Original Research Papers
Cyclin-Dependent Kinase-Mediated Sox2 Phosphorylation Enhances the Ability of Sox2 to Establish the Pluripotent State
Ouyang J, Yu W, Liu J, Zhang N, Florens L, Chen J, Liu H, Washburn M, Pei D, Xie T. Cyclin-dependent Kinase-mediated Sox2 Phosphorylation Enhances the Ability of Sox2 to Establish the Pluripotent State. J Biol Chem. 2015;290:22782-22794.
Twin Promotes the Maintenance and Differentiation of Germline Stem Cell Lineage through Modulating Multiple Pathways
Fu Z, Geng C, Wang H, Yang Z, Weng C, Li H, Deng L, Liu L, Liu N, Ni J, Xie T. Twin Promotes the Maintenance and Differentiation of Germline Stem Cell Lineage through Modulation of Multiple Pathways [published ahead of print November 10 2015]. Cell Rep. 2015.
Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II Via Transcriptional Elongation Control in Mitosis
Liang K, Woodfin AR, Slaughter BD, Unruh JR, Box AC, Rickels RA, Gao X, Haug JS, Jaspersen SL, Shilatifard A. Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis. Mol Cell. 2015;60:435-445.
Serine and SAM responsive complex SESAME regulates histone modification crosstalk by sensing cellular metabolism
Li S, Swanson SK, Gogol M, Florens L, Washburn MP, Workman JL, Suganuma T. Serine and SAM Responsive Complex SESAME Regulates Histone Modification Crosstalk by Sensing Cellular Metabolism [published ahead of print November 3 2015]. Mol Cell. 2015.
Oelz DB, Rubinstein BY, Mogilner A. A Combination of Actin Treadmilling and Cross-Linking Drives Contraction of Random Actomyosin Arrays. Biophys J. 2015;109:1818-1829.
Vilya, a RING domain containing component of the recombination nodule, is required for meiotic double-strand break formation in Drosophila melanogaster
Lake CM, Nielsen RJ, Guo F, Unruh JR, Slaughter BD, Hawley RS. Vilya, a component of the recombination nodule, is required for meiotic double-strand break formation in Drosophila. eLife. 2015;4. doi: 10.7554/eLife.08287.
Wang S, Gao Y, Song X, Ma X, Zhu X, Mao Y, Yang Z, Ni J, Li H, Malanowski KE, Anoja P, Park J, Haug J, Xie T. Wnt signaling-mediated redox regulation maintains the germ line stem cell differentiation niche. eLife. 2015;4. doi: 10.7554/eLife.08174.
Hand/foot splitting and the 're-evolution' of mesopodial skeletal elements during the evolution and radiation of chameleons
Diaz RE, Jr., Trainor PA. Hand/foot splitting and the 're-evolution' of mesopodial skeletal elements during the evolution and radiation of chameleons. BMC Evol Biol. 2015;15:184.
Structured-illumination with particle averaging reveals novel rolesfor yeast centrosome components during duplication
Burns S, Avena JS, Unruh JR, Yu Z, Smith SE, Slaughter BD, Winey M, Jaspersen SL. Structured illumination with particle averaging reveals novel roles for yeast centrosome components during duplication [published ahead of print September 16 2015]. eLife. 2015;4.
Challis RC, Tian H, Wang J, He J, Jiang J, Chen X, Yin W, Connelly T, Ma L, Yu CR, Pluznick JL, Storm DR, Huang L, Zhao K, Ma M. An Olfactory Cilia Pattern in the Mammalian Nose Ensures High Sensitivity to Odors [published ahead of print September 15 2015]. Curr Biol. 2015.
Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation
Sun Y, Nien CY, Chen K, Liu HY, Johnston J, Zeitlinger J, Rushlow C. Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation [published ahead of print September 4 2015]. Genome Res. 2015.
Diaz RE, Jr., Anderson CV, Baumann DP, Kupronis R, Jewell D, Piraquive C, Kupronis J, Winter K, Greek TJ, Trainor PA. Captive Care, Raising, and Breeding of the Veiled Chameleon (Chamaeleo calyptratus) [published ahead of print August 28 2015]. Cold Spring Harb Protoc. 2015.
The Veiled Chameleon (Chamaeleo calyptratus Dumeril and Dumeril 1851): A Model for Studying Reptile Body Plan Development and Evolution
Diaz RE, Jr., Anderson CV, Baumann DP, Kupronis R, Jewell D, Piraquive C, Kupronis J, Winter K, Bertocchini F, Trainor PA. The Veiled Chameleon (Chamaeleo calyptratus Dumeril and Dumeril 1851): A Model for Studying Reptile Body Plan Development and Evolution [published ahead of print August 28 2015]. Cold Spring Harb Protoc. 2015.
Chen FX, Woodfin AR, Gardini A, Rickels RA, Marshall SA, Smith ER, Shiekhattar R, Shilatifard A. PAF1, a Molecular Regulator of Promoter-Proximal Pausing by RNA Polymerase II [published ahead of print August 19 2015]. Cell. 2015.
McLennan R, Schumacher LJ, Morrison JA, Teddy JM, Ridenour DA, Box AC, Semerad CL, Li H, McDowell W, Kay D, Maini PK, Baker RE, Kulesa PM. VEGF Signals induce trailblazer cell identity that Drives Neural Crest Migration [published ahead of print August 19 2015]. Dev Biol. 2015:DBIO15209.
Chal J, Oginuma M, Al Tanoury Z, Gobert B, Sumara O, Hick A, Bousson F, Zidouni Y, Mursch C, Moncuquet P, Tassy O, Vincent S, Miyanari A, Bera A, Garnier JM, Guevara G, Hestin M, Kennedy L, Hayashi S, Drayton B, Cherrier T, Gayraud-Morel B, Gussoni E, Relaix F, Tajbakhsh S, Pourquie O. Differentiation of pluripotent stem cells to muscle fiber to model Duchenne muscular dystrophy [published ahead of print August 3 2015]. Nat Biotechnol. 2015.
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. Regeneration of Sensory Hair Cells Requires Localized Interactions between the Notch and Wnt Pathways. Dev Cell. 2015;34:267-282.
Zakari M, Trimble Ross R, Peak A, Blanchette M, Seidel C, Gerton JL. The SMC Loader Scc2 Promotes ncRNA Biogenesis and Translational Fidelity. PLoS Genet. 2015;11:E1005308. doi:1005310.1001371/journal.pgen.1005308.
Fel L, Rubinstein B. Stability of axisymmetric liquid bridges [published ahead of print July 15 2015]. Z Angew Math Phys. 2015:1-25.
Haga-Yamanaka S, Ma L, Yu CR. Tuning Properties and Dynamic Range of Type 1 Vomeronasal receptors. Frontiers Neurosci. 2015;9:244. doi:210.3389/fnins.2015.00244.
Masuda Y, Takahashi H, Sato S, Tomomori-Sato C, Saraf A, Washburn MP, Florens L, Conaway RC, Conaway JW, Hatakeyama S. TRIM29 regulates the assembly of DNA repair proteins into damaged chromatin. Nat Commun. 2015;6:7299. doi: 7210.1038/ncomms8299.
Stower MJ, Diaz RE, Carrera Fernandez L, White Crother M, Crother B, Marco A, Trainor PA, Srinivas S, Bertocchini F. Bi-modal strategy of gastrulation in reptiles [published ahead of print June 20 2015]. Dev Dyn. 2015.
Thi-Kim Vu H, Rink JC, McKinney SA, McClain M, Lakshmanaperumal N, Alexander R, Sánchez Alvarado A. Stem cells and fluid flow drive cyst formation in an invertebrate excretory organ. eLife. 2015;4: doi: 10.7554/eLife.07405.
Pan L, Hildebrand K, Stutz C, Thoma N, Baumann P. Minishelterins separate telomere length regulation and end protection in fission yeast. Genes & Dev. 2015;29:1164-1174.
Analysis of dynamic changes in retinoid induced transcription and epigenetic profiles of murine Hox clusters in ES cells
De Kumar B, Parrish ME, Slaughter BD, Unruh JR, Gogol M, Seidel C, Paulson A, Li H, Gaudenz K, Peak A, McDowell W, Fleharty B, Ahn Y, Lin C, Smith E, Shilatifard A, Krumlauf R. Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells. Genome Res. 2015;25:1229-1243.
Lemieux B, Blanchette M, Monette A, Mouland AJ, Wellinger RJ, Chabot B. A Function for the hnRNP A1/A2 Proteins in Transcription Elongation. PLoS One. 2015;10:e0126654. doi: 0126610.0121371/journal.pone.0126654.
Neural Crest Migration is Driven by a Few Trailblazer Cells with a Unique Molecular Signature Narrowly Confined to the Invasive Front
McLennan R, Schumacher LJ, Morrison JA, Teddy JM, Ridenour DA, Box AC, Semerad CL, Li H, McDowell W, Kay D, Maini PK, Baker RE, Kulesa PM. Neural crest migration is driven by a few trailblazer cells with a unique molecular signature narrowly confined to the invasive front. Development. 2015;142:2014-2025.
Morphew MK, O'Toole ET, Page CL, Pagratis M, Meehl J, Giddings T, Gardner JM, Ackerson C, Jaspersen SL, Winey M, Hoenger A, McIntosh JR. Metallothionein as a clonable tag for protein localization by electron microscopy of cells [published ahead of print May 15 2015]. J Microsc. 2015.
Watanabe S, Tan D, Lakshminarasimhan M, Washburn MP, Erica Hong EJ, Walz T, Peterson CL. Structural analyses of the chromatin remodelling enzymes INO80-C and SWR-C. Nat Commun. 2015;6:7108. doi: 7110.1038/ncomms8108doi.
ARP2/3 complex is required for directional migration of neural stem cell-derived oligodendrocyte precursors in electric fields
Li Y, Wang PS, Lucas G, Li R, Yao L. ARP2/3 complex is required for directional migration of neural stem cell-derived oligodendrocyte precursors in electric fields. Stem Cell Res Therapy. 2015;6:41. doi: 10.1186/s13287-015-0042-0.
Acrofacial Dysostosis, Cincinnati Type, a Mandibulofacial Dysostosis Snydrome 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. Acrofacial Dysostosis, Cincinnati Type, a Mandibulofacial Dysostosis Syndrome with Limb Anomalies, Is Caused by POLR1A Dysfunction. Am J Hum Genet. 2015;96:765-774.
Weems JC, Slaughter BD, Unruh JR, Hall SM, McLaird MB, Gilmore JM, Washburn MP, Florens L, Yasukawa T, Aso T, Conaway JW, Conaway RC. Assembly of the Elongin A Ubiquitin Ligase Is Regulated by Genotoxic and Other Stresses. J Biol Chem. 2015;290:15030-15041.
Wang X, Wei L, Cramer JM, Leibowitz BJ, Judge C, Epperly M, Greenberger J, Wang F, Li L, Stelzner MG, Dunn JC, Martin MG, Lagasse E, Zhang L, Yu J. Pharmacologically blocking p53-dependent apoptosis protects intestinal stem cells and mice from radiation. Sci Rep. 2015;5:8566. doi: 8510.1038/srep08566.
Yan J, Hao C, DeLucia M, Swanson S, Florens L, Washburn MP, Ahn J, Skowronski J. CyclinA2-Cyclin-dependent Kinase Regulates SAMHD1 Protein Phosphohydrolase Domain. J Biol Chem. 2015;209:13279-13292.
In vivo mechanical loading rapidly activates β-catenin signaling in osteocytes through a prostaglandin mediated mechanism
Lara-Castillo N, Kim-Weroha NA, Kamel MA, Javaheri B, Ellies DL, Krumlauf RE, Thiagarajan G, Johnson ML. In vivo mechanical loading rapidly activates beta-catenin signaling in osteocytes through a prostaglandin mediated mechanism. Bone. 2015;76:58-66.
Improving Label-Free Quantitative Proteomics Strategies by Distributing Shared Peptides and Stabilizing Variance
Zhang Y, Wen Z, Washburn MP, Florens L. Improving label-free quantitative proteomics strategies by distributing shared peptides and stabilizing variance. Anal Chem. 2015;87:4749-4756.
Zhu J, Heinecke D, Mulla W, Bradford WD, Rubinstein B, Box A, Haug JS, Li R. Single-Cell Based Quantitative Assay of Chromosome Transmission Fidelity [published ahead of print April 1 2015]. G3 (Bethesda). 2015.
Kurosaka H, Trainor PA, Leroux-Berger M, Iulianella A. Cranial Nerve Development Requires Co-Ordinated Shh and Canonical Wnt Signaling. PLoS One. 2015;10:e0120821.
Morrison JA, Box AC, McKinney MC, McLennan R, Kulesa PM. Quantitative single cell gene expression profiling in the avian embryo. Dev Dyn. 2015;244:774-784.
Evaluation of Commercially Available RNA Amplification Kits for RNA Sequencing Using Very Low Input Amounts of Total RNA
Shanker S, Paulson A, Edenberg HJ, Peak A, Perera A, Alekseyev YO, Beckloff N, Bivens NJ, Donnelly R, Gillaspy AF, Grove D, Gu W, Jafari N, Kerley-Hamilton JS, Lyons RH, Tepper C, Nicolet CM. Evaluation of commercially available RNA amplification kits for RNA sequencing using very low input amounts of total RNA. J Biomol Tech. 2015;26:4-18.
He Q, Johnston J, Zeitlinger J. ChIP-nexus enables improved detection of in vivo transcription factor binding footprints. Nat Biotechnol. 2015;33:395-401.
Banks CAS, Boanca G, Lee ZT, Florens L, Washburn MP. Proteins interacting with cloning scars: a source of false positive protein-protein interactions. Sci Rep. 2015;5:8530. doi:10.1038/srep08530
Luo Z, Gao X, Lin C, Smith ER, Marshall SA, Swanson SK, Florens L, Washburn MP, Shilatifard A. Zic2 is an enhancer-binding factor required for embryonic stem cell specification. Mol Cell. 2015;57:685-694.
Skaar JR, Ferris AL, Wu X, Saraf A, Khanna KK, Florens L, Washburn MP, Hughes SH, Pagano M. The Integrator complex controls the termination of transcription at diverse classes of gene targets. Cell Res. 2015;25:288-305.
Chen G, Mulla WA, Kucharavy A, Tsai HJ, Rubinstein B, Conkright J, McCroskey S, Bradford WD, Weems L, Haug JS, Seidel CW, Berman J, Li R. Targeting the Adaptability of Heterogeneous Aneuploids. Cell. 2015;160:771-784.
MBTPS1/SKI-S1P proprotein convertase is required for ECM signaling and axial elongation during somitogenesis and vertebral development
Achilleos A, Huffman NT, Marcinkiewicyz E, Seidah NG, Chen Q, Dallas SL, Trainor PA, Gorski JP. MBTPS1/SKI-1/S1P proprotein convertase is required for ECM signaling and axial elongation during somitogenesis and vertebral development. Hum Mol Genet. 2015;24:2884-2898.
Heparan Sulfate Proteoglycans Regulate Fgf Signaling and Cell Polarity during Collective Cell Migration
Venero Galanternik M, Kramer KL, Piotrowski T. Heparan Sulfate Proteoglycans Regulate Fgf Signaling and Cell Polarity during Collective Cell Migration. Cell Rep. 2015;10:414-428.
Kumar RP, Dobi KC, Baylies MK, Abmayr SM. Muscle cell fate choice requires the T-box transcription factor midline in Drosophila. Genetics. 2015;199:777-791.
Kannan R, Helston RM, Dannebaum RO, Baumann P. Diverse mechanisms for spliceosome-mediated 3' end processing of telomerase RNA. Nat Commun. 2015;6:6104. doi:10.1038/ncomms7104.
MED26 regulates the transcription of snRNA genes through the recruitment of little elongation complex
Takahashi H, Takigawa I, Watanabe M, Anwar D, Shibata M, Tomomori-Sato C, Sato S, Ranjan A, Seidel CW, Tsukiyama T, Mizushima W, Hayashi M, Ohkawa Y, Conaway JW, Conaway RC, Hatakeyama S. MED26 regulates the transcription of snRNA genes through the recruitment of little elongation complex. Nat Commun. 2015;6:5941. doi: 10.1038/ncomms6941.
Suraneni P, Fogelson B, Rubinstein B, Noguera P, Volkmann N, Hanein D, Mogilner A, Li R. A mechanism of leading-edge protrusion in the absence of Arp2/3 complex. Mol Biol Cell. 2015;26:901-912.
Characterization of human CDK12 and CDK13 complexes in CTD phosphorylation, gene transcription and RNA processing
Liang K, Gao X, Gilmore JM, Florens L, Washburn MP, Smith E, Shilatifard A. Characterization of Human Cyclin-Dependent Kinase 12 (CDK12) and CDK13 Complexes in C-Terminal Domain Phosphorylation, Gene Transcription, and RNA Processing. Mol Cell Biol. 2015;35:928-938.
Retinoic Acid Activity in UndifferentiatedNeural Progenitors is Sufficient to Fulfill its Role in Restricting Fgf8 Expression for Somitogenesis
Cunningham TJ, Brade T, Sandell LL, Lewandoski M, Trainor PA, Colas A, Mercola M, Duester G. Retinoic Acid Activity in Undifferentiated Neural Progenitors Is Sufficient to Fulfill Its Role in Restricting Fgf8 Expression for Somitogenesis. PLoS One. 2015;10:e0137894.