Complete list of Churchman lab publications can be found here.
Publications and pre-prints since 2011
Drexler HL, Choquet K, Churchman LS (2019) Human co-transcriptional splicing kinetics and coordination revealed by direct nascent RNA sequencing. bioRxiv, :611020. https://doi.org/10.1101/611020
Tye BW, Commins N, Ryazanova LV, Wühr M, Springer M, Pincus D, Churchman LS (2019) Proteotoxicity from aberrant ribosome biogenesis compromises cell fitness. eLife, 8
Doris SM, Chuang J, Viktorovskaya O, Murawska M, Spatt D, Churchman LS, Winston F (2018) Spt6 Is Required for the Fidelity of Promoter Selection. Molecular Cell, 72(4):687–699.e6.
Mischo HE, Chun Y, Harlen KM, Smalec BM, Dhir S, Churchman LS, Buratowski S (2018) Cell-Cycle Modulation of Transcription Termination Factor Sen1. Molecular Cell, 70(2):312–326.e7.
Dronamraju R, Jha DK, Eser U, Adams AT, Dominguez D, Choudhury R, Chiang Y-C, Rathmell WK, Emanuele MJ, Churchman LS, Strahl BD (2018) Set2 methyltransferase facilitates cell cycle progression by maintaining transcriptional fidelity. Nucleic Acids Research, 46(3):1331–1344.
Jin Y, Eser U, Struhl K, Churchman LS (2017) The Ground State and Evolution of Promoter Region Directionality. Cell, 170(5):889–898.e10.
Winter GE, Mayer A, Buckley DL, Erb MA, Roderick JE, Vittori S, Reyes JM, Iulio J di, Souza A, Ott CJ, Roberts JM, Zeid R, Scott TG, Paulk J, Lachance K, Olson CM, Dastjerdi S, Bauer S, Lin CY, Gray NS, Kelliher MA, Churchman LS, Bradner JE (2017) BET Bromodomain Proteins Function as Master Transcription Elongation Factors Independent of CDK9 Recruitment. Molecular Cell, 67(1):5–18.e19.
Boswell SA, Snavely A, Landry HM, Churchman LS, Gray JM, Springer M (2017) Total RNA-seq to identify pharmacological effects on specific stages of mRNA synthesis. Nature Chemical Biology, 13(5):501–507.
Harlen KM, Churchman LS (2017) Subgenic Pol II interactomes identify region-specific transcription elongation regulators. Molecular Systems Biology, 13(1):900.
Eser U, Churchman LS (2016) FIDDLE: An integrative deep learning framework for functional genomic data inference. bioRxiv, :081380. https://doi.org/10.1101/081380
Harlen KM, Trotta KL, Smith EE, Mosaheb MM, Fuchs SM, Churchman LS (2016) Comprehensive RNA Polymerase II Interactomes Reveal Distinct and Varied Roles for Each Phospho-CTD Residue. Cell Reports, 15(10):2147–2158.
Couvillion MT, Soto IC, Shipkovenska G, Churchman LS (2016) Synchronized mitochondrial and cytosolic translation programs. Nature, 533(7604):499–503.
Mayer A, Iulio J di, Maleri S, Eser U, Vierstra J, Reynolds A, Sandstrom R, Stamatoyannopoulos JA, Churchman LS (2015) Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution. Cell, 161(3):541–554.
Padovan-Merhar O, Nair GP, Biaesch AG, Mayer A, Scarfone S, Foley SW, Wu AR, Churchman LS, Singh A, Raj A (2015) Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms. Molecular Cell, 58(2):339–352.
Marquardt S, Escalante-Chong R, Pho N, Wang J, Churchman LS, Springer M, Buratowski S (2014) A chromatin-based mechanism for limiting divergent noncoding transcription. Cell, 157(7):1712–1723
Reviews, commentaries and protocols since 2011
Isaac RS, Churchman LS (2019) The Long and the Short of the RNA Polymerase C-Terminal Domain and Phase Separation. Molecular Cell, 73(6):1087–1088.
Isaac RS, McShane E, Churchman LS (2018) The Multiple Levels of Mitonuclear Coregulation. Annual Review of Genetics, 52:511–533.
Mayer A, Churchman LS (2017) A Detailed Protocol for Subcellular RNA Sequencing (subRNA-seq). Current protocols in molecular biology / edited by Frederick M. Ausubel... [et al.], 120:4.29.1–4.29.18.
Mayer A, Landry HM, Churchman LS (2017) Pause & go: from the discovery of RNA polymerase pausing to its functional implications. Current Opinion in Cell Biology, 46:72–80.
Harlen KM, Churchman LS (2017) The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain. Nature Reviews. Molecular Cell Biology, 18(4):263–273.
Churchman LS (2017) Not Just Noise: Genomics and Genetics Bring Long Noncoding RNAs into Focus. Molecular Cell, 65(1):1–2.
Couvillion MT, Churchman LS (2017) Mitochondrial Ribosome (Mitoribosome) Profiling for Monitoring Mitochondrial Translation In Vivo. Current Protocols in Molecular Biology, 533:4.28.1–4.28.25.
Elting MW, Leslie SR, Churchman LS, Korlach J, McFaul CMJ, Leith JS, Levene MJ, Cohen AE, Spudich JA (2013) Single-molecule fluorescence imaging of processive myosin with enhanced background suppression using linear zero-mode waveguides (ZMWs) and convex lens induced confinement (CLIC). Optics Express, 21(1):1189–1202.
Churchman LS, Weissman JS (2012) Native elongating transcript sequencing (NET-seq). Current protocols in molecular biology / edited by Frederick M. Ausubel... [et al.], Chapter 4:Unit 4.14.1–17.
Terzi N, Churchman LS, Vasiljeva L, Weissman J, Buratowski S (2011) H3K4 trimethylation by Set1 promotes efficient termination by the Nrd1-Nab3-Sen1 pathway. Molecular and Cellular Biology, 31(17):3569–3583.
Churchman LS, Weissman JS (2011) Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature, 469(7330):368–373.
Mortensen KI, Churchman LS, Spudich JA, Flyvbjerg H (2010) Optimized localization analysis for single-molecule tracking and super-resolution microscopy. Nature Methods, 7(5):377–381.
Bassik MC, Lebbink RJ, Churchman LS, Ingolia NT, Patena W, LeProust EM, Schuldiner M, Weissman JS, McManus MT (2009) Rapid creation and quantitative monitoring of high coverage shRNA libraries. Nature Methods, 6(6):443–445.
Churchman LS, Spudich JA (2012) Colocalization of fluorescent probes: accurate and precise registration with nanometer resolution. Cold Spring Harbor Protocols, 2012(2):141–149.
Churchman LS, Spudich JA (2012) Single-molecule high-resolution colocalization of single probes. Cold Spring Harbor Protocols, 2012(2):242–245.
Churchman LS, Spudich JA (2007) Colocalization of Fluorescent Probes: Accurate and Precise Registration with Nanometer Resolution. Single-Molecule Techniques: A Laboratory Manual, :73–84.
Churchman LS, Flyvbjerg H, Spudich JA (2006) A non-Gaussian distribution quantifies distances measured with fluorescence localization techniques. Biophysical Journal, 90(2):668–671.
Churchman LS, Okten Z, Rock RS, Dawson JF, Spudich JA (2005) Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time. Proceedings of the National Academy of Sciences of the United States of America, 102(5):1419–1423.
Okten Z, Churchman LS, Rock RS, Spudich JA (2004) Myosin VI walks hand-over-hand along actin. Nature Structural & Molecular Biology, 11(9):884–887.