roca et al.   GENES & DEVELOPMENT

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

A METTL3–METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation

(2013) Jianzhao Liu et al.   Nature Chemical Biology

Live-Cell Visualization of Pre-mRNA Splicing with Single-Molecule Sensitivity

(2013) Robert M. Martin et al.   Cell Reports

Correction: Cell-Type Specific Features of Circular RNA Expression

(2013) Julia Salzman et al.   PLoS Genetics

The Cellular EJC Interactome Reveals Higher-Order mRNP Structure and an EJC-SR Protein Nexus

(2012) Guramrit Singh et al.   CELL

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

(2012) Kate D. Meyer et al.   CELL

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

(2012) H. Tilgner et al.   GENOME RESEARCH

Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution

(2012) L. Windhager et al.   GENOME RESEARCH

ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility

(2012) Guanqun Zheng et al.   MOLECULAR CELL

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex

(2012) Jérôme Saulière et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types

(2012) Julia Salzman et al.   PLoS One

Circular RNAs are abundant, conserved, and associated with ALU repeats

(2012) W. R. Jeck et al.   RNA

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

Cross-Regulation between an Alternative Splicing Activator and a Transcription Repressor Controls Neurogenesis

(2011) Bushra Raj et al.   MOLECULAR CELL

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

(2011) Sanjeev Shukla et al.   NATURE

N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO

(2011) Guifang Jia et al.   Nature Chemical Biology

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain

(2011) Adam Ameur et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

U2 snRNA is inducibly pseudouridylated at novel sites by Pus7p and snR81 RNP

(2010) Guowei Wu et al.   EMBO JOURNAL

Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation

(2010) J. Y. Ip et al.   GENOME RESEARCH

Relationship between nucleosome positioning and DNA methylation

(2010) Ramakrishna K. Chodavarapu et al.   NATURE

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

Spliceosomal snRNA modifications and their function

(2010) John Karijolich et al.   RNA Biology

Regulation of Alternative Splicing by Histone Modifications

(2010) R. F. Luco et al.   SCIENCE

Patterns of exon-intron architecture variation of genes in eukaryotic genomes

(2009) Liucun Zhu et al.   BMC GENOMICS

The Spliceosome: Design Principles of a Dynamic RNP Machine

(2009) Markus C. Wahl et al.   CELL

Biased Chromatin Signatures around Polyadenylation Sites and Exons

(2009) Noah Spies et al.   MOLECULAR CELL

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

The Peculiarities of Large Intron Splicing in Animals

(2009) Samuel Shepard et al.   PLoS One

7SK snRNP/P-TEFb couples transcription elongation with alternative splicing and is essential for vertebrate development

(2009) M. Barboric et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II

(2009) C. Hodges et al.   SCIENCE

Oxidative demethylation of 3-methylthymine and 3-methyluracil in single-stranded DNA and RNA by mouse and human FTO

(2008) Guifang Jia et al.   FEBS LETTERS

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

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE