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Items: 33


The Long and the Short of the RNA Polymerase C-Terminal Domain and Phase Separation.

Isaac RS, Churchman LS.

Mol Cell. 2019 Mar 21;73(6):1087-1088. doi: 10.1016/j.molcel.2019.03.004.


Proteotoxicity from aberrant ribosome biogenesis compromises cell fitness.

Tye BW, Commins N, Ryazanova LV, Wühr M, Springer M, Pincus D, Churchman LS.

Elife. 2019 Mar 7;8. pii: e43002. doi: 10.7554/eLife.43002.


Spt6 Is Required for the Fidelity of Promoter Selection.

Doris SM, Chuang J, Viktorovskaya O, Murawska M, Spatt D, Churchman LS, Winston F.

Mol Cell. 2018 Nov 15;72(4):687-699.e6. doi: 10.1016/j.molcel.2018.09.005. Epub 2018 Oct 11.


The Multiple Levels of Mitonuclear Coregulation.

Isaac RS, McShane E, Churchman LS.

Annu Rev Genet. 2018 Nov 23;52:511-533. doi: 10.1146/annurev-genet-120417-031709. Epub 2018 Sep 19. Review.


Cell-Cycle Modulation of Transcription Termination Factor Sen1.

Mischo HE, Chun Y, Harlen KM, Smalec BM, Dhir S, Churchman LS, Buratowski S.

Mol Cell. 2018 Apr 19;70(2):312-326.e7. doi: 10.1016/j.molcel.2018.03.010. Epub 2018 Apr 12.


Set2 methyltransferase facilitates cell cycle progression by maintaining transcriptional fidelity.

Dronamraju R, Jha DK, Eser U, Adams AT, Dominguez D, Choudhury R, Chiang YC, Rathmell WK, Emanuele MJ, Churchman LS, Strahl BD.

Nucleic Acids Res. 2018 Feb 16;46(3):1331-1344. doi: 10.1093/nar/gkx1276.


A Detailed Protocol for Subcellular RNA Sequencing (subRNA-seq).

Mayer A, Churchman LS.

Curr Protoc Mol Biol. 2017 Oct 2;120:4.29.1-4.29.18. doi: 10.1002/cpmb.44.


The Ground State and Evolution of Promoter Region Directionality.

Jin Y, Eser U, Struhl K, Churchman LS.

Cell. 2017 Aug 24;170(5):889-898.e10. doi: 10.1016/j.cell.2017.07.006. Epub 2017 Aug 10.


Mitochondrial Ribosome (Mitoribosome) Profiling for Monitoring Mitochondrial Translation In Vivo.

Couvillion MT, Churchman LS.

Curr Protoc Mol Biol. 2017 Jul 5;119:4.28.1-4.28.25. doi: 10.1002/cpmb.41.


BET Bromodomain Proteins Function as Master Transcription Elongation Factors Independent of CDK9 Recruitment.

Winter GE, Mayer A, Buckley DL, Erb MA, Roderick JE, Vittori S, Reyes JM, di Iulio J, 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.

Mol Cell. 2017 Jul 6;67(1):5-18.e19. doi: 10.1016/j.molcel.2017.06.004. Epub 2017 Jun 29.


Pause & go: from the discovery of RNA polymerase pausing to its functional implications.

Mayer A, Landry HM, Churchman LS.

Curr Opin Cell Biol. 2017 Jun;46:72-80. doi: 10.1016/ Epub 2017 Mar 28. Review.


Total RNA-seq to identify pharmacological effects on specific stages of mRNA synthesis.

Boswell SA, Snavely A, Landry HM, Churchman LS, Gray JM, Springer M.

Nat Chem Biol. 2017 May;13(5):501-507. doi: 10.1038/nchembio.2317. Epub 2017 Mar 6.


The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain.

Harlen KM, Churchman LS.

Nat Rev Mol Cell Biol. 2017 Apr;18(4):263-273. doi: 10.1038/nrm.2017.10. Epub 2017 Mar 1. Review.


Not Just Noise: Genomics and Genetics Bring Long Noncoding RNAs into Focus.

Churchman LS.

Mol Cell. 2017 Jan 5;65(1):1-2. doi: 10.1016/j.molcel.2016.12.017.


Subgenic Pol II interactomes identify region-specific transcription elongation regulators.

Harlen KM, Churchman LS.

Mol Syst Biol. 2017 Jan 2;13(1):900. doi: 10.15252/msb.20167279.


Comprehensive RNA Polymerase II Interactomes Reveal Distinct and Varied Roles for Each Phospho-CTD Residue.

Harlen KM, Trotta KL, Smith EE, Mosaheb MM, Fuchs SM, Churchman LS.

Cell Rep. 2016 Jun 7;15(10):2147-2158. doi: 10.1016/j.celrep.2016.05.010. Epub 2016 May 26.


Synchronized mitochondrial and cytosolic translation programs.

Couvillion MT, Soto IC, Shipkovenska G, Churchman LS.

Nature. 2016 May 26;533(7604):499-503. doi: 10.1038/nature18015. Epub 2016 May 11.


Genome-wide profiling of RNA polymerase transcription at nucleotide resolution in human cells with native elongating transcript sequencing.

Mayer A, Churchman LS.

Nat Protoc. 2016 Apr;11(4):813-33. doi: 10.1038/nprot.2016.047. Epub 2016 Mar 24.


Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution.

Mayer A, di Iulio J, Maleri S, Eser U, Vierstra J, Reynolds A, Sandstrom R, Stamatoyannopoulos JA, Churchman LS.

Cell. 2015 Apr 23;161(3):541-554. doi: 10.1016/j.cell.2015.03.010.


Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms.

Padovan-Merhar O, Nair GP, Biaesch AG, Mayer A, Scarfone S, Foley SW, Wu AR, Churchman LS, Singh A, Raj A.

Mol Cell. 2015 Apr 16;58(2):339-52. doi: 10.1016/j.molcel.2015.03.005. Epub 2015 Apr 9.


A Chromatin-Based Mechanism for Limiting Divergent Noncoding Transcription.

Marquardt S, Escalante-Chong R, Pho N, Wang J, Churchman LS, Springer M, Buratowski S.

Cell. 2014 Jul 17;158(2):462. doi: 10.1016/j.cell.2014.06.038. Epub 2014 Jul 17. No abstract available.


A chromatin-based mechanism for limiting divergent noncoding transcription.

Marquardt S, Escalante-Chong R, Pho N, Wang J, Churchman LS, Springer M, Buratowski S.

Cell. 2014 Jun 19;157(7):1712-23. doi: 10.1016/j.cell.2014.04.036.


Single-molecule fluorescence imaging of processive myosin with enhanced background suppression using linear zero-mode waveguides (ZMWs) and convex lens induced confinement (CLIC).

Elting MW, Leslie SR, Churchman LS, Korlach J, McFaul CM, Leith JS, Levene MJ, Cohen AE, Spudich JA.

Opt Express. 2013 Jan 14;21(1):1189-202. doi: 10.1364/OE.21.001189.


Native elongating transcript sequencing (NET-seq).

Churchman LS, Weissman JS.

Curr Protoc Mol Biol. 2012 Apr;Chapter 4:Unit 4.14.1-17. doi: 10.1002/0471142727.mb0414s98.


Single-molecule high-resolution colocalization of single probes.

Churchman LS, Spudich JA.

Cold Spring Harb Protoc. 2012 Feb 1;2012(2):242-5. doi: 10.1101/pdb.prot067926.


Colocalization of fluorescent probes: accurate and precise registration with nanometer resolution.

Churchman LS, Spudich JA.

Cold Spring Harb Protoc. 2012 Feb 1;2012(2):141-9. doi: 10.1101/pdb.top067918.


H3K4 trimethylation by Set1 promotes efficient termination by the Nrd1-Nab3-Sen1 pathway.

Terzi N, Churchman LS, Vasiljeva L, Weissman J, Buratowski S.

Mol Cell Biol. 2011 Sep;31(17):3569-83. doi: 10.1128/MCB.05590-11. Epub 2011 Jun 27.


Nascent transcript sequencing visualizes transcription at nucleotide resolution.

Churchman LS, Weissman JS.

Nature. 2011 Jan 20;469(7330):368-73. doi: 10.1038/nature09652.


Optimized localization analysis for single-molecule tracking and super-resolution microscopy.

Mortensen KI, Churchman LS, Spudich JA, Flyvbjerg H.

Nat Methods. 2010 May;7(5):377-81. doi: 10.1038/nmeth.1447. Epub 2010 Apr 4.


Rapid creation and quantitative monitoring of high coverage shRNA libraries.

Bassik MC, Lebbink RJ, Churchman LS, Ingolia NT, Patena W, LeProust EM, Schuldiner M, Weissman JS, McManus MT.

Nat Methods. 2009 Jun;6(6):443-5. doi: 10.1038/nmeth.1330. Epub 2009 May 17.


A non-Gaussian distribution quantifies distances measured with fluorescence localization techniques.

Churchman LS, Flyvbjerg H, Spudich JA.

Biophys J. 2006 Jan 15;90(2):668-71. Epub 2005 Oct 28.


Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time.

Churchman LS, Okten Z, Rock RS, Dawson JF, Spudich JA.

Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1419-23. Epub 2005 Jan 24.


Myosin VI walks hand-over-hand along actin.

Okten Z, Churchman LS, Rock RS, Spudich JA.

Nat Struct Mol Biol. 2004 Sep;11(9):884-7. Epub 2004 Aug 1.


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