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Transcriptome-wide interrogation of the functional intronome by spliceosome profiling

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/bies.201300156openalex-snapshot

The functional consequences of intron retention: Alternative splicing coupled to NMD as a regulator of gene expression

inferredcites →https://doi.org/10.1007/s00439-017-1791-xopenalex-snapshot

Intron retention as a component of regulated gene expression programs

inferredcites →https://doi.org/10.1016/0092-8674(91)90466-copenalex-snapshot

Isolation and characterization of the gene encoding yeast debranching enzyme

inferredcites →https://doi.org/10.1016/j.cell.2009.02.009openalex-snapshot

The Spliceosome: Design Principles of a Dynamic RNP Machine

inferredcites →https://doi.org/10.1016/j.cell.2011.08.044openalex-snapshot

Introns within Ribosomal Protein Genes Regulate the Production and Function of Yeast Ribosomes

inferredcites →https://doi.org/10.1016/j.cell.2012.05.043openalex-snapshot

Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions

inferredcites →https://doi.org/10.1016/j.cell.2012.09.019openalex-snapshot

Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

inferredcites →https://doi.org/10.1016/j.cell.2012.10.007openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.cell.2013.12.026openalex-snapshot

Global Analysis of mRNA Isoform Half-Lives Reveals Stabilizing and Destabilizing Elements in Yeast

inferredcites →https://doi.org/10.1016/j.cell.2015.03.010openalex-snapshot

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

inferredcites →https://doi.org/10.1016/j.cell.2015.03.027openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.celrep.2012.03.013openalex-snapshot

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

inferredcites →https://doi.org/10.1016/j.gde.2017.10.010openalex-snapshot

Targeting splicing abnormalities in cancer

inferredcites →https://doi.org/10.1016/j.molcel.2006.07.011openalex-snapshot

A Spliceosomal Intron Binding Protein, IBP160, Links Position-Dependent Assembly of Intron-Encoded Box C/D snoRNP to Pre-mRNA Splicing

inferredcites →https://doi.org/10.1016/j.molcel.2008.05.003openalex-snapshot

A Conformational Rearrangement in the Spliceosome Sets the Stage for Prp22-Dependent mRNA Release

inferredcites →https://doi.org/10.1016/j.molcel.2009.09.040openalex-snapshot

The Evolutionarily Conserved Core Design of the Catalytic Activation Step of the Yeast Spliceosome

inferredcites →https://doi.org/10.1016/j.tibs.2008.06.001openalex-snapshot

Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense?

inferredcites →https://doi.org/10.1016/j.tig.2017.03.001openalex-snapshot

Splicing Factor Mutations in Myelodysplasias: Insights from Spliceosome Structures

inferredcites →https://doi.org/10.1016/j.ymeth.2013.09.013openalex-snapshot

RIPiT-Seq: A high-throughput approach for footprinting RNA:protein complexes

inferredcites →https://doi.org/10.1016/s0021-9258(18)69089-1openalex-snapshot

Group II intron self-splicing. Alternative reaction conditions yield novel products.

inferredcites →https://doi.org/10.1017/s1355838202021088openalex-snapshot

Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis

inferredcites →https://doi.org/10.1038/36142openalex-snapshot

Group II intron splicing in vivo by first-step hydrolysis

inferredcites →https://doi.org/10.1038/nature07509openalex-snapshot

Alternative isoform regulation in human tissue transcriptomes

inferredcites →https://doi.org/10.1038/nature07584openalex-snapshot

Spliceosomal cleavage generates the 3′ end of telomerase RNA

inferredcites →https://doi.org/10.1038/nature19316openalex-snapshot

Cryo-EM structure of the spliceosome immediately after branching

inferredcites →https://doi.org/10.1038/nature21079openalex-snapshot

Cryo-EM structure of a human spliceosome activated for step 2 of splicing

inferredcites →https://doi.org/10.1038/nbt.1628openalex-snapshot

Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe

inferredcites →https://doi.org/10.1038/ncomms10237openalex-snapshot

A generic strategy for CRISPR-Cas9-mediated gene tagging

inferredcites →https://doi.org/10.1038/nmeth.3317openalex-snapshot

HISAT: a fast spliced aligner with low memory requirements

inferredcites →https://doi.org/10.1038/nprot.2012.016openalex-snapshot

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

inferredcites →https://doi.org/10.1038/nrg2484openalex-snapshot

RNA-Seq: a revolutionary tool for transcriptomics

inferredcites →https://doi.org/10.1038/nrg3645openalex-snapshot

Ribosome profiling: new views of translation, from single codons to genome scale

inferredcites →https://doi.org/10.1038/nrm.2017.86openalex-snapshot

Mechanistic insights into precursor messenger RNA splicing by the spliceosome

inferredcites →https://doi.org/10.1038/nrm4069openalex-snapshot

Ribosome profiling reveals the what, when, where and how of protein synthesis

inferredcites →https://doi.org/10.1038/nsmb.2327openalex-snapshot

Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo

inferredcites →https://doi.org/10.1038/nsmb.2951openalex-snapshot

The RNA helicase Aquarius exhibits structural adaptations mediating its recruitment to spliceosomes

inferredcites →https://doi.org/10.1042/bj20061181openalex-snapshot

Identification of a mitochondrial alcohol dehydrogenase in Schizosaccharomyces pombe: new insights into energy metabolism

inferredcites →https://doi.org/10.1073/pnas.1218353110openalex-snapshot

Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans

inferredcites →https://doi.org/10.1073/pnas.1612729114openalex-snapshot

Metal dependence and branched RNA cocrystal structures of the RNA lariat debranching enzyme Dbr1

inferredcites →https://doi.org/10.1073/pnas.201407298openalex-snapshot

A computational analysis of sequence features involved in recognition of short introns

inferredcites →https://doi.org/10.1093/bioinformatics/bts559openalex-snapshot

Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads

inferredcites →https://doi.org/10.1093/biostatistics/kxs001openalex-snapshot

Modeling RNA degradation for RNA-Seq with applications

inferredcites →https://doi.org/10.1093/emboj/cdf359openalex-snapshot

Lariat formation and a hydrolytic pathway in plant chloroplast group II intron splicing

inferredcites →https://doi.org/10.1093/nar/25.10.2030openalex-snapshot

Precise branch point mapping and quantification of splicing intermediates

inferredcites →https://doi.org/10.1093/nar/gki934openalex-snapshot

Structure-function analysis of yeast RNA debranching enzyme (Dbr1), a manganese-dependent phosphodiesterase

inferredcites →https://doi.org/10.1093/nar/gkn073openalex-snapshot

Human branch point consensus sequence is yUnAy

inferredcites →https://doi.org/10.1093/nar/gkt1304openalex-snapshot

PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution

inferredcites →https://doi.org/10.1093/nar/gku1303openalex-snapshot

Microarrays for identifying binding sites and probing structure of RNAs

inferredcites →https://doi.org/10.1101/gad.1030602openalex-snapshot

5′ exon interactions within the human spliceosome establish a framework for exon junction complex structure and assembly

inferredcites →https://doi.org/10.1101/gad.1557907openalex-snapshot

Introns play an essential role in splicing-dependent formation of the exon junction complex

inferredcites →https://doi.org/10.1101/gr.131037.111openalex-snapshot

Genome-wide analysis of long noncoding RNA stability

inferredcites →https://doi.org/10.1101/gr.162503.113openalex-snapshot

Cnidarian microRNAs frequently regulate targets by cleavage

inferredcites →https://doi.org/10.1101/gr.166819.113openalex-snapshot

LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq

inferredcites →https://doi.org/10.1101/gr.182899.114openalex-snapshot

Genome-wide discovery of human splicing branchpoints

inferredcites →https://doi.org/10.1101/gr.202820.115openalex-snapshot

Large-scale analysis of branchpoint usage across species and cell lines

inferredcites →https://doi.org/10.1101/pdb.prot080713openalex-snapshot

3′-End Labeling of RNA with [5′-32P]Cytidine 3′,5′-Bis(Phosphate) and T4 RNA Ligase 1

inferredcites →https://doi.org/10.1111/j.1432-1033.1996.00779.xopenalex-snapshot

Computational Method to Predict Mitochondrially Imported Proteins and their Targeting Sequences

inferredcites →https://doi.org/10.1126/science.1158993openalex-snapshot

Both Catalytic Steps of Nuclear Pre-mRNA Splicing Are Reversible

inferredcites →https://doi.org/10.1126/science.1203357openalex-snapshot

Comparative Functional Genomics of the Fission Yeasts

inferredcites →https://doi.org/10.1126/science.aac7629openalex-snapshot

Structure of a yeast spliceosome at 3.6-angstrom resolution

inferredcites →https://doi.org/10.1126/science.aac8159openalex-snapshot

Structural basis of pre-mRNA splicing

inferredcites →https://doi.org/10.1126/science.aag0291openalex-snapshot

Structure of a yeast activated spliceosome at 3.5 Å resolution

inferredcites →https://doi.org/10.1126/science.aag2235openalex-snapshot

Structure of a yeast catalytic step I spliceosome at 3.4 Å resolution

inferredcites →https://doi.org/10.1146/annurev-biophys-062215-011149openalex-snapshot

Group II Intron Self-Splicing

inferredcites →https://doi.org/10.1186/s13059-015-0848-1openalex-snapshot

Transcriptome-wide RNA processing kinetics revealed using extremely short 4tU labeling

inferredcites →https://doi.org/10.1261/rna.033910.112openalex-snapshot

Antisense-targeted immuno-EM localization of the pre-mRNA path in the spliceosomal C complex

inferredcites →https://doi.org/10.1261/rna.038638.113openalex-snapshot

The spliceosome catalyzes debranching in competition with reverse of the first chemical reaction

inferredcites →https://doi.org/10.1261/rna.040980.113openalex-snapshot

Endogenous U2·U5·U6 snRNA complexes in S. pombe are intron lariat spliceosomes

inferredcites →https://doi.org/10.1261/rna.052829.115openalex-snapshot

Sequencing of lariat termini in S. cerevisiae reveals 5′ splice sites, branch points, and novel splicing events

inferredcites →https://doi.org/10.1371/journal.pcbi.1005515openalex-snapshot

Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimates

inferredcites →https://doi.org/10.1534/genetics.106.058560openalex-snapshot

Introns Regulate RNA and Protein Abundance in Yeast

inferredcites →https://doi.org/10.3389/fphys.2016.00598openalex-snapshot

Cutting a Long Intron Short: Recursive Splicing and Its Implications

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.52679/tabcj.2020.0010openalex-snapshot

Bio-genesis and deregulation of circular ribonucleic acid and their role in human cancer

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