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RNA sequencing of Stentor cell fragments reveals key processes underlying cellular regeneration

https://doi.org/10.1101/232363
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What this work says

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

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Properties of Saccharomyces cerevisiae wee1 and its differential regulation of p34CDC28 in response to G1 and G2 cyclins.
inferredcites →https://doi.org/10.1002/jmor.1050840207openalex-snapshot
A cytochemical and cytological study of differentiation in normal and reorganizational stages of Stentor coeruleus
inferredcites →https://doi.org/10.1002/wrna.1332openalex-snapshot
The Ccr4‐Not complex is a key regulator of eukaryotic gene expression
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Molecular Cloning and Characterization of Meichroacidin (Male Meiotic MetaphaseChromosome-AssociatedAcidic Protein)
inferredcites →https://doi.org/10.1016/j.cub.2005.11.042openalex-snapshot
SAK/PLK4 Is Required for Centriole Duplication and Flagella Development
inferredcites →https://doi.org/10.1016/j.cub.2016.12.057openalex-snapshot
The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell
inferredcites →https://doi.org/10.1038/nbt.1883openalex-snapshot
Full-length transcriptome assembly from RNA-Seq data without a reference genome
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot
Fast and sensitive protein alignment using DIAMOND
inferredcites →https://doi.org/10.1038/nprot.2014.006openalex-snapshot
Full-length RNA-seq from single cells using Smart-seq2
inferredcites →https://doi.org/10.1042/bj20090500openalex-snapshot
Human Ccr4–Not complexes contain variable deadenylase subunits
inferredcites →https://doi.org/10.1042/bj3550609openalex-snapshot
The kinase DYRK phosphorylates protein-synthesis initiation factor eIF2Bɛ at Ser539 and the microtubule-associated protein tau at Thr212: potential role for DYRK as a glycogen synthase kinase 3-priming kinase
inferredcites →https://doi.org/10.1046/j.1365-2443.2002.00592.xopenalex-snapshot
Roles of aurora‐A kinase in mitotic entry and G2 checkpoint in mammalian cells
inferredcites →https://doi.org/10.1074/jbc.c000873200openalex-snapshot
Chromosome Condensation by a Human Condensin Complex inXenopus Egg Extracts
inferredcites →https://doi.org/10.1093/bioinformatics/btp348openalex-snapshot
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btu031openalex-snapshot
InterProScan 5: genome-scale protein function classification
inferredcites →https://doi.org/10.1093/emboj/21.3.355openalex-snapshot
Identification of a ubiquitin–protein ligase subunit within the CCR4–NOT transcription repressor complex
inferredcites →https://doi.org/10.1093/molbev/mst024openalex-snapshot
Ultrafast Approximation for Phylogenetic Bootstrap
inferredcites →https://doi.org/10.1093/molbev/msx148openalex-snapshot
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
inferredcites →https://doi.org/10.1093/nar/gki198openalex-snapshot
MAFFT version 5: improvement in accuracy of multiple sequence alignment
inferredcites →https://doi.org/10.1093/nar/gkv1248openalex-snapshot
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
inferredcites →https://doi.org/10.1093/nar/gkv259openalex-snapshot
Significance of ligand interactions involving Hop2-Mnd1 and the RAD51 and DMC1 recombinases in homologous DNA repair and XX ovarian dysgenesis
inferredcites →https://doi.org/10.1101/076331openalex-snapshot
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper
inferredcites →https://doi.org/10.1101/240788openalex-snapshot
The Transcriptional Program of Regeneration in the Giant Single Cell, Stentor coeruleus
inferredcites →https://doi.org/10.1101/gad.10.7.851openalex-snapshot
Differential effects of cdk2 and cdk3 on the control of pRb and E2F function during G1 exit.
inferredcites →https://doi.org/10.1101/gad.279406.116openalex-snapshot
The C2H2-ZF transcription factor Zfp335 recognizes two consensus motifs using separate zinc finger arrays
inferredcites →https://doi.org/10.1101/gad.7.10.1850openalex-snapshot
Heterodimerization of the transcription factors E2F-1 and DP-1 leads to cooperative trans-activation.
inferredcites →https://doi.org/10.1111/j.1462-2920.2010.02193.xopenalex-snapshot
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
inferredcites →https://doi.org/10.1111/j.1742-4658.2009.07261.xopenalex-snapshot
LIN54 is an essential core subunit of the DREAM/LINC complex that binds to the cdc2 promoter in a sequence‐specific manner
inferredcites →https://doi.org/10.1111/jeu.12216openalex-snapshot
Tetrahymena Expresses More than a Hundred Proteins with Lipid‐binding MORN Motifs that can Differ in their Subcellular Localisations
inferredcites →https://doi.org/10.1126/science.129.3361.1483openalex-snapshot
Regulation of Mitosis in Stentor coeruleus
inferredcites →https://doi.org/10.1126/science.aam6496openalex-snapshot
Self-repairing cells: How single cells heal membrane ruptures and restore lost structures
inferredcites →https://doi.org/10.1172/jci60818openalex-snapshot
DYRK2 priming phosphorylation of c-Jun and c-Myc modulates cell cycle progression in human cancer cells
inferredcites →https://doi.org/10.1186/s13059-014-0410-6openalex-snapshot
Corset: enabling differential gene expression analysis for de novoassembled transcriptomes
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1371/journal.pbio.1001861openalex-snapshot
The Kinase Regulator Mob1 Acts as a Patterning Protein for Stentor Morphogenesis
inferredcites →https://doi.org/10.1371/journal.pone.0095567openalex-snapshot
Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia

What points at this work

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

inferred← citeshttps://doi.org/10.1101/240788openalex-snapshot
The Transcriptional Program of Regeneration in the Giant Single Cell, Stentor coeruleus
inferred← citeshttps://doi.org/10.1371/journal.pgen.1007390openalex-snapshot
Danger signals activate a putative innate immune system during regeneration in a filamentous fungus
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