Research Output 1972 2019

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2016

Transcription upregulation via force-induced direct stretching of chromatin

Tajik, A., Zhang, Y., Wei, F., Sun, J., Jia, Q., Zhou, W., Singh, R., Khanna, N., Belmont, A. S. & Wang, N., Dec 1 2016, In : Nature Materials. 15, 12, p. 1287-1296 10 p.

Research output: Contribution to journalArticle

chromatin
Transcription
Tetrahydrofolate Dehydrogenase
Stretching
Chromatin

ZSCAN5B and primate-specific paralogs bind RNA polymerase III genes and extra-TFIIIC (ETC) sites to modulate mitotic progression

Sun, Y., Zhang, H., Kazemian, M., Troy, J. M., Seward, C., Lu, X. & Stubbs, L. J., Jan 1 2016, In : Oncotarget. 7, 45, p. 72571-72592 22 p.

Research output: Contribution to journalArticle

RNA Polymerase III
Primates
Transfer RNA
Genes
Cell Cycle
2015

A dietary phytochemical alters caste-associated gene expression in honey bees

Mao, W., Schuler, M. A. & Berenbaum, M. R., Aug 2015, In : Science Advances. 1, 7, e1500795.

Research output: Contribution to journalArticle

Honey
Bees
Phytochemicals
Social Class
Larva

Association of ORCA/LRWD1 with repressive histone methyl transferases mediates heterochromatin organization

Giri, S. & Prasanth, S. G., Jan 1 2015, In : Nucleus. 6, 6, p. 435-441 7 p.

Research output: Contribution to journalArticle

Heterochromatin
Transferases
Histones
Lysine
Histone Code

BEND3 mediates transcriptional repression and heterochromatin organization

Khan, A. & Prasanth, S. G., Oct 20 2015, In : Transcription. 6, 5, p. 102-105 4 p.

Research output: Contribution to journalArticle

Heterochromatin
Transcription
Gene expression
Gene Expression
Chromatin Assembly and Disassembly

BEND3 represses rDNA transcription by stabilizing a NoRC component via USP21 deubiquitinase

Khan, A., Giri, S., Wang, Y., Chakraborty, A., Ghosh, A. K., Anantharaman, A., Aggarwal, V., Sathyan, K. M., Ha, T., Kannanganattu, P. K. & Prasanth, S. G., Jul 7 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 27, p. 8338-8343 6 p.

Research output: Contribution to journalArticle

Ubiquitin-Specific Proteases
Ribosomal DNA
rRNA Genes
DNA Methylation
Ribosomes

Contribution of clinically derived mutations in ERG11 to azole resistance in Candida albicans

Flowers, S. A., Colón, B., Whaley, S. G., Schuler, M. A. & David Rogers, P., Jan 1 2015, In : Antimicrobial Agents and Chemotherapy. 59, 1, p. 450-460 11 p.

Research output: Contribution to journalArticle

Azoles
Amino Acid Substitution
Candida albicans
Fluconazole
Mutation

CRISPR/Cas9-mediated genome modification in the mollusc, Crepidula fornicata

Perry, K. J. & Henry, J. J., Feb 1 2015, In : Genesis. 53, 2, p. 237-244 8 p.

Research output: Contribution to journalArticle

Clustered Regularly Interspaced Short Palindromic Repeats
Catenins
Mollusca
Gene Transfer Techniques
Genome

Deployment of regulatory genes during gastrulation and germ layer specification in a model spiralian mollusc Crepidula

Perry, K. J., Lyons, D. C., Truchado-Garcia, M., Fischer, A. H. L., Helfrich, L. W., Johansson, K. B., Diamond, J. C., Grande, C. & Henry, J. J., Oct 1 2015, In : Developmental Dynamics. 244, 10, p. 1215-1248 34 p.

Research output: Contribution to journalArticle

Germ Layers
Gastrulation
Mollusca
Regulator Genes
Gastrula

Glacier moraine formation-mimicking colloidal particle assembly in microchanneled, bioactive hydrogel for guided vascular network construction

Lee, M. K., Rich, M. H., Shkumatov, A., Jeong, J. H., Boppart, M. D., Bashir, R., Gillette, M. U., Lee, J. & Kong, H., Jan 1 2015, In : Advanced Healthcare Materials. 4, 2, p. 195-201 7 p.

Research output: Contribution to journalArticle

Ice Cover
Glaciers
Hydrogel
Microchannels
Hydrogels

Growth differentiation factor-15 encodes a novel microRNA 3189 that functions as a potent regulator of cell death

Jones, M. F., Ling Li, X., Subramanian, M., Shabalina, S. A., Hara, T., Zhu, Y., Huang, J., Yang, Y., Wakefield, L. M., Kannanganattu, P. K. & Lal, A., Oct 9 2015, In : Cell Death and Differentiation. 22, 10, p. 1641-1653 13 p.

Research output: Contribution to journalArticle

Growth Differentiation Factor 15
MicroRNAs
Primates
Cell Death
Apoptosis

Lysine deacetylases regulate the heat shock response including the age-associated impairment of HSF1

Zelin, E. & Freeman, B. C., Apr 10 2015, In : Journal of Molecular Biology. 427, 7, p. 1644-1654 11 p.

Research output: Contribution to journalArticle

Heat-Shock Response
Lysine
Shock
Hot Temperature
Cell Aging

MSX2 mediates entry of human pluripotent stem cells into mesendoderm by simultaneously suppressing SOX2 and activating NODAL signaling

Wu, Q., Zhang, L., Su, P., Lei, X., Liu, X., Wang, H., Lu, L., Bai, Y., Xiong, T., Li, D., Zhu, Z., Duan, E., Jiang, E., Feng, S., Han, M., Xu, Y., Wang, F. & Zhou, J., Dec 1 2015, In : Cell Research. 25, 12, p. 1314-1332 19 p.

Research output: Contribution to journalArticle

Pluripotent Stem Cells
Homeobox Genes
Muscles
Homeodomain Proteins
Germ Layers

Orc1 binding to mitotic chromosomes precedes spatial patterning during G1 phase and assembly of the origin recognition complex in human cells

Kara, N., Hossain, M., Prasanth, S. G. & Stillman, B., May 8 2015, In : Journal of Biological Chemistry. 290, 19, p. 12355-12369 15 p.

Research output: Contribution to journalArticle

Origin Recognition Complex
G1 Phase
Chromosomes
Cells
Chromatin

Overcoming steric hindrances during replication of peripheral heterochromatin

Zhironkina, O. A., Kurchashova, S. Y., Brattseva, A. L., Cherepaninets, V. D., Strelkova, O. S., Belmont, A. S. & Kireev, I. I., Mar 1 2015, In : Cell and Tissue Biology. 9, 2, p. 110-118 9 p.

Research output: Contribution to journalArticle

Heterochromatin
Lamins
Chromatin
Nuclear Lamina
S Phase

Rapid mitogenic regulation of the mTORC1 Inhibitor, DEPTOR, by phosphatidic acid

Yoon, M. S., Rosenberger, C. L., Wu, C., Truong, N., Sweedler, J. V. & Chen, J., May 7 2015, In : Molecular cell. 58, 3, p. 549-556 8 p.

Research output: Contribution to journalArticle

Phosphatidic Acids
Phospholipase D
Unsaturated Fatty Acids
Mitogens
mechanistic target of rapamycin complex 1

Roles of progesterone receptor A and B isoforms during human endometrial decidualization

Kaya, H. S., Hantak, A. M., Stubbs, L. J., Taylor, R. N., Bagchi, I. C. & Bagchi, M. K., Jun 1 2015, In : Molecular Endocrinology. 29, 6, p. 882-895 14 p.

Research output: Contribution to journalArticle

Protein Isoforms
Progesterone Receptors
Stromal Cells
Cell Differentiation
Pregnancy

Spiralian gastrulation: Germ layer formation, morphogenesis, and fate of the blastopore in the slipper snail Crepidula fornicata

Lyons, D. C., Perry, K. J. & Henry, J. J., Jun 24 2015, In : EvoDevo. 6, 1, 24.

Research output: Contribution to journalArticle

Gastrula
Germ Layers
Gastrulation
morphogenesis
Snails

Synaptopodin couples epithelial contractility to α-actinin-4-dependent junction maturation

Kannan, N. & Tang, V., Oct 26 2015, In : Journal of Cell Biology. 211, 2, p. 407-434 28 p.

Research output: Contribution to journalArticle

Actinin
Intercellular Junctions
Vinculin
Actins
Myosin Type II

Taranis Protects Regenerating Tissue from Fate Changes Induced by the Wound Response in Drosophila

Schuster, K. J. & Smith-Bolton, R., Jul 6 2015, In : Developmental cell. 34, 1, p. 119-128 10 p.

Research output: Contribution to journalArticle

Drosophila
Tissue
Wounds and Injuries
Regeneration
Genes

Task-related differential expression of four cytochrome P450 genes in honeybee appendages

Mao, W., Schuler, M. A. & Berenbaum, M. R., Oct 1 2015, In : Insect Molecular Biology. 24, 5, p. 582-588 7 p.

Research output: Contribution to journalArticle

appendages
cytochrome P-450
Cytochrome P-450 Enzyme System
honey bees
Leg

The preRC protein ORCA organizes heterochromatin by assembling histone H3 lysine 9 methyltransferases on chromatin

Giri, S., Aggarwal, V., Pontis, J., Shen, Z., Chakraborty, A., Khan, A., Mizzen, C. A., Kannanganattu, P. K., Ait-Si-Ali, S., Ha, T. & Prasanth, S. G., Apr 29 2015, In : eLife. 2015, 4, p. 1-54 54 p.

Research output: Contribution to journalArticle

Heterochromatin
Methyltransferases
Histones
Lysine
Chromatin

Trithorax regulates systemic signaling during drosophila imaginal disc regeneration

Skinner, A., Khan, S. J. & Smith-Bolton, R., Oct 15 2015, In : Development (Cambridge). 142, 20, p. 3500-3511 12 p.

Research output: Contribution to journalArticle

Imaginal Discs
Drosophila
Regeneration
regeneration
animal
2014

A cleavage clock regulates features of lineage-specific differentiation in the development of a basal branching metazoan, the ctenophore Mnemiopsis leidyi

Fischer, A. H. L., Pang, K., Henry, J. Q. & Martindale, M. Q., Jan 31 2014, In : EvoDevo. 5, 1, 4.

Research output: Contribution to journalArticle

Ctenophora
Mnemiopsis leidyi
metazoan
cleavage
branching

A distant downstream enhancer directs essential expression of Tbx18 in urogenital tissues

Bolt, C. C., Elso, C. M., Lu, X., Pan, F., Kispert, A. & Stubbs, L. J., Aug 15 2014, In : Developmental Biology. 392, 2, p. 483-493 11 p.

Research output: Contribution to journalArticle

Homozygote
Phenotype
Mutation
Inner Ear
Point Mutation

Aip1 destabilizes cofilin-saturated actin filaments by severing and accelerating monomer dissociation from ends

Nadkarni, A. V. & Brieher, W. M., Dec 1 2014, In : Current Biology. 24, 23, p. 2749-2757 9 p.

Research output: Contribution to journalArticle

Actin Depolymerizing Factors
microfilaments
Actin Cytoskeleton
actin
Actins

A novel small-molecule tumor necrosis factor α inhibitor attenuates inflammation in a hepatitis mouse model

Ma, L., Gong, H., Zhu, H., Ji, Q., Su, P., Liu, P., Cao, S., Yao, J., Jiang, L., Han, M., Ma, X., Xiong, D., Luo, H. R., Wang, F., Zhou, J. & Xu, Y., Jan 1 2014, In : Journal of Biological Chemistry. 289, 18, p. 12457-12466 10 p.

Research output: Contribution to journalArticle

Computer-Aided Design
Drug Design
Hepatitis
Tumor Necrosis Factor-alpha
Inflammation

Comparing label-free quantitative peptidomics approaches to characterize diurnal variation of peptides in the rat suprachiasmatic nucleus

Southey, B. R., Lee, J. E., Zamdborg, L., Atkins, N., Mitchell, J. W., Li, M., Gillette, M. L., Kelleher, N. L. & Sweedler, J. V., Jan 7 2014, In : Analytical chemistry. 86, 1, p. 443-452 10 p.

Research output: Contribution to journalArticle

Rats
Labels
Peptides
Neuropeptides
Secretogranin II

Deep vertebrate roots for mammalian zinc finger transcription factor subfamilies

Liu, H., Chang, L. H., Sun, Y., Lu, X. & Stubbs, L. J., Mar 2014, In : Genome biology and evolution. 6, 3, p. 510-525 16 p.

Research output: Contribution to journalArticle

zinc finger motif
Zinc Fingers
Vertebrates
vertebrate
Transcription Factors
Porcine respiratory and reproductive syndrome virus
Gene Expression Regulation
Viruses
Gene expression
Cell Cycle

Dynamic phosphorylation of HP1α regulates mitotic progression in human cells

Chakraborty, A., Kannanganattu, P. K. & Prasanth, S. G., Mar 12 2014, In : Nature communications. 5, 3445.

Research output: Contribution to journalArticle

phosphorylation
Phosphorylation
progressions
Cells
proteins

Fluorescence imaging with one-nanometer accuracy (fiona)

Wang, Y., Cai, E., Sheung, J., Lee, S. H., Teng, K. W. & Selvin, P. R., Sep 26 2014, In : Journal of Visualized Experiments. 91, e51774.

Research output: Contribution to journalArticle

Optical Imaging
Fluorescence
Imaging techniques
Quantum Dots
Semiconductor quantum dots

Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax

Fang, X., Nevo, E., Han, L., Levanon, E. Y., Zhao, J., Avivi, A., Larkin, D., Jiang, X., Feranchuk, S., Zhu, Y., Fishman, A., Feng, Y., Sher, N., Xiong, Z., Hankeln, T., Huang, Z., Gorbunova, V., Zhang, L., Zhao, W., Wildman, D. & 33 others, Xiong, Y., Gudkov, A., Zheng, Q., Rechavi, G., Liu, S., Bazak, L., Chen, J., Knisbacher, B. A., Lu, Y., Shams, I., Gajda, K., Farré, M., Kim, J., Lewin, H. A., Ma, J., Band, M. R., Bicker, A., Kranz, A., Mattheus, T., Schmidt, H., Seluanov, A., Azpurua, J., McGowen, M. R., Ben Jacob, E., Li, K., Peng, S., Zhu, X., Liao, X., Li, S., Krogh, A., Zhou, X., Brodsky, L. & Wang, J., Jun 3 2014, In : Nature communications. 5, 3966.

Research output: Contribution to journalArticle

Spalax
Mole Rats
genome
rats
Rats

High-efficiency motor neuron differentiation from human pluripotent stem cells and the function of Islet-1

Qu, Q., Li, D., Louis, K. R., Li, X., Yang, H., Sun, Q., Crandall, S. R., Tsang, S., Zhou, J., Cox, C. L., Cheng, J. & Wang, F., Mar 13 2014, In : Nature communications. 5, 3449.

Research output: Contribution to journalArticle

Pluripotent Stem Cells
stem cells
Motor Neurons
Stem cells
neurons

HSP70 transgene directed motion to nuclear speckles facilitates heat shock activation

Khanna, N., Hu, Y. & Belmont, A. S., May 19 2014, In : Current Biology. 24, 10, p. 1138-1144 7 p.

Research output: Contribution to journalArticle

Speckle
Transgenes
transgenes
heat stress
Shock

Ins and outs of spiralian gastrulation

Lyons, D. C. & Henry, J. J., Jan 1 2014, In : International Journal of Developmental Biology. 58, 6-8, p. 413-428 16 p.

Research output: Contribution to journalArticle

Gastrulation
Cell Lineage
Morphogenesis
Embryonic Structures
Platyhelminths

Label-Free Characterization of Emerging Human Neuronal Networks

Mir, M., Kim, T., Majumder, A., Xiang, M., Wang, R., Liu, S. C., Gillette, M. L., Stice, S. & Popescu, G., Apr 1 2014, In : Scientific reports. 4, 4434.

Research output: Contribution to journalArticle

Process Assessment (Health Care)
Nervous System
Longitudinal Studies
Stem Cells
Neurons

Lanthionine synthetase C-like protein 2 (LanCL2) is a novel regulator of Akt

Zeng, M., Van Der Donk, W. A. & Chen, J., Dec 1 2014, In : Molecular biology of the cell. 25, 24, p. 3954-3961 8 p.

Research output: Contribution to journalArticle

Ligases
Protein C
Phosphorylation
Phosphotransferases
lanthionine

MicroRNA-146b promotes myogenic differentiation and modulates multiple gene targets in muscle cells

Khanna, N., Ge, Y. & Chen, J., Jun 23 2014, In : PloS one. 9, 6, e100657.

Research output: Contribution to journalArticle

MicroRNAs
microRNA
myocytes
Muscle Cells
Muscle

Molecular chaperone-mediated nuclear protein dynamics

Echtenkamp, F. J. & Freeman, B. C., Jan 1 2014, In : Current Protein and Peptide Science. 15, 3, p. 216-224 9 p.

Research output: Contribution to journalArticle

Molecular Chaperones
Nuclear Proteins
Proteins
Foster Home Care
Accessories

MOV10 and FMRP Regulate AGO2 Association with MicroRNA Recognition Elements

Kenny, P. J., Zhou, H., Kim, M., Skariah, G., Khetani, R. S., Drnevich, J., Arcila, M. L., Kosik, K. S. & Ceman, S., Dec 11 2014, In : Cell Reports. 9, 5, p. 1729-1741 13 p.

Research output: Contribution to journalArticle

MicroRNAs
RNA
Fragile X Mental Retardation Protein
RNA Helicases
Messenger RNA

Neuromolecular responses to social challenge: Common mechanisms across mouse, stickleback fish, and honey bee

Rittschof, C. C., Bukhari, S. A., Sloofman, L. G., Troy, J. M., Caetano-Anollés, D., Cash-Ahmed, A., Kent, M., Lu, X., Sanogo, Y. O., Weisner, P. A., Zhang, H., Bell, A. M., Ma, J., Sinha, S., Robinson, G. E. & Stubbs, L. J., Dec 16 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 50, p. 17929-17934 6 p.

Research output: Contribution to journalArticle

Smegmamorpha
Honey
Bees
Fishes
Energy Metabolism

Oscillatory behavior of neutrophils under opposing chemoattractant gradients supports a winner-take-all mechanism

Byrne, M. B., Kimura, Y., Kapoor, A., He, Y., Mattam, K. S., Hasan, K. M., Olson, L. N., Wang, F., Kenis, P. J. A. & Rao, C. V., Jan 21 2014, In : PloS one. 9, 1, e85726.

Research output: Contribution to journalArticle

chemoattractants
Chemotactic Factors
neutrophils
chemotaxis
Neutrophils

PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity

Yoon, J. H., De, S., Srikantan, S., Abdelmohsen, K., Grammatikakis, I., Kim, J., Kim, K. M., Noh, J. H., White, E. J. F., Martindale, J. L., Yang, X., Kang, M. J., Wood, W. H., Noren Hooten, N., Evans, M. K., Becker, K. G., Tripathi, V., Kannanganattu, P. K., Wilson, G. M., Tuschl, T. & 3 others, Ingolia, N. T., Hafner, M. & Gorospe, M., Jan 1 2014, In : Nature communications. 5, 5248.

Research output: Contribution to journalArticle

Ribonucleosides
genome
crosslinking
Immunoprecipitation
Crosslinking

Phosphorylation-dephosphorylation cycle of HP1á governs accurate mitotic progression

Chakraborty, A. & Prasanth, S. G., Jun 1 2014, In : Cell Cycle. 13, 11, p. 1663-1670 8 p.

Research output: Contribution to journalArticle

Phosphorylation
Prometaphase
Mitosis
Chromatin
heterochromatin-specific nonhistone chromosomal protein HP-1

Prolonged in vivo imaging of Xenopus laevis

Hamilton, P. W. & Henry, J. J., Aug 2014, In : Developmental Dynamics. 243, 8, p. 1011-1019 9 p.

Research output: Contribution to journalArticle

Xenopus laevis
Larva
Anesthetics
Anesthesia
Xenopus

Retinoic acid regulation by CYP26 in vertebrate lens regeneration

Thomas, A. G. & Henry, J. J., Feb 15 2014, In : Developmental Biology. 386, 2, p. 291-301 11 p.

Research output: Contribution to journalArticle

Tretinoin
Lenses
Vertebrates
Regeneration
Cornea

Single molecule FRET reveals pore size and opening mechanism of a mechano-sensitive ion channel

Wang, Y., Liu, Y., Deberg, H. A., Nomura, T., Hoffman, M. T. O., Rohde, P. R., Schulten, K., Martinac, B. & Selvin, P. R., Jan 1 2014, In : eLife. 3, p. e01834

Research output: Contribution to journalArticle

Molecular Models
Energy Transfer
Molecular Dynamics Simulation
Ion Channels
Liposomes

Single molecule FRET reveals pore size and opening mechanism of a mechano-sensitive ion channel

Wang, Y., Liu, Y., DeBerg, H. A., Nomura, T., Hoffman, M. T., Rohde, P. R., Schulten, K. J., Martinac, B. & Selvin, P. R., Feb 18 2014, In : eLife. 2014, 3, e01834.

Research output: Contribution to journalArticle

Molecular Models
Energy Transfer
Molecular Dynamics Simulation
Ion Channels
Liposomes

Small quantum dots conjugated to nanobodies as immunofluorescence probes for nanometric microscopy

Wang, Y., Cai, E., Rosenkranz, T., Ge, P., Teng, K. W., Lim, S. J., Smith, A. M., Chung, H. J., Sachs, F., Green, W. N., Gottlieb, P. & Selvin, P. R., Dec 17 2014, In : Bioconjugate Chemistry. 25, 12, p. 2205-2211 7 p.

Research output: Contribution to journalArticle

Single-Domain Antibodies
Quantum Dots
Antibodies
Semiconductor quantum dots
Fluorescent Antibody Technique