2023
Transcriptome profiling of the Caenorhabditis elegans intestine reveals that ELT-2 negatively and positively regulates intestinal gene expression within the context of a gene regulatory network.
Williams RTP, King DC, Mastroianni IR, Hill JL, Apenes NW, Ramirez G, Miner EC, Moore A, Coleman K, Osborne Nishimura E.
Genetics. 2023 May 15:iyad088. doi: 10.1093/genetics/iyad088. PMID: 37183501
- Protocol collection: Dissociation and FACS isolation of embryonic and post-embryonic C. elegans intestine cells for RNA-seq analysis
- Synchronized C. elegans culture on NGM plates for FACS isolation of intestine cells
- Embryo stage C. elegans dissociation for FACS isolation and RNA-seq analysis of intestine-specific cells
- L1 stage C. elegans dissociation for FACS isolation and RNA-seq analysis of intestine-specific cells
- L3 stage C. elegans dissociation for FACS isolation and RNA-seq analysis of intestine-specific cells
- FACS isolation of intestine-specific C. elegans cells
- NCBI GEO Accession = Series GSE214581. This contains raw counts, normalized counts, and rlog stabilized counts, big wig files, gtf files, and methods information.
- SRA Run Selector PRJNA885900. This contains all the raw .fastq files.
- Github Repository for Williams_et_al. This contains software, analytical pipelines, and figure generation.
Transcriptome profiling of the Caenorhabditis elegans intestine reveals that ELT-2 negatively and positively regulates intestinal gene expression within the context of a gene regulatory network
Williams RTP, King DC, Mastroianni IR, Hill JL, Apenes NW, Ramirez G, Miner EC, Moore A, Coleman K, Osborne Nishimura E
BioRXIV. [Preprint] March 21, 2023. doi: https://doi.org/10.1101/2021.08.29.457787
2022
Hand Dissection of Caenorhabditis elegans Intestines
Hill JL, Moore A, Williams RTP, Osborne Nishimura E
J Vis Exp. 2022. Sep 13;(187). doi: 10.3791/64120. PMID: 36190277 DOI: 10.3791/64120
- Part of the collection – Methods for Microbiome Research in Caenorhabditis elegans
Hyper-active RAS/MAPK introduces cancer-specific mitotic vulnerabilities
Herman JA, Romain RR, Hoellerbauer P, Shirnekhi HK, King DC, DeLuca KF, Osborne Nishimura E, Paddison PJ, DeLuca JG.
Proc Natl Acad Sci U S A. 2022 Oct 11;119(41):e2208255119. doi: 10.1073/pnas.2208255119.
The ERM-1 membrane-binding domain directs erm-1 mRNA localization to the plasma membrane in the C. elegans embryo.
Winkenbach LP, Parker DM, Williams RTP, Nishimura EO.
Development. 2022 Nov 15;149(22):dev200930. doi: 10.1242/dev.200930.
PMID: 36314842
Translation of the ERM-1 membrane-binding domain directs erm-1 mRNA localization to the plasma membrane in the C. elegans embryo
Winkenbach LP, Parker DP, Williams RTP, Osborne Nishimura E
BioRXIV. [Preprint] May 11, 2022 doi: https://doi.org/10.1101/2022.05.11.491546
It’s Just a Phase: Exploring the Relationship Between mRNA, Biomolecular Condensates, and Translational Control
Parker DM, Winkenbach LP, Osborne Nishimura E
Review Front Genet. 2022. Jun 27; 13:931220. doi: 10.3389/fgene.2022.931220. eCollection 2022.
2021
Improved methods for protein and single-molecule RNA detection in C. elegans embryos
Parker DM, Winkenbach LP, Parker A, Boyson S, Osborne Nishimura E
Current Protocols. 2021. Nov;1(11):e299. doi: 10.1002/cpz1.299.
- github – smFISH IF Methods
- online resources for the single molecule imaging workshop at C. elegans 2022
The transcription factor ELT-2 positively and negatively impacts direct target genes to modulate the Caenorhabditis elegans intestinal transcriptome
King DC¹ and Williams RTP¹, Mastroianni IR, Hill J, Apenas NW, Ramirez G, Osborne Nishimura E.
BioRXIV. [Preprint] August 29, 2021. doi: https://doi.org/10.1101/2021.08.29.457787
¹Authors contributed equally.
Improved methods for protein and single-molecule RNA detection in C. elegans embryos
Parker DM, Winkenbach LP, Parker A, Boyson S, Osborne Nishimura E
BioRXIV. [Preprint] May 8, 2021. doi: https://doi.org/10.1101/2021.05.07.443170
LCD-Composer: an intuitive, composition-centric method enabling the identification and detailed functional mapping of low-complexity domains
Cascarina AM, King DC, Osborne Nishimura E, Ross ED
NAR Genom Bioinform (2021) May 26;3(2):lqab048. doi: 10.1093/nargab/lqab048
2020
mRNA localization is linked to translation regulation in the Caenorhabditis elegans germ lineage
Parker DM, Winkenbach LP, Boyson S, Saxton MN, Daidone C, Al-Mazaydeh ZA, Nishimura MT, Mueller F, Osborne Nishimura E.
Development (2020) Jul 8;147(13):dev186817. doi: 10.1242/dev.186817.
YTHDF2 destabilizes m6A-modified neural-specific RNAs to restrain differentiation in induced pluripotent stem cells
Heck AM, Russo J, Wilusz J, Nishimura EO, Wilusz CJ.
RNA (2020) Jun;26(6):739-755. doi: 10.1261/rna.073502.119.
Widespread roles for piRNAs and WAGO-class siRNAs in shaping the germline transcriptome of Caenorhabditis elegans
Reed KJ, Svendsen JM, Brown KC, Montgomery BE, Marks TN, Vijayasarathy T, Parker DM, Nishimura EO, Updike DL, Montgomery TA.
Nucleic Acids Res (2020) Feb 28;48(4):1811-1827. doi: 10.1093/nar/gkz1178.
2019
TIR domains of plant immune receptors are NAD+-cleaving enzymes that promote cell death
Wan L, Essuman K, Anderson RG, Sasaki Y, Monteiro F, Chung EH, Osborne Nishimura E, DiAntonio A, Milbrandt J, Dangl JL, Nishimura MT
Science. (2019) 23 Aug; 365, 6455, p799-803.
2018
A Strategy To Isolate Modifiers of Caenorhabditis elegans Lethal Mutations: Investigating the Endoderm Specifying Ability of the Intestinal Differentiation GATA Factor ELT-2
Wiesenfahrt T, Duanmu J, Snider F, Moerman D, Au V, Li-Leger E, Flibotte S, Parker DM, Marshall CJ, Nishimura E, Mains PE, and McGhee JD.
G3 (2018) May 4; 8(5):1425-1437. doi: 10.1534/g3.118.200079.
Quantitating transcription factor redundancy: The relative roles of the ELT-2 and ELT-7 GATA factors in the C. elegans endoderm
Dineen A¹ and Osborne Nishimura E¹, Goszczynski B, Rothman JH, McGhee JD.
Dev Biol (2018) Jan 29. pii: S0012-1606(17)30690-5.
¹Authors contributed equally.
2017
TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death in Arabidopsis
Nishimura MT, Anderson RG, Cherkis KA, Law TF, Liu QL, Machius M, Nimchuk ZL, Yang L, Chung EH, El Kasmi F, Hyunh M, Osborne Nishimura E, Sondek JE, Dangl JL.
Proc Natl Acad Sci (2017) Mar 7;114(10):E2053-E2062.
2016
Polar Positioning of Phase-Separated Liquid Compartments in Cells Regulated by an mRNA Competition Mechanism
Saha S, Weber CA, Nousch M, Adame-Arana O, Hoege C, Hein MY, Osborne-Nishimura E, Mahamid J, Jahnel M, Jawerth L, Pozniakovski A, Eckmann CR, Jülicher F, Hyman AA.
Cell (2016) Sep 8;166(6):1572-1584.e16.
Probing and rearranging the transcription factor network controlling the C. elegans endoderm
Wiesenfahrt T, Osborne Nishimura E, Berg JY, McGhee JD.
Worm (2016) June 10; e1198869
A Transcriptional Lineage of the Early C. elegans Embryo
Tintori SC, Osborne Nishimura E, Golden P, Lieb JD, Goldstein B.
Dev Cell (2016) Aug 22;38(4):430-44.
- Interactive visualizer of differential gene expression in the early C. elegans embryo
- NCBI GEO: GSE77944
The function and regulation of the GATA factor ELT-2 in the C. elegans endoderm
Wiesenfahrt T, Berg JY, Osborne Nishimura E, Robinson AG, Goszczynski B, Lieb JD, McGhee JD.
Development (2016) Feb 1;143(3):483-91.
2015
Asymmetric Transcript Discovery by RNA-seq in C. elegans Blastomeres Identifies neg-1, a Gene Important for Anterior Morphogenesis
Osborne Nishimura E , Zhang JC, Werts AD, Goldstein B, Lieb JD.
PLoS Genetics (2015) Apr 13;11(4):e1005117.
For more publications see Erin’s page