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 they have 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:

Papers selected 05.04.22

Topolewski P, Zakrzewska KE, Walczak J, et al. (2022) Phenotypic variability, not noise, accounts for most of the cell-to-cell heterogeneity in IFN-γ and oncostatin M signaling responses. Science signaling 15(721): eabd9303.

Ma Y, Budde MW, Mayalu MN, et al. (2022) Synthetic mammalian signaling circuits for robust cell population control. Cell 185(6): 967–979.e12.

Snetkova V, Ypsilanti AR, Akiyama JA, et al. (2021) Ultraconserved enhancer function does not require perfect sequence conservation. Nature genetics 53(4): 521–528.

Konstantinides N, Holguera I, Rossi AM, et al. (2022) A complete temporal transcription factor series in the fly visual system. Nature 604(7905): 316–322.

Previously discussed papers:

Papers selected 03.16.22

Marklund E, Mao G, Yuan J, et al. (2022) Sequence specificity in DNA binding is mainly governed by association. Science 375(6579): 442–445.

Rao S, Ahmad K and Ramachandran S (2021) Cooperative binding between distant transcription factors is a hallmark of active enhancers. Molecular cell 81(8): 1651–1665.e4.

Traets JJ, van der Burght SN, Rademakers S, et al. (2021) Mechanism of life-long maintenance of neuron identity despite molecular fluctuations. eLife 10. DOI: 10.7554/eLife.66955.

Ursu O, Neal JT, Shea E, et al. (2022) Massively parallel phenotyping of coding variants in cancer with Perturb-seq. Nature biotechnology. DOI: 10.1038/s41587-021-01160-7.

01.26.22: Seczynska M, Bloor S, Cuesta SM, et al. (2021) Genome surveillance by HUSH-mediated silencing of intronless mobile elements. Nature. DOI: 10.1038/s41586-021-04228-1.

01.19.22: Duveau F, Vande Zande P, Metzger BP, et al. (2021) Mutational sources of trans-regulatory variation affecting gene expression in Saccharomyces cerevisiae. eLife 10. DOI: 10.7554/eLife.67806.

01.05.22: Bintu L, Yong J, Antebi YE, et al. (2016) Dynamics of epigenetic regulation at the single-cell level. Science 351(6274): 720–724.

12.08.21: Hocker JD, Poirion OB, Zhu F, et al. (2021) Cardiac cell type-specific gene regulatory programs and disease risk association. Science advances 7(20). DOI: 10.1126/sciadv.abf1444.

11.10.21: Rinzema NJ, Sofiadis K, Tjalsma SJD, et al. (2021) Building regulatory landscapes: enhancer recruits cohesin to create contact domains, engage CTCF sites and activate distant genes. bioRxiv. DOI: 10.1101/2021.10.05.463209.

11.03.21: de Almeida BP, Reiter F, Pagani M, et al. (2021) DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of enhancers. bioRxiv. DOI: 10.1101/2021.10.05.463203.

10.27.21: Li YE, Preissl S, Hou X, et al. (2021) An atlas of gene regulatory elements in adult mouse cerebrum. Nature 598(7879): 129–136.

10.20.21: Garcia DA, Johnson TA, Presman DM, et al. (2021) An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors. Molecular cell 81(7): 1484–1498.e6.

10.06.21: Child MB 6th, Bateman JR, Jahangiri A, et al. (2021) Live imaging and biophysical modeling support a button-based mechanism of somatic homolog pairing in Drosophila. eLife 10. DOI: 10.7554/eLife.64412.

09.29.21: Wan Y, Anastasakis DG, Rodriguez J, et al. (2021) Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection. Cell 184(11): 2878–2895.e20.

09.08.21: Zhang Y, Ho TD, Buchler NE, et al. (2021) Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions. Genome research. DOI: 10.1101/gr.275145.120.

09.01.21: Desai RV, Chen X, Martin B, et al. (2021) A DNA-repair pathway can affect transcriptional noise to promote cell fate transitions. Science. DOI: 10.1126/science.abc6506.

08.25.21: Soochit W, Sleutels F, Stik G, et al. (2021) CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells. Nature cell biology 23(8): 881–893.

08.18.21: Tak YE, Horng JE, Perry NT, et al. (2021) Augmenting and directing long-range CRISPR-mediated activation in human cells. Nature methods. DOI: 10.1038/s41592-021-01224-1.

07.21.21: Sanford EM, Emert BL, Coté A, et al. (2020) Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals. eLife 9. DOI: 10.7554/eLife.59388.

07.14.21: Sönmezer C, Kleinendorst R, Imanci D, et al. (2021) Molecular Co-occupancy Identifies Transcription Factor Binding Cooperativity In Vivo. Molecular cell 81(2): 255–267.e6.

07.07.21: Tycko J, DelRosso N, Hess GT, et al. (2020) High-Throughput Discovery and Characterization of Human Transcriptional Effectors. Cell 183(7): 2020–2035.e16.

06.30.21: Ng AHM, Khoshakhlagh P, Rojo Arias JE, et al. (2021) A comprehensive library of human transcription factors for cell fate engineering. Nature biotechnology 39(4): 510–519.

06.23.21: Li J, Hsu A, Hua Y, et al. (2020) Single-gene imaging links genome topology, promoter-enhancer communication and transcription control. Nature structural & molecular biology 27(11): 1032–1040.

05.12.21: Hanna RE, Hegde M, Fagre CR, et al. (2021) Massively parallel assessment of human variants with base editor screens. Cell 184(4): 1064–1080.e20.

05.05.21: Kharerin H and Bai L (2021) Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast. PLoS computational biology 17(1): e1008560.

04.28.21: Takei Y, Yun J, Zheng S, et al. (2021) Integrated spatial genomics reveals global architecture of single nuclei. Nature 590(7845): 344–350.

04.21.21: Emert BL, Cote CJ, Torre EA, et al. (2021) Variability within rare cell states enables multiple paths toward drug resistance. Nature biotechnology. DOI: 10.1038/s41587-021-00837-3.

04.14.21: Choi J, Lysakovskaia K, Stik G, et al. (2021) Evidence for additive and synergistic action of mammalian enhancers during cell fate determination. eLife 10. DOI: 10.7554/eLife.65381.

03.03.21: Henninger JE, Oksuz O, Shrinivas K, et al. (2021) RNA-Mediated Feedback Control of Transcriptional Condensates. Cell 184(1): 207–225.e24.

02.24.21: Thomas HF, Kotova E, Jayaram S, et al. (2021) Temporal dissection of an enhancer cluster reveals distinct temporal and functional contributions of individual elements. Molecular cell. DOI: 10.1016/j.molcel.2020.12.047.

02.17.21: Tanaka H, Takizawa Y, Takaku M, et al. (2020) Interaction of the pioneer transcription factor GATA3 with nucleosomes. Nature communications 11(1): 4136.

02.10.21: Akdemir KC, Le VT, Kim JM, et al. (2020) Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure. Nature genetics 52(11): 1178–1188.

02.03.21: Klosin A, Oltsch F, Harmon T, et al. (2020) Phase separation provides a mechanism to reduce noise in cells. Science 367(6476): 464–468.

01.20.21: Bergen, V., Lange, M., Peidli, S., Wolf, F. A. & Theis, F. J. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat. Biotechnol. (2020) doi:10.1038/s41587-020-0591-3

01.06.21: Domcke, S. et al. A human cell atlas of fetal chromatin accessibility. Science 370, (2020)

Cao, J. et al. A human cell atlas of fetal gene expression. Science 370, (2020)

12.16.20: Wong, E. S. et al. Deep conservation of the enhancer regulatory code in animals. Science 370, (2020)

12.09.20: Kent, S. et al. Phase-Separated Transcriptional Condensates Accelerate Target-Search Process Revealed by Live-Cell Single-Molecule Imaging. Cell Rep. 33, 108248 (2020)

11.11.20: Ballaré, C. et al. Nucleosome-Driven Transcription Factor Binding and Gene Regulation. Mol. Cell 49, 67–79 (2013)

11.04.20: Ireland, W. T. et al. Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time. Elife 9, (2020)

10.21.20: Chiasson, M. A. et al. Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact. Elife 9, (2020)

10.14.20: Houri-Zeevi, L., Korem Kohanim, Y., Antonova, O. & Rechavi, O. Three Rules Explain Transgenerational Small RNA Inheritance in C. elegans. Cell 182, 1186–1197.e12 (2020)

10.07.20: Chen, S. Y. et al. Optogenetic Control Reveals Differential Promoter Interpretation of Transcription Factor Nuclear Translocation Dynamics. Cell Syst (2020)

09.23.20: Jaeger, M. G. et al. Selective Mediator dependence of cell-type-specifying transcription. Nat. Genet. (2020) doi:10.1038/s41588-020-0635-0

09.16.20: Sigalova, O. M., Shaeiri, A., Forneris, M., Furlong, E. E. & Zaugg, J. B. Predictive features of gene expression variation reveal mechanistic link with differential expression. Mol. Syst. Biol. 16, e9539 (2020)

09.09.20: Hoppe, C. et al. Modulation of the Promoter Activation Rate Dictates the Transcriptional Response to Graded BMP Signaling Levels in the Drosophila Embryo. Dev. Cell (2020) doi:10.1016/j.devcel.2020.07.007

09.02.20: Hafner, A. et al. Quantifying the Central Dogma in the p53 Pathway in Live Single Cells. Cell Syst 10, 495–505.e4 (2020)

08.26.20: Partridge, E. C. et al. Occupancy maps of 208 chromatin-associated proteins in one human cell type. Nature 583, 720–728 (2020)

08.12.20: Quintero-Cadena, P., Lenstra, T. L. & Sternberg, P. W. RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting. Mol. Cell (2020) doi:10.1016/j.molcel.2020.05.030

08.05.20: Fitz, J. et al. Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction. Nat. Genet. (2020) doi:10.1038/s41588-020-0605-6

07.29.20: Long, Y. et al. RNA is essential for PRC2 chromatin occupancy and function in human pluripotent stem cells. Nat. Genet. (2020) doi:10.1038/s41588-020-0662-x

07.22.20: Ramaker, R. C. et al. Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations. Genome Res. (2020) doi:10.1101/gr.260463.119

07.15.20: Wheat, J. C. et al. Single-molecule imaging of transcription dynamics in somatic stem cells. Nature (2020) doi:10.1038/s41586-020-2432-4

07.01.20: Jost, M. et al. Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs. Nat. Biotechnol. 38, 355–364 (2020)

06.24.20: Fulco, C. P. et al. Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. Nat. Genet. 51, 1664–1669 (2019)

06.17.20: Tsujimura, T. et al. Controlling gene activation by enhancers through a drug-inducible topological insulator. Elife 9, (2020)

05.27.20: Anderson, C. et al. Natural variation in stochastic photoreceptor specification and color preference in Drosophila. Elife 6, (2017)

05.20.20: Bialek, W., Gregor, T. & Tkačik, G. Action at a distance in transcriptional regulation. arXiv [q-bio.SC] (2019)

05.13.20: Slobodin, B. et al. Transcription Dynamics Regulate Poly(A) Tails and Expression of the RNA Degradation Machinery to Balance mRNA Levels. Mol. Cell (2020)

05.06.20: Poramba-Liyanage, D. W. et al. Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes. Genome Res. (2020)

04.15.20: Hackett, S. R. et al. Learning causal networks using inducible transcription factors and transcriptome-wide time series. Mol. Syst. Biol. 16, e9174 (2020)

04.08.20: Chen, J. et al. Pervasive functional translation of noncanonical human open reading frames. Science 367, 1140–1146 (2020)

04.01.20: Yokoshi, M., Segawa, K. & Fukaya, T. Visualizing the Role of Boundary Elements in Enhancer-Promoter Communication. Mol. Cell (2020)

03.04.20: Palii, C. G. et al. Single-Cell Proteomics Reveal that Quantitative Changes in Co-expressed Lineage-Specific Transcription Factors Determine Cell Fate. Cell Stem Cell 24, 812–820.e5 (2019)

02.19.20: Hendy, O., Campbell, J., Jr, Weissman, J. D., Larson, D. R. & Singer, D. S. Differential context-specific impact of individual core promoter elements on transcriptional dynamics. Mol. Biol. Cell 28, 3360–3370 (2017)

02.05.20: Shi, Z. et al. Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide. Mol. Cell 67, 71–83.e7 (2017)

01.29.20: Davidson, I. F. et al. DNA loop extrusion by human cohesin. Science 366, 1338–1345 (2019)

01.22.20: McFaline-Figueroa, J. L. et al. A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition. Nat. Genet. 51, 1389–1398 (2019)

01.15.20: Feldman, D. et al. Optical Pooled Screens in Human Cells. Cell 179, 787–799.e17 (2019)

12.11.19: Gibson, B. A. et al. Organization of Chromatin by Intrinsic and Regulated Phase Separation. Cell 179, 470–484.e21 (2019)

12.04.19: Viets, K. et al. Characterization of Button Loci that Promote Homologous Chromosome Pairing and Cell-Type-Specific Interchromosomal Gene Regulation. Dev. Cell 51, 341–356.e7 (2019)

11.20.19: Bartman, C. R. et al. Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation. Mol. Cell 73, 519–532.e4 (2019)

11.13.19: Lord, N. D. et al. Stochastic antagonism between two proteins governs a bacterial cell fate switch. Science 366, 116–120 (2019)

11.06.19: Huertas, J., MacCarthy, C. M., Schöler, H. & Cojocaru, V. Nucleosomal DNA dynamics mediate Oct4 pioneer factor binding. bioRxiv 634386 (2019).

10.02.19: Lim, B., Heist, T., Levine, M. & Fukaya, T. Visualization of Transvection in Living Drosophila Embryos. Mol. Cell 70, 287–296.e6 (2018).

09.25.19: Benabdallah, N. S. et al. Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation. Molecular Cell, (2019).

08.28.19: Tsai, A., Alves, M. R. & Crocker, J. Multi-enhancer transcriptional hubs confer phenotypic robustness. Elife 8, (2019).

08.21.19: Jin, Y., Eser, U., Struhl, K. & Churchman, L. S. The Ground State and Evolution of Promoter Region Directionality. Cell 170, 889–898.e10 (2017).

08.07.19: Wilson, M. D. et al. Species-specific transcription in mice carrying human chromosome 21. Science 322, 434–438 (2008).

07.31.19: Ghavi-Helm, Y. et al. Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression. Nat. Genet. (2019). doi:10.1038/s41588-019-0462-3

07.17.19: Schmiedel, J. M. & Lehner, B. Determining protein structures using deep mutagenesis. Nat. Genet. 51, 1177–1186 (2019).

07.10.19: Falk, M. et al. Heterochromatin drives compartmentalization of inverted and conventional nuclei. Nature 570, 395–399 (2019).

07.03.19: Paliou, C. et al. Preformed chromatin topology assists transcriptional robustness of Shh during limb development. Proc. Natl. Acad. Sci. U. S. A. 116, 12390–12399 (2019).

Williamson, I. et al. Developmentally regulated Shh expression is robust to TAD perturbations. bioRxiv 609941 (2019). doi:10.1101/609941

06.19.19: Haberle, V. et al. Transcriptional cofactors display specificity for distinct types of core promoters. Nature 570, 122–126 (2019).

06.12.19: McSwiggen, D. T. et al. Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation. Elife 8, (2019).

05.29.19: Yamada, S. et al. The Drosophila Pioneer Factor Zelda Modulates the Nuclear Microenvironment of a Dorsal Target Enhancer to Potentiate Transcriptional Output. Curr. Biol. 29, 1387–1393.e5 (2019).

05.22.19: Bashor, C. J. et al. Complex signal processing in synthetic gene circuits using cooperative regulatory assembliesScience 364, 593–597 (2019).

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

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