Publications

Translational activators align mRNAs at the small mitoribosomal subunit for translation initiation

Bridgers JB*, Carlström A*, Sherpa D*, Couvillion MT, Rovšnik U, Gao J, Wan B, Shao S#, Ott M#, Churchman LS#

Nature Structural & Molecular Biology 33(2), 245–258

Copper depletion boosts CNS leukemia therapy by inhibiting nucleotide synthesis through impairment of mitochondrial complex IV activity

Wong AYL, Myers JW, Prakash G, Ma A, Brook JR, Petrova B, Bulut B, White R 3rd, Merz C, de Souza M, Maynard AG, Wang P, Yu A, Pohl NK, Weitman M, Silverman LB, Stegmaier K, Churchman LS, Cole PD, Brady DC, Kanarek N

Nature Cancer

Transcription arrest induces formation of RNA granules in mitochondria

Hansen KG, Baxter-Koenigs A, Weiss CA, McShane E, Churchman LS

Life Science Alliance 8(9), e202403082

A molecular switch at the yeast mitoribosomal tunnel exit controls cytochrome b synthesis

Carlström A, Bridgers JB, Couvillion M, Singh AP, Forné I, Imhof A, Churchman LS#, Ott M#

Nucleic Acids Research 53(13)

Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing

Choquet K, Chaumont LP, Bache S, Baxter-Koenigs AR, Churchman LS

Genome Research 35(4), 712–724

Context-specific inhibition of mitochondrial ribosomes by phenicol and oxazolidinone antibiotics

Bibel B, Raskar T, Couvillion M, Lee M, Kleinman JI, Takeuchi-Tomita N, Churchman LS, Fraser JS, Fujimori DG

Nucleic Acids Research 53(3)

RNA polymerases reshape chromatin architecture and couple transcription on individual fibers

Tullius TW, Isaac RS, Ranchalis J, Dubocanin D, Churchman LS#, Stergachis AB#

Molecular Cell 84(17), 3209–3222.e5

Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle

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#

Molecular Cell 84, 2765–2784.e16

A kinetic dichotomy between mitochondrial and nuclear gene expression processes

McShane E, Couvillion M, Ietswaart R, Prakash G, Smalec BM, Soto I, Baxter-Koenigs AR, Choquet K, Churchman LS

Molecular Cell 84(8), 1541–1555.e11

Post-transcriptional splicing can occur in a slow-moving zone around the gene

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

eLife 12

Proteome-scale movements and compartment connectivity during the eukaryotic cell cycle

Litsios A, Grys BT, 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

Cell 187, 1490–1507.e21

Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA

Isaac RS, Tullius TW*, Hansen KG*, Dubocanin D, Couvillion M, Stergachis AB#, Churchman LS#

Nature Structural & Molecular Biology 31, 568–577

Structural basis of LRPPRC-SLIRP-dependent translation by the mitoribosome

Singh V, Moran JC, Itoh Y, Soto IC, Fontanesi F, Couvillion M, Huynen MA, Churchman LS, Barrientos A, Amunts A

Nature Structural & Molecular Biology 31(12), 1838–1847

Regulators of mitonuclear balance link mitochondrial metabolism to mtDNA expression

Kramer NJ*, Prakash G*, Choquet K, Soto I, Petrova B, Merens HE, Kanarek N, Churchman LS

Nature Cell Biology 25, 1575–1589

Intronic small nucleolar RNAs regulate host gene splicing through base pairing with their adjacent intronic sequences

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 MS

Genome Biology 24, 160

Elongation rate of RNA polymerase II affects pausing patterns across 3' UTRs

Khitun A, Brion C, Moqtaderi Z, Geisberg JV, Churchman LS, Struhl K

Journal of Biological Chemistry 299(11), 105289

Balanced mitochondrial and cytosolic translatomes underlie the biogenesis of human respiratory complexes

Soto I*, Couvillion M*, Hansen KG, McShane E, Moran JC, Barrientos A, Churchman LS

Genome Biology 23(1), 170

Transcription elongation is finely tuned by dozens of regulatory factors

Couvillion M*, Harlen KM*, Lachance KC*, Trotta KL, Smith E, Brion C, Smalec BM, Churchman LS

eLife 11

Essential histone chaperones collaborate to regulate transcription and chromatin integrity

Viktorovskaya O, Chuang J, Jain D, Reim NI, López-Rivera F, Murawska M, Spatt D, Churchman LS, Park PJ, Winston F

Genes & Development 35(9-10), 698–712

GeneWalk identifies relevant gene functions for a biological context using network representation learning

Ietswaart R, Gyori BM, Bachman JA, Sorger PK, Churchman LS

Genome Biology 22(1), 55

Single-molecule regulatory architectures captured by chromatin fiber sequencing

Stergachis AB, Debo BM, Haugen E, Churchman LS, Stamatoyannopoulos JA

Science 368, 1449–1454

Splicing kinetics and coordination revealed by direct nascent RNA sequencing through nanopores

Drexler HL, Choquet K, Churchman LS

Molecular Cell 77(5), 985–998.e8

Proteotoxicity from aberrant ribosome biogenesis compromises cell fitness

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

eLife 8

Spt6 is required for the fidelity of promoter selection

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

Molecular Cell 72(4), 687–699.e6

Cell-cycle modulation of transcription termination factor Sen1

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

Molecular Cell 70(2), 312–326.e7

Set2 methyltransferase facilitates cell cycle progression by maintaining transcriptional fidelity

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

Nucleic Acids Research 46(3), 1331–1344

The ground state and evolution of promoter region directionality

Jin Y*, Eser U*, Struhl K#, Churchman LS#

Cell 170(5), 889–898.e10

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#

Molecular Cell 67(1), 5–18.e19

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

Nature Chemical Biology 13(5), 501–507

Subgenic Pol II interactomes identify region-specific transcription elongation regulators

Harlen KM, Churchman LS

Molecular Systems Biology 13(1), 900

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 Reports 15(10), 2147–2158

Synchronized mitochondrial and cytosolic translation programs

Couvillion MT, Soto IC, Shipkovenska G, Churchman LS

Nature 533(7604), 499–503

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 161(3), 541–554

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

Molecular Cell 58(2), 339–352

A splicing factor's unexpected detour to the mitochondrial surface

Raicu AM, Churchman LS

Molecular Cell 86(7), 1195–1196

The regulation and function of post-transcriptional RNA splicing

Choquet K, Patop IL, Churchman LS

Nature Reviews Genetics 26(6), 378–394

Central dogma rates in human mitochondria

McShane E, Churchman LS

Human Molecular Genetics 33(R1), R34–R41

Human mitoribosome profiling: a re-engineered approach tailored to study mitochondrial translation

Soto I, Couvillion M, Churchman LS

Methods in Molecular Biology 2661, 257–280

Revealing nascent RNA processing dynamics with nano-COP

Drexler HL, Choquet K, Merens HE, Tang PS, Simpson JT, Churchman LS

Nature Protocols 16(3), 1343–1375

The long and the short of the RNA polymerase C-terminal domain and phase separation

Isaac RS, Churchman LS

Molecular Cell 73(6), 1087–1088

The multiple levels of mitonuclear coregulation

Isaac RS, McShane E, Churchman LS

Annual Review of Genetics 52, 511–533

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

Mayer A, Landry HM, Churchman LS

Current Opinion in Cell Biology 46, 72–80

A detailed protocol for subcellular RNA sequencing (subRNA-seq)

Mayer A, Churchman LS

Current Protocols in Molecular Biology 120, 4.29.1–4.29.18

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

Harlen KM, Churchman LS

Nature Reviews Molecular Cell Biology 18(4), 263–273

Not just noise: genomics and genetics bring long noncoding RNAs into focus

Churchman LS

Molecular Cell 65(1), 1–2

Mitochondrial ribosome (mitoribosome) profiling for monitoring mitochondrial translation in vivo

Couvillion MT, Churchman LS

Current Protocols in Molecular Biology 119, 4.28.1–4.28.25

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

Mayer A, Churchman LS

Nature Protocols 11(4), 813–833

Native elongating transcript sequencing (NET-seq)

Churchman LS, Weissman JS

Current Protocols in Molecular Biology Chapter 4, Unit 4.14.1–17

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 CMJ, Leith JS, Levene MJ, Cohen AE, Spudich JA

Optics Express 21(1), 1189–1202

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

Churchman LS, Spudich JA

Cold Spring Harbor Protocols 2012(2), 141–149

Single-molecule high-resolution colocalization of single probes

Churchman LS, Spudich JA

Cold Spring Harbor Protocols 2012(2), 242–245

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

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

Molecular and Cellular Biology 31(17), 3569–3583

Nascent transcript sequencing visualizes transcription at nucleotide resolution

Churchman LS, Weissman JS

Nature 469(7330), 368–373

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

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

Nature Methods 7(5), 377–381

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

Nature Methods 6(6), 443–445

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

Churchman LS, Flyvbjerg H, Spudich JA

Biophysical Journal 90(2), 668–671

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

Churchman LS, Ökten Z, Rock RS, Dawson JF, Spudich JA

Proceedings of the National Academy of Sciences 102(5), 1419–1423

Myosin VI walks hand-over-hand along actin

Ökten Z, Churchman LS, Rock RS, Spudich JA

Nature Structural & Molecular Biology 11(9), 884–887