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 :

07.18.18 : Nicolas D et al. Modulation of transcriptional burstfrequency by histone acetylation. Proc Natl Acad Sci U S A. 2018 Jul3;115(27):7153-7158.

Latest pitches (07.11.2018) :

Max = Liu G et al. Inherited DNA methylation primes the establishment of accessible chromatin during genome activation. Genome Res. 2018 Jul;28(7):998-1007.

Max (2) = Cho WK et al. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates. Science. 2018 Jun 21.

Max (3) = Chong S et al. Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Science. 2018 Jun 21.

Jeff = Liu G et al. Inherited DNA methylation primes the establishment of accessible chromatin during genome activation. Genome Res. 2018 Jul;28(7):998-1007.

Avi = Matreyek KA et al. Multiplex assessment of protein variant abundance by massively parallel sequencing. Nat Genet. 2018 Jun;50(6):874-882.

Kai = Hnisz D et al. A Phase Separation Model for Transcriptional Control. Cell. 2017 Mar 23;169(1):13-23.

Siqi = Nicolas D et al. Modulation of transcriptional burstfrequency by histone acetylation. Proc Natl Acad Sci U S A. 2018 Jul3;115(27):7153-7158.

Dana = Liu G et al. Inherited DNA methylation primes the establishment of accessible chromatin during genome activation. Genome Res. 2018 Jul;28(7):998-1007.

Ryan = Hawkins JA et al. Indel-correcting DNA barcodes for high throughput sequencing. Proc Natl Acad Sci U S A. 2018 Jul 3;115(27):E6217-E6226.

Previously discussed papers :

06.28.2018 : 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.

06.13.2018 : Diss G, Lehner B. The genetic landscape of a physical interaction. Elife. 2018 Apr 11;7. pii: e32472.

06.13.2018 : 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.

06.06.2018 : Osterwalder M et al. Enhancer redundancy provides phenotypic robustness in mammalian development. Nature. 2018 Feb 8;554(7691):239-243.

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