Our Publications

Complete list of Churchman lab publications can be found here.
*equal authorship; #co-corresponding authorship; Churchman Lab members in bold text.

Churchman lab publications

Tullius TW, Isaac RS, Ranchalis, J, Dubocanin, D, Churchman LS#, Stergachis AB# (2024) RNA polymerases reshape chromatin and coordinate transcription on individual fibers. Mol Cell, 84, 3209-3222.e5.

Ietswaart R#*, Smalec BM*, Xu A*, Choquet K, McShane E, Jowhar ZM, Guegler CK, Baxter-Koenigs AR, West ER, Fu BXH, Gilbert L, Floor SN#, Churchman LS#. (2024) Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle. Mol Cell, 84, 2765-2784.e16.

McShane E, Couvillion M, Ietswaart R, Prakash G, Smalec BM, Soto I, Baxter-Koenigs AR, Choquet K, Churchman LS. (2024) A kinetic dichotomy between mitochondrial and nuclear gene expression drives OXPHOS biogenesis. Mol. Cell 84, 1541–1555.e11.

Coté A, O’Farrell A, Dardani I, Dunagin M, Coté C, Wan Y, Bayatpour S, Drexler HL, Alexander KA, Chen F, Wassie AT, Patel R, Pham K, Boyden ES, Berger S, Phillips-Cremins J, Churchman LS & Raj A. (2004) Post-transcriptional splicing can occur in a slow-moving zone around the gene. Elife 12.

Litsios A, Grys B T, Kraus OZ, Friesen H, Ross C, Masinas MPD, Forster DT, Couvillion MT, Timmermann S, Billmann M, Myers C, Johnsson N, Churchman LS, Boone C & Andrews BJ. (2004) Proteome-scale movements and compartment connectivity during the eukaryotic cell cycle. Cell 187, 1490–1507.e21.

Isaac SR, Tullius TW*, Hansen KG*, Dubocanin D, Couvillion M, Stergachis AB#, Churchman LS#. (2024) Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA. Nat. Struct. Mol. Biol. 31, 568–577.

Kramer NJ*, Prakash G*, Choquet K, Soto I, Petrova B, Merens HE, Kanarek N, Churchman LS. (2023) Regulators of mitonuclear balance link mitochondrial metabolism to mtDNA expression. Nat. Cell Biol., 25, 1575–1589.

Martell DJ, Merens HE, Caulier A, Fiorini C, Ulirsch J, Ietswaart R, Choquet K, Graziadei G, Brancaleoni V, Cappellini MD, Scott C, Roberts N, Proven M, Roy NBA, Babbs C, Higgs DR, Sankaran VG#, Churchman LS#. (2023) RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation. Dev. Cell 58, 2112–2127.e4.

Choquet K, Baxter-Koenigs AR, Dülk SL, Smalec BM, Rouskin S, Churchman LS. (2023) Pre-mRNA splicing order is predetermined and maintains splicing fidelity across multi-intronic transcripts. Nat. Struct. Mol. Biol. 1–13.

Bergeron D, Faucher-Giguère L, Emmerichs A-K, Choquet K, Song KS, Deschamps-Francoeur G, Fafard-Couture É, Rivera A, Couture S, Churchman LS, Heyd F. Abou Elela S, Scott M S. (2023) Intronic small nucleolar RNAs regulate host gene splicing through base pairing with their adjacent intronic sequences. Genome Biol. 24, 160.

Soto I*, Couvillion M*, Hansen KG, McShane E, Moran JC, Barrientos A, Churchman LS. (2022) Balanced mitochondrial and cytosolic translatomes underlie the biogenesis of human respiratory complexes. Genome Biol. 23(1):170.

Couvillion M*, Harlen KM*, Lachance KC*, Trotta KL, Smith E, Brion C, Smalec BM, Churchman LS. (2022) Transcription elongation is finely tuned by dozens of regulatory factors. Elife, 11.

Tye BW, Churchman LS. (2021) Hsf1 activation by proteotoxic stress requires concurrent protein synthesis. (2021) Mol Biol Cell., 32(19):1800–1806.

Viktorovskaya O, Chuang J, Jain D, Reim NI, López-Rivera F, Murawska M, Spatt D, Churchman LS, Park PJ, Winston F. (2021) Essential histone chaperones collaborate to regulate transcription and chromatin integrity. Genes Dev. 35(9-10):698–712.

Ietswaart, R, Gyori BM, Bachman JA, Sorger PK, Churchman LS. (2021) GeneWalk identifies relevant gene functions for a biological context using network representation learning. Genome Biol 22(1):55.

Drexler, HL, Choquet K, Merens HE, Tang PS, Simpson JT and Churchman LS. (2021) Revealing nascent RNA processing dynamics with nano-COP. Nat Protoc. 6(3):1343–1375

Stergachis AB, Debo BM, Haugen E, Churchman LS, Stamatoyannopoulos JA. (2020) Single-molecule regulatory architectures captured by chromatin fiber sequencing. Science 368:1449–54.

Fischer J, Song YS, Yosef N, di Iulio J, Churchman LS, Choder M. (2020) The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5’ and 3' gene regions. J Biol Chem., 295:11435-11454.

Drexler HL, Choquet K, Churchman LS (2020) Splicing kinetics and coordination revealed by direct nascent RNA sequencing through nanopores. Molecular Cell, 77(5):985-998.e8.

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.

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*, di Iulio J* 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

McShane E, Churchman LS. (2024) Central dogma rates in human mitochondria. Hum Mol Genet, 33(R1):R34–R41.

Merens HE, Choquet K, Baxter-Koenigs AR, Churchman LS. (2024) Timing is everything: advances in quantifying splicing kinetics. Trends Cell Biol.

Soto I, Couvillion M, Churchman LS. (2024) Human mitoribosome profiling: A re-engineered approach tailored to study mitochondrial translation. Methods Mol Biol 2661:257–280.

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.

Earlier publications

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.

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.

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, 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.

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.

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.