Alumni

Maternal Smc3 protects the integrity of the zygotic genome through DNA replication and mitosis
Yueh WT, Singh VP, Gerton JL. [published ahead of print December 23 2021]. Development. 2021;148.

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.

Med23 Regulates Sox9 Expression during Craniofacial Development
Dash S, Bhatt S, Falcon KT, Sandell LL, Trainor PA. J Dent Res. 2021;100:406-414.

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.

Elongin functions as a loading factor for Mediator at ATF6alpha-regulated ER stress response genes
He Y, Sato S, Tomomori-Sato C, Chen S, Goode ZH, Conaway JW, Conaway RC. Proc Natl Acad Sci U S A. 2021;118:e2108751118. doi: 10.1073/pnas.2108751118.

Double emulsions with ultrathin shell by microfluidic step-emulsification
Ge X, Rubinstein BY, He Y, Bruce FNO, Li L, Leshansky AM, Li Z. [published ahead of print March 9 2021]. Lab Chip. 2021.

Differential gene expression profiling of adult murine hematopoietic stem cells
Park IK, He Y, Lin F, Laerum OD, Tian Q, Bumgarner R, Klug CA, Li K, Kuhr C, Doyle MJ, Xie T, Schummer M, Sun Y, Goldsmith A, Clarke MF, Weissman IL, Hood L, Li L. Blood. 2002;99:488-498.

Multiple roles for PARP1 in ALC1-dependent nucleosome remodeling
Ooi SK, Sato S, Tomomori-Sato C, Zhang Y, Wen Z, Banks CAS, Washburn MP, Unruh JR, Florens L, Conaway RC, Conaway JW.  Proc Natl Acad Sci U S A. 2021;118:e2107277118. doi: 2107277110.2107271073/pnas.2107277118.
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.

A Comprehensive Survey of the Plasmodium Life Cycle by Genomic, Transcriptomic, and Proteomic Analyses
Hall N, Karras M, Raine JD, Carlton JM, Kooij TW, Berriman M, Florens L, Janssen CS, Pain A, Christophides GK, James K, Rutherford K, Harris B, Harris D, Churcher C, Quail MA, Ormond D, Doggett J, Trueman HE, Mendoza J, Bidwell SL, Rajandream MA, Carucci DJ, Yates JR, 3rd, Kafatos FC, Janse CJ, Barrell B, Turner CM, Waters AP, Sinden RE. Science.2005;307:82-86.

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

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

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

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

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

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.

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

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

An adaptable chromosome preparation methodology for use in invertebrate research organisms
Guo L, Accorsi A, He S, Guerrero-Hernandez C, Sivagnanam S, McKinney S, Gibson M, Sanchez Alvarado A. BMC Biol. 2018;16:25. doi: 10.1186/s12915-12018-10497-12914.
Original Data

Analysis of lamprey meis genes reveals that conserved inputs from hox, Meis and Pbx proteins control their expression in the hindbrain and neural tube
Parker HJ, De Kumar B, Pushel I, Bronner ME, Krumlauf R. Dev Biol. 2021:61-76.
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

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.

Hedgehog signaling is required for endomesodermal patterning and germ cell development in the sea anemone Nematostella vectensis
Chen CY, McKinney SA, Ellington LR, Gibson MC. eLife. 2020;9:e54573. doi: 54510.54577.54554/eLife.54573.
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

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

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

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

wtf genes are prolific dual poison-antidote meiotic drivers
Nuckolls NL*, Bravo Núñez 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

Reviews, Commentaries, Chapters or Books
Genetic Villains: Killer Meiotic Drivers
Bravo Nunez MA*, Nuckolls NL*, Zanders SE. [published ahead of print February 27 2018]. Trends Genet.2018.
*contributed equally to this work.

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

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

Gamma-Tubulin Is Required for Bipolar Spindle Assembly and for Proper Kinetochore Microtubule Attachments during Prometaphase I in Drosophila Oocytes.
Hughes SE, Beeler JS, Seat A, Slaughter BD, Unruh JR, Bauerly E, Matthies HJ, Hawley RS. PLoS Genet. 2011;7:e1002209.

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;15:662-676.
Original Data

The SAGA chromatin-modifying complex: the sum of its parts is greater than thewhole
Soffers JHM, Workman JL. Genes Dev. 2020;34:1287-1303.

SAGA Structures Provide Mechanistic Models for Gene Activation
Soffers JHM, Popova VV, Workman JLW. [published ahead of print March 16 2020]. Trends Biochem Sci. 2020.

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

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

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

wtf genes are prolific dual poison-antidote meiotic drivers
Nuckolls NL*, Bravo Núñez 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

Reviews, Commentaries, Chapters or Books
Genetic Villains: Killer Meiotic Drivers
Bravo Nunez MA*, Nuckolls NL*, Zanders SE. [published ahead of print February 27 2018]. Trends Genet.2018.
*contributed equally to this work.

PCP and Wnt pathway components act in parallel during zebrafish mechanosensory hair cell orientation
Joaquin Navajas Acedo, Matthew G Voas, Richard L Alexander, Thomas Woolley, Jay Unruh, Hua Li, Cecilia Moens, Tatjana Piotrowski. (2019) Nature Communications
Original Data

Evolutionary Origin and Nomenclature of Vertebrate Wnt11-Family Genes
Postlethwait JH, Navajas Acedo J, Piotrowski T. Zebrafish. 2019;16:469-476.

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

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

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

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

Reviews, Commentaries, Chapters or Books
When mothers leave their mark.
Barajas-Azpeleta R, Si K. eLife. 2019;8:e48899. doi: 48810.47554/eLife.48899.

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

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

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

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.

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.

Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events
Noe Gonzalez, M., Conaway, J. W., & Conaway, R. C.  Journal of Visualized Experiments. (147), e59497.

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 Feb 1. pii: genetics.301911.2019. doi: 10.1534/genetics.119.301911. [Epub ahead of print]

Analysis of membrane proteins localizing to the inner nuclear envelope in living cells.
Smoyer CJ, Katta SS, Gardner JM, Stoltz L, McCroskey S, Bradford WD, McClain M, Smith SE, Slaughter BD, Unruh JR, Jaspersen SL. J Cell Biol. 2016 Nov 21;215(4):575-590. Epub 2016 Nov 9.

Breaking down the wall: the nuclear envelope during mitosis.
Smoyer CJ, Jaspersen SL. Curr Opin Cell Biol. 2014 Feb;26:1-9. doi: 10.1016/j.ceb.2013.08.002. Epub 2013 Sep 4. Review.

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 Feb 17;204(4):523-39. doi: 10.1083/jcb.201307043. Epub 2014 Feb 10.

Destination: inner nuclear membrane.
Katta SS, Smoyer CJ, Jaspersen SL. Trends Cell Biol. 2014 Apr;24(4):221-9. doi: 10.1016/j.tcb.2013.10.006. Epub 2013 Nov 19. Review.

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 Dec;2(12):1703-18. doi: 10.1534/g3.112.004614. Epub 2012 Dec 1.

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 Jul;23(13):2546-59. doi: 10.1091/mbc.E11-07-0600. Epub 2012 May 16.

The SUN protein Mps3 is required for spindle pole body insertion into the nuclear membrane and nuclear envelope homeostasis.
Friederichs JM, Ghosh S, Smoyer CJ, McCroskey S, Miller BD, Weaver KJ, Delventhal KM, Unruh J, Slaughter BD, Jaspersen SL. PLoS Genet. 2011 Nov;7(11):e1002365. doi: 10.1371/journal.pgen.1002365. Epub 2011 Nov 17.

Targeting of the SUN protein Mps3 to the inner nuclear membrane by the histone variant H2A.Z.
Gardner JM, Smoyer CJ, Stensrud ES, Alexander R, Gogol M, Wiegraebe W, Jaspersen SL. J Cell Biol. 2011 May 2;193(3):489-507. doi: 10.1083/jcb.201011017. Epub 2011 Apr 25.

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. 28(9):904-917.

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

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

A global change in RNA Polymerase II pausing during the Drosophila mid bastula transition. eLife 2013 doi: 10.7554/eLife.00861
Chen, K., Johnston, J., Shao, W., Meier, S., Staber, C., and Zeitlinger, J.

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.

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.

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

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

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

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

NIPBL Controls RNA Biogenesis to Prevent Activation of the Stress Kinase PKR.
Yuen KC, Xu B, Krantz, ID, and Gerton, JL (2016) Cell Rep. Jan 5;14(1):93-102.

Etiology and pathogenesis of the cohesinopathies.
Zakari M, Yuen K, Gerton JL. (2015) Wiley Interdiscip Rev Dev Biol. Sep-Oct;4(5):489-504.

Mef2c-F10N enhancer drive β-galactosidase (LacZ) and Cre recombinase mice facilitate analyses of gene function and lineage fate in neural crest cells. 
Aoto, K, Sandell, L.L., Butler Tjaden, N.E., Yuen, K.C., Watt, K.E., Black B.L., Durnin, M., and Trainor, P.A. (2015) Dev Biol, 402(1):3-16 

From skeleton to cytoskeleton: osteocalcin transforms vascular fibroblasts to myofibroblasts via angiotensin II and Toll-like receptor 4.
Yuen CY, Wong SL, Lau CW, Tsang SY, Xu A, Zhu Z, Ng CF, Yao X, Kong SK, Lee HK, Huang Y. (2012) Circ Res. 111(3):e55-66.

Telmisartan inhibits vasoconstriction via PPARγ-dependent expression and activation of endothelial nitric oxide synthase.
Yuen, C.Y., Wong, W.T., Tian, X.Y., Wong, S.L., Lau, C. W., Yu, J., Tomlinson, B., Yao, X. and Huang, Y. Cardiovasc Res, 90(1):122-129.