Cohen Lab

Journal Club

The Cohen Lab journal club meets at 10:00 AM on Wednesdays in Couch 4304.

Every few 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, the lab votes on the papers that will populate the coming weeks’ discussions.

Previously-Discussed Papers

10/5/22: Asimi V et al. Hijacking of transcriptional condensates by endogenous retroviruses. Nature Genetics (2022) [doi: 10.1038/s41588-022-01132-w]

9/14/22: Lin X et al. Nested epistasis enhancer networks for robust genome regulation. Science (2022) [doi: 10.1126/science.abk3512]

9/7/22: Pachano T et al. Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness. Nature Genetics (2021) [doi: 10.1038/s41588-021-00888-x]

8/31/22: Neumayr C et al. Differential cofactor dependencies define distinct types of human enhancers. Nature (2022) [doi: 10.1038/s41586-022-04779-x]

8/17/22: Bergman DT et al. Compatibility rules of human enhancer and promoter sequences. Nature (2022) [doi: 10.1038/s41586-022-04877-w]

8/10/22: Bal E et al. Super-enhancer hypermutation alters oncogene expression in B cell lymphoma. Nature (2022) [doi: 10.1038/s41586-022-04906-8]

8/3/22: Choi J et al. A time-resolved, multi-symbol molecular recorder via sequential genome editing. Nature (2022) [doi: 10.1038/s41586-022-04922-8]

7/13/22: Konstantinides N et al. A complete temporal transcription factor series in the fly visual system. Nature (2022) [doi: 10.1038/s41586-022-04564-w]

7/6/22: Snetkova V et al. Ultraconserved enhancer function does not require perfect sequence conservation. Nature Genetics (2021) [doi: 10.1038/s41588-021-00812-3]

6/8/22: Ma Y et al. Synthetic mammalian signaling circuits for robust cell population control. Cell (2022) [doi: 10.1016/j.cell.2022.01.026]

5/18/22: Topolewski P et al. Phenotypic variability, not noise, accounts for most of the cell-to-cell heterogeneity in IFN-gamma and oncostatin M signaling responses. Science Signaling (2022) [doi: 10.1126/scisignal.abd9303]

4/19/22: Marklund E et al. Sequence specificity in DNA binding is mainly governed by association. Science (2022) [doi: 10.1126/science.abg7427]

4/13/22: Rao S et al. Cooperative binding between distant transcription factors is a hallmark of active enhancers. Molecular Cell (2021) [doi: 10.1016/j.molcel.2021.02.014]

4/6/22: Traets JJH et al. Mechanism of life-long maintenance of neuron identity despite molecular fluctuations. eLife (2021) [doi: 10.7554/eLife.66955]

3/23/22: Ursu O et al. Massively parallel phenotyping of coding variants in cancer with Perturb-seq. Nature Biotechnology (2022) [doi: 10.1038/s41587-021-01160-7]

2/23/22: Seczynska M et al. Genome surveillance by HUSH-mediated silencing of intronless mobile elements. Nature (2022) [doi: 10.1038/s41586-021-04228-1]

2/2/22: Duveau F et al. Mutational sources of trans-regulatory variation affecting gene expression in Saccharomyces cerevisiae. eLife (2021) [doi: 10.7554/eLife.67806]

1/26/22: Bintu L et al. Dynamics of epigenetic regulation at the single-cell level. Science (2016) [doi: 10.1126/science.aab2956]

12/8/21: Hocker JD et al. Cardiac cell type-specific gene regulatory programs and disease risk association. Science Advances (2021) [doi: 10.1126/sciadv.abf1444]

11/10/21: Rinzema NJ et al. Building regulatory landscapes: enhancer recruits cohesin to create contact domains, engage CTCF sites and activate distant genes. bioRχiv Preprint (2021) [doi: 10.1101/2021.10.05.463209]

11/3/21: de Almeida BP et al. DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of enhancers. bioRχiv Preprint (2021) [doi: 10.1101/2021.10.05.463203]

10/27/21: Li YE et al. An atlas of gene regulatory elements in adult mouse cerebrum. Nature (2021) [doi: 10.1038/s41586-021-03604-1]

10/20/21: Garcia DA et al. An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors. Molecular Cell (2021) [doi: 10.1016/j.molcel.2021.01.013]

10/6/21: Child MB et al. Live imaging and biophysical modeling support a button-based mechanism of somatic homolog pairing in Drosophila. eLife (2021) [doi: 10.7554/eLife.64412]

9/29/21: Wan YH et al. Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection. Cell (2021) [doi: 10.1016/j.cell.2021.04.012]

9/8/21: Zhang YN et al. Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions. Genome Research (2021) [doi: 10.1101/gr.275145.120]

9/1/21: Desai RV et al. A DNA repair pathway can regulate transcriptional noise to promote cell fate transitions. Science (2021) [doi: 10.1126/science.abc6506]

8/25/21: Soochit W et al. CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells. Nature Cell Biology (2021) [doi: 10.1038/s41556-021-00722-w]

8/18/21: Tak YE et al. Augmenting and directing long-range CRISPR-mediated activation in human cells. Nature Methods (2021) [doi: 10.1038/s41592-021-01224-1]

7/21/21: Sanford EM et al. Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals. eLife (2020) [doi: 10.7554/eLife.59388]

7/14/21: Sonmezer C et al. Molecular Co-occupancy Identifies Transcription Factor Binding Cooperativity In Vivo. Molecular Cell (2021) [doi: 10.1016/j.molcel.2020.11.015]

7/7/21: Tycko J et al. High-Throughput Discovery and Characterization of Human Transcriptional Effectors. Cell (2020) [doi: 10.1016/j.cell.2020.11.024]

6/30/21: Ng AHM et al. A comprehensive library of human transcription factors for cell fate engineering. Nature Biotechnology (2021) [doi: 10.1038/s41587-020-0742-6]

6/23/21: Li JR et al. Single-gene imaging links genome topology, promoter-enhancer communication and transcription control. Nature Structural & Molecular Biology (2020) [doi: 10.1038/s41594-020-0493-6]

5/12/21: Hanna RE et al. Massively parallel assessment of human variants with base editor screens. Cell (2021) [doi: 10.1016/j.cell.2021.01.012]

5/5/21: Kharerin H, Bai L Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast. PLOS Computational Biology (2021) [doi: 10.1371/journal.pcbi.1008560]

4/28/21: Takei Y et al. Integrated spatial genomics reveals global architecture of single nuclei. Nature (2021) [doi: 10.1038/s41586-020-03126-2]

4/21/21: Emert BL et al. Variability within rare cell states enables multiple paths toward drug resistance. Nature Biotechnology (2021) [doi: 10.1038/s41587-021-00837-3]

4/14/21: Choi J et al. Evidence for additive and synergistic action of mammalian enhancers during cell fate determination. eLife (2021) [doi: 10.7554/eLife.65381]

3/3/21: Henninger JE et al. RNA-Mediated Feedback Control of Transcriptional Condensates. Cell (2021) [doi: 10.1016/j.cell.2020.11.030]

2/24/21: Thomas HF et al. Temporal dissection of an enhancer cluster reveals distinct temporal and functional contributions of individual elements. Molecular Cell (2021) [doi: 10.1016/j.molcel.2020.12.047]

2/17/21: Tanaka H et al. Interaction of the pioneer transcription factor GATA3 with nucleosomes. Nature Communications (2020) [doi: 10.1038/s41467-020-17959-y]

2/10/21: Akdemir KC et al. Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure. Nature Genetics (2020) [doi: 10.1038/s41588-020-0708-0]

2/3/21: Klosin A et al. Phase separation provides a mechanism to reduce noise in cells. Science (2020) [doi: 10.1126/science.aav6691]

1/20/21: Bergen V et al. Generalizing RNA velocity to transient cell states through dynamical modeling. Nature Biotechnology (2020) [doi: 10.1038/s41587-020-0591-3]

1/6/21: Domcke S et al. A human cell atlas of fetal chromatin accessibility. Science (2020) [doi: 10.1126/science.aba7612]

12/16/20: Wong ES et al. Deep conservation of the enhancer regulatory code in animals. Science (2020) [doi: 10.1126/science.aax8137]

12/9/20: Kent S et al. Phase-Separated Transcriptional Condensates Accelerate Target-Search Process Revealed by Live-Cell Single-Molecule Imaging. Cell Reports (2020) [doi: 10.1016/j.celrep.2020.108248]

11/11/20: Ballare C et al. Nucleosome-Driven Transcription Factor Binding and Gene Regulation. Molecular Cell (2013) [doi: 10.1016/j.molcel.2012.10.019]

11/4/20: Ireland WT et al. Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time. eLife (2020) [doi: 10.7554/eLife.55308]

10/21/20: Chiasson MA et al. Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact. eLife (2020) [doi: 10.7554/eLife.58026]

10/14/20: Houri-Zeevi L et al. Three Rules Explain Transgenerational Small RNA Inheritance in C. elegans. Cell (2020) [doi: 10.1016/j.cell.2020.07.022]

10/7/20: Chen SY et al. Optogenetic Control Reveals Differential Promoter Interpretation of Transcription Factor Nuclear Translocation Dynamics. Cell Systems (2020) [doi: 10.1016/j.cels.2020.08.009]

9/23/20: Jaeger MG et al. Selective Mediator dependence of cell-type-specifying transcription. Nature Genetics (2020) [doi: 10.1038/s41588-020-0635-0]

9/16/20: Sigalova OM et al. Predictive features of gene expression variation reveal mechanistic link with differential expression. Molecular Systems Biology (2020) [doi: 10.15252/msb.20209539]

9/9/20: Hoppe C et al. Modulation of the Promoter Activation Rate Dictates the Transcriptional Response to Graded BMP Signaling Levels in the Drosophila Embryo. Developmental Cell (2020) [doi: 10.1016/j.devcel.2020.07.007]

9/2/20: Hafner A et al. Quantifying the Central Dogma in the p53 Pathway in Live Single Cells. Cell Systems (2020) [doi: 10.1016/j.cels.2020.05.001]

8/26/20: Partridge EC et al. Occupancy maps of 208 chromatin-associated proteins in one human cell type. Nature (2020) [doi: 10.1038/s41586-020-2023-4]

8/12/20: Quintero-Cadena P et al. RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting. Molecular Cell (2020) [doi: 10.1016/j.molcel.2020.05.030]

8/5/20: Fitz J et al. Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction. Nature Genetics (2020) [doi: 10.1038/s41588-020-0605-6]

7/29/20: Long YC et al. RNA is essential for PRC2 chromatin occupancy and function in human pluripotent stem cells. Nature Genetics (2020) [doi: 10.1038/s41588-020-0662-x]

7/22/20: Ramaker RC et al. Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations. Genome Research (2020) [doi: 10.1101/gr.260463.119]

7/15/20: Wheat JC et al. Single-molecule imaging of transcription dynamics in somatic stem cells. Nature (2020) [doi: 10.1038/s41586-020-2432-4]

7/1/20: Jost M et al. Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs. Nature Biotechnology (2020) [doi: 10.1038/s41587-019-0387-5]

6/24/20: Fulco CP et al. Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. Nature Genetics (2019) [doi: 10.1038/s41588-019-0538-0]

6/17/20: Tsujimura T et al. Controlling gene activation by enhancers through a drug-inducible topological insulator. eLife (2020) [doi: 10.7554/eLife.47980]

5/27/20: Anderson C et al. Natural variation in stochastic photoreceptor specification and color preference in Drosophila. eLife (2017) [doi: 10.7554/eLife.29593]

5/20/20: Bialek W et al. Action at a distance in transcriptional regulation. arΧiv Preprint (2019) [doi: 10.48550/arXiv.1912.08579]

5/13/20: Slobodin B et al. Transcription Dynamics Regulate Poly(A) Tails and Expression of the RNA Degradation Machinery to Balance mRNA Levels. Molecular Cell (2020) [doi: 10.1016/j.molcel.2020.03.022]

5/6/20: Poramba-Liyanage DW et al. Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes. Genome Research (2020) [doi: 10.1101/gr.256255.119]

4/15/20: Hackett SR et al. Learning causal networks using inducible transcription factors and transcriptome-wide time series. Molecular Systems Biology (2020) [doi: 10.15252/msb.20199174]

4/8/20: Chen J et al. Pervasive functional translation of noncanonical human open reading frames. Science (2020) [doi: 10.1126/science.aay0262]

4/1/20: Yokoshi M et al. Visualizing the Role of Boundary Elements in Enhancer-Promoter Communication. Molecular Cell (2020) [doi: 10.1016/j.molcel.2020.02.007]

3/4/20: Palii CG et al. Single-Cell Proteomics Reveal that Quantitative Changes in Co-expressed Lineage-Specific Transcription Factors Determine Cell Fate. Cell Stem Cell (2019) [doi: 10.1016/j.stem.2019.02.006]

2/19/20: Hendy O et al. Differential context-specific impact of individual core promoter elements on transcriptional dynamics. Molecular Biology Of The Cell (2017) [doi: 10.1091/mbc.E17-06-0408]

2/5/20: Shi Z et al. Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide. Molecular Cell (2017) [doi: 10.1016/j.molcel.2017.05.021]

1/29/20: Davidson IF et al. DNA loop extrusion by human cohesin. Science (2019) [doi: 10.1126/science.aaz3418]

1/22/20: McFaline-Figueroa JL et al. A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition. Nature Genetics (2019) [doi: 10.1038/s41588-019-0489-5]

1/15/20: Feldman D et al. Optical Pooled Screens in Human Cells. Cell (2019) [doi: 10.1016/j.cell.2019.09.016]

12/11/19: Gibson BA et al. Organization of Chromatin by Intrinsic and Regulated Phase Separation. Cell (2019) [doi: 10.1016/j.cell.2019.08.037]

12/4/19: Viets K et al. Characterization of Button Loci that Promote Homologous Chromosome Pairing and Cell-Type-Specific Interchromosomal Gene Regulation. Developmental Cell (2019) [doi: 10.1016/j.devcel.2019.09.007]

11/20/19: Bartman CR et al. Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation. Molecular Cell (2019) [doi: 10.1016/j.molcel.2018.11.004]

11/13/19: Lord ND et al. Stochastic antagonism between two proteins governs a bacterial cell fate switch. Science (2019) [doi: 10.1126/science.aaw4506]

11/6/19: Huertas J et al. Nucleosomal DNA Dynamics Mediate Oct4 Pioneer Factor Binding. Biophysical Journal (2020) [doi: 10.1016/j.bpj.2019.12.038]

10/2/19: Lim B et al. Visualization of Transvection in Living Drosophila Embryos. Molecular Cell (2018) [doi: 10.1016/j.molcel.2018.02.029]

9/25/19: Benabdallah NS et al. Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation. Molecular Cell (2019) [doi: 10.1016/j.molcel.2019.07.038]

8/28/19: Tsai A et al. Multi-enhancer transcriptional hubs confer phenotypic robustness. eLife (2019) [doi: 10.7554/eLife.45325]

8/21/19: Jin Y et al. The Ground State and Evolution of Promoter Region Directionality. Cell (2017) [doi: 10.1016/j.cell.2017.07.006]

8/7/19: Wilson MD et al. Species-specific transcription in mice carrying human chromosome 21. Science (2008) [doi: 10.1126/science.1160930]

7/31/19: Ghavi-Helm Y et al. Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression. Nature Genetics (2019) [doi: 10.1038/s41588-019-0462-3]

7/17/19: Schmiedel JM, Lehner B Determining protein structures using deep mutagenesis. Nature Genetics (2019) [doi: 10.1038/s41588-019-0431-x]

7/10/19: Falk M et al. Heterochromatin drives compartmentalization of inverted and conventional nuclei. Nature (2019) [doi: 10.1038/s41586-019-1275-3]

7/3/19: Paliou C et al. Preformed chromatin topology assists transcriptional robustness of Shh during limb development. PNAS (2019) [doi: 10.1073/pnas.1900672116]

6/19/19: Haberle V et al. Transcriptional cofactors display specificity for distinct types of core promoters. Nature (2019) [doi: 10.1038/s41586-019-1210-7]

6/12/19: McSwiggen DT et al. Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation. eLife (2019) [doi: 10.7554/eLife.47098]

5/29/19: Yamada S et al. The Drosophila Pioneer Factor Zelda Modulates the Nuclear Microenvironment of a Dorsal Target Enhancer to Potentiate Transcriptional Output. Current Biology (2019) [doi: 10.1016/j.cub.2019.03.019]

5/22/19: Bashor CJ et al. Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies. Science (2019) [doi: 10.1126/science.aau8287]

7/18/18: Nicolas D et al. Modulation of transcriptional burst frequency by histone acetylation. PNAS (2018) [doi: 10.1073/pnas.1722330115]

6/28/18: Recillas-Targa F et al. Position-effect protection and enhancer blocking by the chicken beta-globin insulator are separable activities. PNAS (2002) [doi: 10.1073/pnas.102179399]

6/20/18: Diss G, Lehner B The genetic landscape of a physical interaction. eLife (2018) [doi: 10.7554/eLife.32472]

6/13/18: Shen N et al. Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding. Cell Systems (2018) [doi: 10.1016/j.cels.2018.02.009]

6/6/18: Osterwalder M et al. Enhancer redundancy provides phenotypic robustness in mammalian development. Nature (2018) [doi: 10.1038/nature25461]

5/9/18: Moretto F et al. A regulatory circuit of two lncRNAs and a master regulator directs cell fate in yeast. Nature Communications (2018) [doi: 10.1038/s41467-018-03213-z]

5/2/18: Batut PJ, Gingeras TR Conserved noncoding transcription and core promoter regulatory code in early Drosophila development. eLife (2017) [doi: 10.7554/eLife.29005]

4/25/18: Ren G et al. CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression. Molecular Cell (2017) [doi: 10.1016/j.molcel.2017.08.026]

1/31/18: Corrales M et al. Clustering of Drosophila housekeeping promoters facilitates their expression. Genome Research (2017) [doi: 10.1101/gr.211433.116]

1/24/18: Jiang SY et al. Dissecting Nucleosome Function with a Comprehensive Histone H2A and H2B Mutant Library. G3-Genes Genomes Genetics (2017) [doi: 10.1534/g3.117.300252]

12/13/17: Ye ZQ et al. Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1. Nucleic Acids Research (2016) [doi: 10.1093/nar/gkw659]

2/10/16: Burrows CK et al. Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs. PLOS Genetics (2016) [doi: 10.1371/journal.pgen.1005793]

2/3/16: Sorrells TR et al. Intersecting transcription networks constrain gene regulatory evolution. Nature (2015) [doi: 10.1038/nature14613]

1/27/16: Kellogg RA et al. Digital signaling decouples activation probability and population heterogeneity. eLife (2015) [doi: 10.7554/eLife.08931]

1/20/16: van Dijk D et al. Competition between binding sites determines gene expression at low transcription factor concentrations. bioRχiv Preprint (2016) [doi: 10.1101/033753]

12/16/15: Jolma A et al. DNA-dependent formation of transcription factor pairs alters their binding specificity. Nature (2015) [doi: 10.1038/nature15518]

12/9/15: Stampfel G et al. Transcriptional regulators form diverse groups with context-dependent regulatory functions. Nature (2015) [doi: 10.1038/nature15545]