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Publications

2020

Original Research Papers

Changes in regeneration-responsive enhancers shape regenerative capacities in vertebrates
Wang W, Hu CK, Zeng A, Alegre D, Hu D, Gotting K, Ortega Granillo A, Wang Y, Robb S, Schnittker R, Zhang S, Alegre D, Li H, Ross E, Zhang N, Brunet A, Sanchez Alvarado A. Changes in regeneration-responsive enhancers shape regenerative capacities in vertebrates. Science. 2020;369: eaaz3090. doi: 10.1126/science.aaz3090.
Original Data

b-Catenin and Associated Proteins Regulate Lineage Differentiation in Ground State Mouse Embryonic Stem Cells
Tao F, Soffers J, Hu D, Chen S, Gao X, Zhang Y, Zhao C, Smith SE, Unruh JR, Zhang D, Tsuchiya D, Venkatraman A, Zhao M, Li Z, Qian P, Parmely T, He XC, Washburn M, Florens L, Perry JM, Zeitlinger J, Workman J, Li L. Stem Cell Rep. 2020. https://www.ncbi.nlm.nih.gov/pubmed/32822591.
Original Data

Atypical meiosis can be adaptive in outcrossed S. pombe due to wtf meiotic drivers 
Bravo Núñez MA, Sabbarini IM, Eide LE, Unckless RL, Zanders SE. eLife. 2020;9:e57936. doi: 57910.57554/eLife.57936. 
Original Data 

The wtf4 meiotic driver utilizes controlled protein aggregation to generate selective cell death.
Nuckolls, NL, Mok, AC, Lange, JJ, Yi, K, Kandola, TS, Hunn, AM, McCroskey, S, Snyder, JL, Bravo Núñez, MA, McClain, ML, McKinney, SA, Wood, C, Halfmann, R, and Zanders, SE. bioRxiv 2020.02.05.935874; doi: https://doi.org/10.1101/2020.02.05.935874 

Wampa is a dynein subunit required for axonemal assembly and male fertility in Drosophila 
Bauerly E, Yi K, Gibson MC. Dev Biol. 2020;463:158-168. 
Original Data 

Differential complex formation via paralogs in the human Sin3 protein interaction network
Adams MK, Banks CAS, Thornton JL, Kempf C, Zhang Y, Miah S, Hao Y, Sardiu ME, Killer M, Hattem G, Murray A, Katt M, Florens LA, Washburn MP. [published ahead of print May 30 2020] Mol Cell Proteomics. 2020.
Original Data

The role of Mediator and Little Elongation Complex in transcription termination
Takahashi H, Ranjan A, Chen S, Suzuki H, Shibata M, Hirose T, Hirose H, Sasaki K, Abe R, Chen K, He Y, Zhang Y, Takigawa I, Tsukiyama T, Watanabe M, Fujii S, Iida M, Yamamoto J, Yamaguchi Y, Suzuki Y, Matsumoto M, Nakayama KI, Washburn MP, Saraf A, Florens L, Sato S, Tomomori-Sato C, Conaway RC, Conaway JW, Hatakeyama S. Nat Commun. 2020;11:1063. doi: 10.1038/s41467-020-14849-1.
Original Data

Regulation of Polo Kinase by Matrimony Is Required for Cohesin Maintenance during Drosophila melanogaster Female Meiosis
Bonner AM, Hughes SE, Hawley RS. Curr Biol. 2020;30:715-722e713.
Original Data

Dramatically diverse Schizosaccharomyces pombe wtf meiotic drivers all display high gamete-killing efficiency
Bravo Núñez MA, Sabbarini IM, Eickbush MT, Liang Y, Lange JJ, Kent AM, Zanders SE. PLoS Genet. 2020;16:e1008350. doi: 1008310.1001371/journal.pgen.1008350.
Original Data

 

 

2019

Original Research Papers

Characterization of a metazoan ADA acetyltransferase complex 
Soffers JHM, Li X, Saraf A, Seidel CW, Florens L, Washburn MP, Abmayr SM, Workman JL. Nucleic Acids Res. 2019;47:3383-3394. 
Original Data

BRK phosphorylates SMAD4 for proteasomal degradation and inhibits tumor suppressor FRK to control SNAIL, SLUG, and metastatic potential
Miah S, Banks CAS, Ogunbolude Y, Bagu ET, Berg JM, Saraf A, Tettey TT, Hattem G, Dayebgadoh G, Kempf CG, Sardiu M, Napper S, Florens L, Lukong KE, Washburn MP. Sci Adv. 2019;5:eaaw3113. doi: 3110.1126/sciadv.aaw3113.
Original Data

X chromosome and autosomal recombination are differentially sensitive to disruptions in SC maintenance
Billmyre KK, Cahoon CK, Heenan GM, Wesley ER, Yu Z, Unruh JR, Takeo S, Hawley RS. Proc Natl Acad Sci U S A. 2019;116:21641-21650.
Original Data

PCP and Wnt pathway components act in parallel during zebrafish mechanosensory hair cell orientation
Navajas Acedo J, Voas MG, Alexander R, Woolley T, Unruh JR, Li H, Moens C, Piotrowski T. Nat Commun. 2019;10:3993. doi: 3910.1038/s41467-41019-12005-y.
Original Data

Detecting and Characterizing Protein Self-Assembly in vivo by Flow Cytometry
Venkatesan S, Kandola TS, Rodriguez-Gama A, Box A, Halfmann R. J Vis Exp. 2019;149:e59577. doi: 59510.53791/59577.
Original Data

Biochemical Reduction of the Topology of the Diverse WDR76 Protein Interactome
Dayebgadoh G, Sardiu ME, Florens L, Washburn MP.  [published ahead of print July 30 2019]. J Proteome Res. 2019.
Original Data

Evolutionary origin and nomenclature of vertebrate Wnt11-family genes
Postlethwait JH, Navajas Acedo J, Piotrowski T. [published ahead of print July 12 2019]. Zebrafish. 2019.

Structures of autoinhibited and polymerized forms of CARD9 reveal mechanisms of CARD9 and CARD11 activation
Holliday MJ, Witt A, Rodriguez Gama A, Walters BT, Arthur CP, Halfmann R, Rohou A, Dueber EC, Fairbrother WJ. Nat Commun. 2019;10:3070. doi: 10.1038/s41467-019-10953-z.
Original Data

A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing
Tettey TT, Gao X, Shao W, Story BA, Chitsazan AD, Glaser RL, Seidel CW, Conaway RC, Zeitlinger J, Blanchette M, Conaway JW. Cell Rep. 2019;27:3770-3779 e7.
Original Data

Junctional tumor suppressors interact with 14-3-3 proteins to control planar spindle alignment
Nakajima YI, Lee ZT, McKinney SA, Swanson SK, Florens L, Gibson MC. J Cell Biol. 2019;218:1824-1838.
Original Data

Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events
Noe Gonzalez M, Conaway JW, Conaway RC. J Vis Exp. 2019;147: doi: 10.3791/59497.
Original Data

Reporter-ChIP-nexus reveals strong contribution of the Drosophila initiator sequence to RNA Polymerase pausing
Shao W, Alcantara SG, Zeitlinger J. eLife. 2019;8:e41461. doi: 41410.47554/eLife.41461.
Original Data

Translation affects mRNA stability in a codon-dependent manner in human cells
Wu Q, Medina SG, Kushawah G, DeVore ML, Castellano LA, Hand JM, Wright M, Bazzini AA.  eLife. 2019;8:e45396. doi: 45310.47554/eLife.45396.
Original Data

Distribution of Proteins at the Inner Nuclear Membrane Is Regulated by the Asi1 E3 Ligase in Saccharomyces cerevisiae
Smoyer CJ, Smith SE, Gardner JM, McCroskey S, Unruh JR, Jaspersen SL. Genetics. 2019;211:1269-1282.
Original Data

Characterization of a metazoan ADA acetyltransferase complex
Soffers JHM, Li X, Saraf A, Seidel CW, Florens L, Washburn MP, Abmayr SM, Workman JL. Nucleic Acids Res. 2019;47:3383-3394.
Original Data

scRNA-Seq reveals distinct stem cell populations that drive hair cell regeneration after loss of Fgf and Notch signaling
Lush ME, Diaz DC, Koenecke N, Baek S, Boldt H, St Peter MK, Gaitan-Escudero T, Romero-Carvajal A, Busch-Nentwich EM, Perera AG, Hall KE, Peak A, Haug JS, Piotrowski T.  Elife. 2019;8:e44431. doi: 44410.47554/eLife.44431.
Original Data

Electroporation of short hairpin RNAs for rapid and efficient gene knockdown in the starlet sea anemone, Nematostella vectensis.
Karabulut A, He S, Chen CY, McKinney SA, Gibson MC. Dev Biol. 2019;448:7-15.
Original Data

Oocyte-specific deletion of Hdac8 in mice reveals stage-specific effects on fertility
Singh VP, Yueh WT, Gerton JL, Duncan FE. Reproduction. 2019;157:305-316.
Original Data

Narya, a RING finger domain-containing protein, is required for both meiotic DNA double-strand break formation and crossover maturation in Drosophila melanogaster
Lake CM, Nielsen RJ, Bonner AM, Eche S, White-Brown S, McKim KS, Hawley RS. PLoS Genet. 2019;15:e1007886. doi: 1007810.1001371/journal.pgen.1007886.
Original Data

Functional consequences of the evolution of matrimony, a meiosis-specific inhibitor of Polo kinase
Bonner AM, Hawley RS. Mol Biol Evol. 2019;36:69-83.
Original Data

 

Reviews, Commentaries, Chapters or Books

Cnidofest 2018: The future is bright for cnidarian research
He S, Grasis JA, Nicotra ML, Juliano CE, Schnitzler CE. EvoDevo. 2019;10:20. doi: 10.1186/s13227-13019-10134-13225.

When mothers leave their mark​
Barajas-Azpeleta R, Si K. eLife. 2019;8:e48899. doi: 48810.47554/eLife.48899.

Patrolling the nucleus: inner nuclear membrane-associated degradation
Smoyer CJ, Jaspersen SL. [published ahead of print April 26 2019]. Curr Genet. 2019.

 

 

2018

Original Research Papers

A suppressor of a wtf poison-antidote meiotic driver acts via mimicry of the driver’s antidote
Bravo Nunez MA, Lange JJ, Zanders SE. PLoS Genet. 2018;14:e1007836.  doi: 1007810.1001371/journal.pgen.1007836.
Original Data

An axial Hox code controls axial patterning and tissue segmentation in Nematostella vectensis
He S, Del Viso F, Chen CY, Ikmi A, Kroesen AE, Gibson MC. Science. 2018;361:1377-1380.
Original Data

Antimicrobial peptides modulate long-term memory ​
Barajas-Azpeleta R, Wu J, Gill J, Welte R, Seidel C, McKinney S, Dissel S, Si K. PLoS Genet. 2018;14:e1007440. doi: 1007410.1001371/journal.pgen.1007440.
Original Data

Differential HDAC1/2 network analysis reveals a role for prefoldin/CCT in HDAC1/2 complex assembly
Banks CAS, Miah S, Adams MK, Eubanks CG, Thornton JL, Florens L, Washburn MP. Sci Rep.2018;9:18712.
Original Data

Suppression of m(6)A reader Ythdf2 promotes hematopoietic stem cell expansion
Li Z, Qian P, Shao W, Shi H, He XC, Gogol M, Yu Z, Wang Y, Qi M, Zhu Y, Perry JM, Zhang K, Tao F, Zhou K, Hu D, Han Y, Zhao C, Alexander R, Xu H, Chen S, Peak A, Hall K, Peterson M, Perera A, Haug JS, Parmely T, Li H, Shen B, Zeitlinger J, He C, Li L. Cell Res. 2018. Author Correction: Cell Res 2018:1-14. https://doi.org/10.1038/s41422-018-0072-0. Published online July 2018.;28:904-917.
Original Data

CTD-dependent and -independent mechanisms govern co-transcriptional capping of Pol II transcripts
Noe Gonzalez M, Sato S, Tomomori-Sato C, Conaway JW, Conaway RC. Nat Commun. 2018;9:3392. doi: 3310.1038/s41467-41018-05923-w.

Combined expansion microscopy with structured illumination microscopy for analyzing protein complexes
Y. W, Yu Z, Cahoon CK, Parmely T, Thomas N, Unruh JR, Slaughter BD, Hawley RS. Nature Protocols.2018;13:1869-1895.
Original Data

Suppression of m(6)A reader Ythdf2 promotes hematopoietic stem cell expansion
Li Z, Qian P, Shao W, Shi H, He XC, Gogol M, Yu Z, Wang Y, Qi M, Zhu Y, Perry JM, Zhang K, Tao F, Zhou K, Hu D, Han Y, Zhao C, Alexander R, Xu H, Chen S, Peak A, Hall K, Peterson M, Perera A, Haug JS, Parmely T, Li H, Shen B, Zeitlinger J, He C, Li L. [published ahead of print August 2 2018]. Cell Res.2018.
Original Data

Quantifying nucleation in vivo reveals the physical basis of prion-like phase behavior
Khan T, Kandola TS, Wu J, Venkatesan S, Ketter E, Lange JJ, Rodriguez Gama A, Box A, Unruh JR, Cook M, Halfmann R. Mol Cell.2018;71:155-168.e157.
Original Data

Predicting neuroblastoma using developmental signals and a logic-based model
Kasemeier-Kulesa JC, Schnell S, Woolley T, Spengler JA, Morrison JA, McKinney MC, Pushel I, Wolfe LA, Kulesa PM. Biophys Chem.2018;238:30-38.
Original Data

A structured workflow for mapping human Sin3 histone deacetylase complex interactions using Halo-MudPIT AP-MS
Banks CAS, Thornton JL, Eubanks CG, Adams MK, Miah S, Boanca G, Liu X, Katt ML, Parmely TJ, Florens L, Washburn MP. Mol Cell Proteomics.2018;17:1432-1447.
Original Data

Capicua controls Toll/IL-1 signaling targets independently of RTK regulation
Papagianni A, Fores M, Shao W, He S, Koenecke N, Andreu MJ, Samper N, Paroush Z, Gonzalez-Crespo S, Zeitlinger J, Jimenez G.  Proc Natl Acad Sci U S A.2018;115:1807-1812.
Original Data

 

Reviews, Commentaries, Chapters or Books

Frozen in transcription: Cryo-EM structures of Pol II transcribing through a nucleosome
Noe Gonzalez M, Conaway RC, Conaway JW.  Mol Cell. 2018;72:802-804.

Coupling the roles of Hox genes to regulatory networks patterning cranial neural crest
Parker HJ, Pushel I, Krumlauf R.. Dev Biol. 2018;444 Suppl 1:S67-S78.

Veni, vidi, vici: the success of wtf meiotic drivers in fission yeast
Lopez Hernandez JF, Zanders SE. Yeast.2018;35:447-453.

Systems to study codon effect on post-transcriptional regulation of gene expression
Wu Q, Bazzini AA. Methods.2018;137:82-89.

Genetic Villains: Killer Meiotic Drivers
Bravo Nunez MA, Nuckolls NL, Zanders SE. [published ahead of print February 27 2018]. Trends Genet.2018.

Taking cohesin and condensin in context
Yuen KC, Gerton JL. PLoS Genet.2018;14:e1007118. doi: 10.1371/journal.pgen.1007118.

 

 

 

2017

Original Research Papers

Retinoic acid is required and Fgf, Wnt, and Bmp signaling inhibit posterior lateral line placode induction in zebrafish
Nikaido M, Acedo JN, Hatta K, Piotrowski T. Dev Biol. 2017;431:215-225.
Original Data

HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets
De Kumar B, Parker HJ, Paulson A, Parrish ME, Pushel I, Singh NP, Zhang Y, Slaughter BD, Unruh JR, Florens L, Zeitlinger J, Krumlauf R. Genome Res.2017;27:1501-1512.
Original Data

Superresolution expansion microscopy reveals the three-dimensional organization of the Drosophila synaptonemal complex.
Cahoon CK, Yu Z, Wang Y, Guo F, Unruh JR, Slaughter BD, Hawley RS. Proc Natl Acad Sci U S A.2017;114:E6857-E6866.
Original Data

Condensin II is anchored by TFIIIC and H3K4me3 in the mammalian genome and supports expression of active dense gene clusters
Yuen, KC, Slaughter, BD, and Gerton JL. Sci Adv. 2017;3:e1700191. doi: 1700110.1701126/sciadv.1700191. .
Original Data

wtf genes are prolific dual poison-antidote meiotic drivers
Nuckolls NL, Bravo Nunez MA, Eickbush MT, Young JM, Lange JJ, Yu JS, Smith GR, Jaspersen SL, Malik HS, Zanders SE. eLife. 2017;6:e26033. doi: 26010.27554/eLife.26033.
Original Data

Paused RNA polymerase II inhibits new transcriptional initiation
Shao W, Zeitlinger J. Nat Genet.2017;49:1045-1051..
Original Data

 

Reviews, Commentaries, Chapters or Books

Poly(A) tails: longer is not always better
Castellano LA, Bazzini AA. Nat Struct Mol Biol. 2017;24:1010-1011.

Unravelling the biology of chromatin in health and cancer using proteomic approaches
Eubanks CG, Dayebgadoh G, Liu X, Washburn MP. Expert Rev Proteomics.2017;14:905-915.

Rare syndromes of the head and face: mandibulofacial and acrofacial dysostoses
Terrazas K, Dixon J, Trainor PA, Dixon MJ. WIREs Dev Biol. 2017;6:e263. doi: 210.1002/wdev.1263.

 

 

 

2016

Original Research Papers

TNIP2 is a hub protein in the NF-&(kappa)B network with both protein and RNA mediated interactions.
Banks CA, Boanca G, Lee ZT, Eubanks CG, Hattem GL, Peak A, Weems LE, Conkright JJ, Florens L, Washburn MP. Mol Cell Proteomics. 2016;15:3435-3449.
Original Data

WDR76 Co-Localizes with Heterochromatin Related Proteins and Rapidly Responds to DNA Damage.
Gilmore JM, Sardiu ME, Groppe BD, Thornton JL, Liu X, Dayebgadoh G, Banks CA, Slaughter BD, Unruh JR, Workman JL, Florens L, Washburn MP. PloS One. 2016;11:e0155492. doi: 0155410.0151371/journal.pone.0155492.
Original Data

Proteomic and genomic analyses of the Rvb1 and Rvb2 interaction network upon deletion of R2TP complex components
Lakshminarasimhan M, Boanca G, Banks CA, Hattem GL, Gabriel AE, Groppe BD, Smoyer C, Malanowski KE, Peak A, Florens L, Washburn MP. Mol Cell Proteomics. 2016;15:960-974.
Original Data

Imaging collective cell migration and hair cell regeneration in the sensory lateral line
Venero Galanternik M, Navajas Acedo J, Romero-Carvajal A, Piotrowski T. Methods Cell Biol.2016;134:211-256.
Original Data

 

Reviews, Commentaries, Chapters or Books

A Nucleoporin at the Meiotic Kinetochore
Bonner AM, Hawley RS. Dev Cell. 2016;38:447-448.​

Regulating the construction and demolition of the synaptonemal complex
Cahoon CK, Hawley RS. Nat Struct Mol Biol. 2016;23:369-377.

Meiosis: Cohesins are not just for sisters anymore.
Cahoon CK, Hawley RS. Current Biology. 2016 Jun 11;26(13):R523-5.

Reading and Interpreting the Histone Acylation Code
Soffers JH, Li X, Abmayr SM, Workman JL. Bioinformatics. 2016;14:329-332.​

 

 

 

2015

Original Research Papers

Mef2c-F10N enhancer driven beta-galactosidase (LacZ) and Cre recombinase mice facilitate analyses of gene function and lineage fate in neural crest cells.
Aoto K, Sandell LL, Butler Tjaden NE, Yuen KC, Watt KE, Black BL, Durnin M, Trainor PA. Dev Biol. 2015;402:3-16.

Proteins interacting with cloning scars: a source of false positive protein-protein interactions.
Banks CAS, Boanca G, Lee ZT, Florens L, Washburn MP. Sci Rep. 2015;5:8530. doi:10.1038/srep08530
Original Data

Regeneration of Sensory Hair Cells Requires Localized Interactions between the Notch and Wnt Pathways.
Romero-Carvajal A, Navajas Acedo J, Jiang L, Kozlovskaja-Gumbriene A, Alexander R, Li H, Piotrowski T. Dev Cell. 2015;34:267-282.
Original Data

Acrofacial Dysostosis, Cincinnati Type, a Mandibulofacial Dysostosis Syndrome with Limb Anomalies, Is Caused by POLR1A Dysfunction.
Weaver KN, Watt KE, Hufnagel RB, Navajas Acedo J, Linscott LL, Sund KL, Bender PL, Konig R, Lourenco CM, Hehr U, Hopkin RJ, Lohmann DR, Trainor PA, Wieczorek D, Saal HM. Am J Hum Genet. 2015;96:765-774.
Original Data

 

Reviews, Commentaries, Chapters or Books

Etiology and pathogenesis of the cohesinopathies.
Zakari M, Yuen K, Gerton JL. Wiley Interdiscip Rev Dev Biol. 2015;4:489-504.

 

 

 

2014

Original Research Papers

Controlling for gene expression changes in transcription factor protein networks.
Banks CA, Lee ZT, Boanca G, Lakshminarasimhan M, Groppe BD, Wen Z, Hattem GL, Seidel CW, Florens L, Washburn MP. Mol Cell Proteomics. 2014;13:1510-1522.
Original Data

Discovery of Supernumerary B Chromosomes in Drosophila melanogaster.
Bauerly E, Hughes SE, Vietti DR, Miller DE, McDowell W, Hawley RS. Genetics. 2014;196:1007-1016.
Original Data

The SUN protein Mps3 controls Ndc1 distribution and function on the nuclear membrane.
Chen J, Smoyer CJ, Slaughter BD, Unruh JR, Jaspersen SL. J Cell Biol. 2014;204:523-539.
Original Data

Biochemical Assays for Analyzing Activities of ATP-dependent Chromatin Remodeling Enzymes.
Chen L, Ooi SK, Conaway JW, Conaway RC. J Vis Exp. 2014;92:e51721, doi10.3791/51721.
Original Data

Generation and Purification of Human INO80 Chromatin Remodeling Complexes and Subcomplexes.
Chen L, Ooi SK, Conaway RC, Conaway JW. J Vis Exp. 2014;92:e51720, doi10.3791/51720.

 

Reviews, Commentaries, Chapters or Books

Destination: inner nuclear membrane.
Katta SS, Smoyer CJ, Jaspersen SL. Trends Cell Biol. 2014;24:221-229.

Breaking down the wall: the nuclear envelope during mitosis.
Smoyer CJ, Jaspersen SL. Curr Opin Cell Biol. 2014;26C:1-9.

 

 

 

2013

Original Research Papers
Binding of Drosophila Polo kinase to its regulator Matrimony is noncanonical and involves two separate functional domains.
Bonner AM, Hughes SE, Chisholm JA, Smith SK, Slaughter BD, Unruh JR, Collins KA, Friederichs JM, Florens L, Swanson SK, Pelot MC, Miller DE, Washburn MP, Jaspersen SL, Hawley RS. Proc Natl Acad Sci U S A.2013;110:E1222-1231.
Original Data

Flies get a head start on meiosis.
Cahoon CK, Hawley RS. PLoS Genet. 2013;9:e1004051.

A global change in RNA polymerase II pausing during the Drosophila midblastula transition.
Chen K, Johnston J, Shao W, Meier S, Staber C, Zeitlinger J. eLife. 2013;2:e00861. doi: 00810.07554/eLife.00861.
Original Data

Multiple opposing constraints govern chromosome interactions during meiosis.
Liu DY, Cahoon CK, Burgess S. PLoS Genet. 2013;9:e1003197

 

 

 

2012

Original Research Papers

Genetic analysis of Mps3 SUN domain mutants in Saccharomyces cerevisiae reveals an interaction with the SUN-like protein Slp1.
Friederichs JM, Gardner JM, Smoyer CJ, Whetstine CR, Gogol M, Slaughter BD, Jaspersen SL. G3 (Bethesda). 2012;2:1703-1718.
Original Data

Acetylation of the SUN protein Mps3 by Eco1 regulates its function in nuclear organization.
Ghosh S, Gardner JM, Smoyer CJ, Friederichs JM, Unruh JR, Slaughter BD, Alexander R, Chisholm RD, Lee KK, Workman JL, Jaspersen SL. Mol Biol Cell. 2012;23:2546-2559.