Journal Club

We meet at 10.00 AM on Wednesdays in Room #4304 at 4515 McKinley.

Every couple of weeks, each lab member pitches an article that he or she has recently read. They have two minutes to sell the lab on the exciting findings and merits of the experiments. At the conclusion, we vote on the papers that will populate the coming weeks’ discussions.

Next paper :

06.09.2018 : Osterwalder M et al. Enhancer redundancy provides phenotypic robustness in mammalian development. Nature. 2018 Feb 8;554(7691):239-243.

Latest pitches (05.30.2018) :

Clarice : Recillas-Targa F et al. Position-effect protection and enhancer blocking by the chicken beta-globin insulator are separable activities. Proc Natl Acad Sci U S A. 2002 May 14;99(10):6883-8.

Siqi : Faure AJ, Schmiedel JM, Lehner B. Systematic Analysis of the Determinants of Gene Expression Noise in Embryonic Stem Cells. Cell Syst. 2017 Nov 22;5(5):471-484.e4.

Avi : Osterwalder M et al. Enhancer redundancy provides phenotypic robustness in mammalian development. Nature. 2018 Feb 8;554(7691):239-243.

Jeff : Yu X, Buck M. Defining p53 pioneering capabilities with competitive nucleosome binding assays. Biorxiv. DOI: https://doi.org/10.1101/327635.

Dana : Wei B et al. A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility. Nat Biotechnol. 2018 May 21.

Max : Diss G, Lehner B. The genetic landscape of a physical interaction. Elife. 2018 Apr 11;7. pii: e32472.

Ryan : Shen N et al. Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding. Cell Syst. 2018 Apr 25;6(4):470-483.e8.

 

Previously discussed papers :

05.09.2018 : Moretto F, Wood NE, Kelly G, Doncic A, van Werven FJ. A regulatory circuit of two lncRNAs and a master regulator directs cell fate in yeast. Nat Commun. 2018 Feb 22;9(1):780.

05.02.2018 : Batut PJ, Gingeras TR. Conserved noncoding transcription and core promoter regulatory code in early Drosophila development. Elife. 2017 Dec 20;6. pii: e29005.

04.25.2018 : Ren G, Jin W, Cui K, Rodrigez J, Hu G, Zhang Z, Larson DR, Zhao K. CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression. Mol Cell. 2017 Sep 21;67(6):1049-1058.e6.

01.31.2018 : Corrales M, Rosado A, Cortini R, van Arensbergen J, van Steensel B, Filion GJ. (2017). Clustering of Drosophila housekeeping promoters facilitates their expression. Genome Res. 27:1153-1161.

01.24.2018 : Jiang S, Liu Y, Xu C, et al. Dissecting Nucleosome Function with a Comprehensive Histone H2A and H2B Mutant Library. G3: Genes|Genomes|Genetics. 2017;7(12):3857-3866.

12.13.2017 : Ye Z, Chen Z, Sunkel B, et al. Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1. Nucleic Acids Research. 2016;44(16):7540-7554. doi:10.1093/nar/gkw659.

02.10.2016 : Burrows CK, Banovich NE, Pavlovic BJ, Patterson K, Gallego Romero I, Pritchard JK, Gilad Y. (2016) Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs. PLoS Genet.12(1):e1005793

02.03.2016: Sorrells, T. R., Booth, L. N., Tuch, B. B., & Johnson, A. D. (2015) Intersecting transcription networks constrain gene regulatory evolution. Nature. 523(7560), 361–365.

01.27. 2016 : Kellogg RA, Tian C, Lipniacki T, Quake SR, Tay S (2015) Digital signaling decouples activation probability and population heterogeneity.Elife. 21(4):e08931

01.20.2016 : , , , , , Competition between binding sites determines gene expression at low transcription factor concentrations. Biorxiv.

12.16.2015 : Arttu Jolma, Yimeng Yin, Kazuhiro R. Nitta, Kashyap Dave, Alexander Popov, Minna Taipale, Martin Enge, Teemu Kivioja, Ekaterina Morgunova & Jussi Taipale (2015) DNA-dependent formation of transcription factor pairs alters their binding specificity. Nature. 527,384–388

12.09.2015 : Gerald Stampfel, Tomáš Kazmar, Olga Frank, Sebastian Wienerroither, Franziska Reiter & Alexander Stark (2015) Transcriptional regulators form diverse groups with context-dependent regulatory functions. Nature. 528,147–151