Nishimura Lab Journal Club

Past Journal Clubs:

Spring-Fall 2018 & Spring 2019 Schedule

January 12, 2018SARM1-specific motifs in the TIR domain enable NAD+ loss and regulate injury-induced SARM1 activation.
Summers DW, Gibson DA, DiAntonio A, Milbrandt J
Proc Natl Acad Sci U S A. 2016 Oct 11;113(41):E6271-E6280.
January 19Progressive Decrease of Mitochondrial Motility during Maturation of Cortical Axons In Vitro and In Vivo.
Lewis TL Jr, Turi GF, Kwon SK, Losonczy A, Polleux F.
Curr Biol. 2016 Oct 10;26(19):2602-2608.

Acetylated Tau Obstructs KIBRA-Mediated Signaling in Synaptic Plasticity and Promotes Tauopathy-Related Memory Loss.
Tracy TE1, Sohn PD2, Minami SS1, Wang C1, Min SW1, Li Y3, Zhou Y3, Le D3, Lo I3, Ponnusamy R3, Cong X4, Schilling B4, Ellerby LM4, Huganir RL5, Gan L6.
Neuron. 2016 Apr 20;90(2):245-60.
January 26Neurons generated by direct conversion of fibroblasts reproduce synaptic phenotype caused by autism-associated neuroligin-3 mutation.
Chanda S1, Marro S, Wernig M, Südhof TC.
Proc Natl Acad Sci U S A. 2013 Oct 8;110(41):16622-7.
February 2RobertChromatin accessibility dynamics reveal novel functional enhancers in C. elegans.
Daugherty AC, Yeo RW, Buenrostro JD, Greenleaf WJ, Kundaje A, Brunet A.
Genome Res. 2017 Dec;27(12):2096-2107. doi: 10.1101/gr.226233.117.
February 9DylanIn Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus.
Shah S, Lubeck E, Zhou W, Cai L.
Neuron. 2016 Oct 19;92(2):342-357. doi: 10.1016/j.neuron.2016.10.001.
February 16Phil FoxMyc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation.
Kieffer-kwon KR, Nimura K, Rao SSP, et al. 2017;67(4):566-578.e10. doi: 10.1016/j.molcel.2017.07.013.
February 23BMB Recruitment - no journal club
March 2Matt MarzoA Massively Parallel Reporter Assay of 3′ UTR Sequences Identifies In Vivo Rules for mRNA Degradation.
Rabani M, Pieper L, Chew GL, Schier AF. Mol Cell. 2017;68(6):1083-1094.e5. doi: 10.1016/j.molcel.2017.11.014
March 9David & KhalilModerated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014). Genome Biology, 15(12), 1–21. doi: 10.1186/s13059-014-0550-8
March 16Spring Break - no journal club
March 23Dylan ParkerThe Stress Granule Transcriptome Reveals Principles of mRNA Accumulation in Stress Granules
Khong A, Matheny T, Jain S, Mitchell SF, Wheeler JR, Parker R. The Stress Granule Transcriptome Reveals Principles of mRNA Accumulation in Stress Granules. Mol Cell. 2017;68(4):808-820.e5.
March 30 - April 13No Journal Club
April 20, 2018Dylan ParkerNanos promotes epigenetic reprograming of the germline by down-regulation of the THAP transcription factor LIN-15B
Lee CS, Lu T, Seydoux G. Elife. 2017;6
May 5th, 2018Robert WilliamsCell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics.
Plass M, Solana J, Wolf FA, Ayoub S, Misios A, Glažar P, Obermayer B, Theis FJ, Kocks C, Rajewsky N.
Science. 2018 May 25;360(6391). pii: eaaq1723. doi: 10.1126/science.aaq1723. Epub 2018 Apr 19.
May 25th, 2018Robert and DavidDeactivation of the GATA Transcription Factor ELT-2 Is a Major Driver of Normal Aging in C. elegans.
Mann FG, Van Nostrand EL, Friedland AE, Liu X, Kim SK (2016), PLoS Genet 12(4): e1005956.
June 1st, 2018Dylan ParkerDynamic Axonal Translation in Developing and Mature Visual Circuits.
Shigeoka T, Jung H, Jung J, Turner-Bridger B, Ohk J, Lin JQ, Amieux PS, Holt CE
Cell. 2016 Jun 30;166(1):181-92. doi: 10.1016/j.cell.2016.05.029. Epub 2016 Jun 16.
June 5, 2018LindsayThe mTOR-S6 kinase pathway promotes stress granule assembly.
Aristeidis P. Sfakianos, Laura E. Mellor, Yoke Fei Pang, Paraskevi Kritsiligkou, Hope Needs, Hussein Abou-Hamdan, Laurent Désaubry, Gino B. Poulin, Mark P. Ashe & Alan J. Whitmarsh
Cell Death & Differentiation (2018)
June 12, 2018ErinSummer Writing Workshop
June 19, 2018ErinSummer Writing Workshop II
June 26, 2018 and August 2, 2018ErinHigh-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies.
Youn JY, Dunham WH, Hong SJ, et al.
Mol Cell. 2018;69(3):517-532.e11.
August 9, 2018Robert
Feb 15, 2019LindsayAoki ST, Crittenden SL, Lynch TR, Bingman CA, Wickens M, Kimble J. Nematode germ granule assembly is linked to mRNA repression. BioRXiv
Mar 1, 2019DylanAoki ST, Kershner AM, Bingman CA, Wickens M, and Kimble J. PGL germ granule assembly protein is a base-specific, single-stranded RNase. PNAS February 2, 2016 113 (5) 1279-1284
Mar 15, 2019RobertA lineage-resolved molecular atlas of C. elegans embryogenesis at single cell resolution.
Jonathan S. Packer, Qin Zhu, Chau Huynh, Priya Sivaramakrishnan, Elicia Preston, Hannah Dueck, Derek Stefanik, Kai Tan, Cole Trapnell, Junhyong Kim, Robert H. Waterston, John I. Murray

bioRxiv, DOI: 10.1101/565549
Mar 29, 2019David
April 12, 2019Sam
April 25, 2019RescheduledGenome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation

May AllAbby Dernberg Paper
Oct 11RobertMathies, L.D., et al. (2019). mRNA profiling reveals significant transcriptional differences between a multipotent progenitor and its differentiated sister. BMC Genomics. 20, article number: 427; doi: 10.1186/s12864-019-5821-z
Oct 25DavidShen et al. (2018). Divergence in DNA Specificity among Paralogous
Transcription Factors Contributes to Their
Differential In Vivo Binding. Cell Systems 6, 470–483
April 25, 2018. Published by Elsevier Inc.

Also for perspective on that-
from Harmen Bussemaker (discovered PQM-1)
Dec 13RobertAnzalone AV, et al. (2019). Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019 Dec;576(7785):149-157. doi: 10.1038/s41586-019-1711-4. Epub 2019 Oct 21.

Meeting Location: MRB250
Time: 12:30-2pm