Howard Hughes Medical Institution

Research Output 1988 2018

2018

Affinity capture of polyribosomes followed by RNAseq (ACAPseq), a discovery platform for protein-protein interactions

Peng, X., Emiliani, F., Smallwood, P. M., Rattner, A., Lei, H., Sabbagh, M. F. & Nathans, J., Oct 22 2018, In : eLife. 7

Research output: Contribution to journalArticle

RNA Sequence Analysis
Polyribosomes
Proteins
Immobilized Proteins
High-Throughput Nucleotide Sequencing

Sequence-specific DNA binding activity of the cross-brace zinc finger motif of the piggyBac transposase

Morellet, N., Li, X., Wieninger, S. A., Taylor, J. L., Bischerour, J., Moriau, S., Lescop, E., Bardiaux, B., Mathy, N., Assrir, N., Bétermier, M., Nilges, M., Hickman, A. B., Dyda, F., Craig, N. L. & Guittet, E., Jan 1 2018, In : Nucleic acids research. 46, 5, p. 2660-2677 18 p.

Research output: Contribution to journalArticle

Transposases
Braces
Zinc Fingers
Cysteine
DNA

Though the brain has billions of neurons, wiring it all up may depend upon very simple rules

Kolodkin, A. L., Apr 24 2018, Think Tank: Forty Neuroscientists Explore the Biological Roots of Human Experience. Yale University Press, p. 26-33 8 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Neurons
Brain
2017

Can multidrug-resistant candida auris be reliably identified in clinical microbiology laboratories?

Mizusawa, M., Miller, H., Green, R., Lee, R., Durante, M., Perkins, R., Hewitt, C., Simner, P. J., Carroll, K. C., Hayden, R. T. & Zhang, S. X., Feb 1 2017, In : Journal of Clinical Microbiology. 55, 2, p. 638-640 3 p.

Research output: Contribution to journalShort survey

Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry
Microbiology
Candida

Cerebral Vein Malformations Result from Loss of Twist1 Expression and BMP Signaling from Skull Progenitor Cells and Dura

Tischfield, M. A., Robson, C. D., Gilette, N. M., Chim, S. M., Sofela, F. A., DeLisle, M. M., Gelber, A., Barry, B. J., MacKinnon, S., Dagi, L. R., Nathans, J. & Engle, E. C., 2017, (Accepted/In press) In : Developmental Cell.

Research output: Contribution to journalArticle

Cerebral Veins
Bone Morphogenetic Proteins
Skull
Stem Cells
Craniosynostoses

eIF5A Functions Globally in Translation Elongation and Termination

Schuller, A. P., Wu, C. C. C., Dever, T. E., Buskirk, A. R. & Green, R., Apr 20 2017, In : Molecular Cell. 66, 2, p. 194-205.e5

Research output: Contribution to journalArticle

Ribosomes
Proline
Peptide Initiation Factors
Terminator Codon
3' Untranslated Regions

Establishing Wiring Specificity in Visual System Circuits: From the Retina to the Brain

Zhang, C., Kolodkin, A. L., Wong, R. O. & James, R. E., Jul 25 2017, In : Annual Review of Neuroscience. 40, p. 395-424 30 p.

Research output: Contribution to journalArticle

Retina
Visual Pathways
Brain
Nervous System

Intramembrane proteolysis of astrotactins

Chang, H., Smallwood, P. M., Williams, J. & Nathans, J., Feb 24 2017, In : Journal of Biological Chemistry. 292, 8, p. 3506-3516 11 p.

Research output: Contribution to journalArticle

Proteolysis
Asialoglycoprotein Receptor
CD4 Antigens
Transferrin Receptors
Hair Follicle

Netrin-Mediated Axon Guidance to the CNS Midline Revisited

Hand, R. A. & Kolodkin, A. L., May 17 2017, In : Neuron. 94, 4, p. 691-693 3 p.

Research output: Contribution to journalShort survey

Neurons
Axon Guidance
netrin-1

Neuropilin-2/PlexinA3 Receptors Associate with GluA1 and Mediate Sema3F-Dependent Homeostatic Scaling in Cortical Neurons

Wang, Q., Chiu, S-L., Koropouli, E., Hong, I., Mitchell, S., Easwaran, T. P., Hamilton, N. R., Gustina, A. S., Zhu, Q., Ginty, D. D., Huganir, R. L. & Kolodkin, A. L., Dec 6 2017, In : Neuron. 96, 5, p. 1084-1098.e7

Research output: Contribution to journalArticle

Neuropilin-2
Semaphorins
Neurons
Synapses
AMPA Receptors

Not just Salk

Greider, C., Hopkins, N., Steitz, J., Amon, A., Asai, D., Barres, B., Bass, B., Bassler, B., Birgeneau, R., Bjorkman, P., Botchan, M., Brugge, J., Cech, T., Colwell, R., Craig, N., Delange, T., Eisen, M., Gottesman, S., Green, R., Handelsman, J. & 17 othersKimble, J., King, M. C., Lehmann, R., Marder, E., Mullins, D., O’Shea, E., Schmid, S., Seydoux, G., Spradling, A., Storz, G., Szostak, J., Telesnitsky, A., Tilghman, S., Tjian, R., Vale, R., Wolberger, C. & Zakian, V., Sep 15 2017, In : Science. 357, 6356, p. 1105-1106 2 p.

Research output: Contribution to journalLetter

Peropsin modulates transit of Vitamin A from retina to retinal pigment epithelium

Cook, J. D., Ng, S. Y., Lloyd, M., Eddington, S., Sun, H., Nathans, J., Bok, D., Radu, R. A. & Travis, G. H., Jan 1 2017, In : Journal of Biological Chemistry. 292, 52, p. 21407-21416 10 p.

Research output: Contribution to journalArticle

Retinal Pigments
Retinal Pigment Epithelium
Vitamins
Vitamin A
Pigments

Population growth: Help to make food go further in Egypt

Nathans, J., Jun 7 2017, In : Nature. 546, 7657, p. 210 1 p.

Research output: Contribution to journalLetter

Northern Africa
Egypt
Population Growth
Population Dynamics
Developing Countries

Rapid generation of hypomorphic mutations

Arthur, L. L., Chung, J. J., Jankirama, P., Keefer, K. M., Kolotilin, I., Pavlovic-Djuranovic, S., Chalker, D. L., Grbic, V., Green, R., Menassa, R., True, H. L., Skeath, J. B. & Djuranovic, S., Jan 20 2017, In : Nature Communications. 8, 14112.

Research output: Contribution to journalArticle

mutations
Genes
organisms
genes
Mutation

Reck and Gpr124 Are Essential Receptor Cofactors for Wnt7a/Wnt7b-Specific Signaling in Mammalian CNS Angiogenesis and Blood-Brain Barrier Regulation

Cho, C., Smallwood, P. M. & Nathans, J., Aug 30 2017, In : Neuron. 95, 5, p. 1056-1073.e5

Research output: Contribution to journalArticle

Blood-Brain Barrier
Leucine
Membrane Proteins
Endothelial Cells
Mutagenesis

Regulated Ire1-dependent mRNA decay requires no-go mRNA degradation to maintain endoplasmic reticulum homeostasis in S. Pombe

Guydosh, N. R., Kimmig, P., Walter, P. & Green, R., Sep 25 2017, In : eLife. 6, e29216.

Research output: Contribution to journalArticle

Schizosaccharomyces
RNA Stability
Endoplasmic Reticulum
Homeostasis
Ribosomes

Ribosome pausing, arrest and rescue in bacteria and eukaryotes

Buskirk, A. & Green, R., Mar 19 2017, In : Philosophical Transactions of the Royal Society B: Biological Sciences. 372, 1716, 20160183.

Research output: Contribution to journalReview article

ribosomes
Eukaryota
Ribosomes
eukaryotic cells
Elongation

Slowed decay of mRNAs enhances platelet specific translation

Mills, E. W., Green, R. & Ingolia, N. T., Apr 27 2017, In : Blood. 129, 17, p. e38-e48

Research output: Contribution to journalArticle

Platelets
Blood Platelets
Messenger RNA
RNA Sequence Analysis
Ribosomes

The ABC(E1)s of Ribosome Recycling and Reinitiation

Schuller, A. P. & Green, R., Jun 1 2017, In : Molecular Cell. 66, 5, p. 578-580 3 p.

Research output: Contribution to journalShort survey

Recycling
Ribosomes
Molecular Biology

The laminar organization of the drosophila ellipsoid body is semaphorin-dependent and prevents the formation of ectopic synaptic connections

Xie, X., Tabuchi, M., Brown, M. P., Mitchell, S. P., Wu, M. N. & Kolodkin, A. L., Jun 20 2017, In : eLife. 6, e25328.

Research output: Contribution to journalArticle

Semaphorins
Drosophila
Neurons
Axons
Optogenetics

Translation of poly(A) tails leads to precise mRNA cleavage

Guydosh, N. R. & Green, R., May 1 2017, In : RNA. 23, 5, p. 749-761 13 p.

Research output: Contribution to journalArticle

Ribosomes
Messenger RNA
Polyadenylation
RNA Stability
Nucleotides

Varicose and cheerio collaborate with pebble to mediate semaphorin-1a reverse signaling in Drosophila

Jeong, S., Yang, D. S., Hong, Y. G., Mitchell, S. P., Brown, M. P. & Kolodkin, A. L., Sep 26 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 39, p. E8254-E8263

Research output: Contribution to journalArticle

Semaphorins
Drosophila
Actin Cytoskeleton
Axons
Rho Guanine Nucleotide Exchange Factors

Wiring visual systems: common and divergent mechanisms and principles

Kolodkin, A. L. & Hiesinger, P. R., Feb 1 2017, In : Current Opinion in Neurobiology. 42, p. 128-135 8 p.

Research output: Contribution to journalReview article

Diptera
Fishes
History
2016

Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling

Mohammad, F., Woolstenhulme, C., Green, R. & Buskirk, A., Feb 2 2016, In : Cell Reports. 14, 4, p. 686-694 9 p.

Research output: Contribution to journalArticle

Ribosomes
Bacteria
Messenger RNA
Gene expression
Elongation

Connections Underlying Translation and mRNA Stability

Radhakrishnan, A. & Green, R., Sep 11 2016, In : Journal of Molecular Biology. 428, 18, p. 3558-3564 7 p.

Research output: Contribution to journalReview article

RNA Stability
Messenger RNA
Ribosomes
Untranslated RNA
Protein Stability

Dynamic Regulation of a Ribosome Rescue Pathway in Erythroid Cells and Platelets

Mills, E. W., Wangen, J., Green, R. & Ingolia, N. T., Sep 27 2016, In : Cell Reports. 17, 1, p. 1-10 10 p.

Research output: Contribution to journalArticle

Erythroid Cells
Platelets
Ribosomes
Blood
Blood Platelets

Epigenomic landscapes of retinal rods and cones

Mo, A., Luo, C., Davis, F. P., Mukamel, E. A., Henry, G. L., Nery, J. R., Urich, M. A., Picard, S., Lister, R., Eddy, S. R., Beer, M., Ecker, J. R. & Nathans, J., Mar 7 2016, In : eLife. 5, MARCH2016, e11613.

Research output: Contribution to journalArticle

Retinal Cone Photoreceptor Cells
Retinal Rod Photoreceptor Cells
Vertebrate Photoreceptor Cells
Epigenomics
Cones

Frizzled Receptors in Development and Disease

Wang, Y., Chang, H., Rattner, A. & Nathans, J., 2016, (Accepted/In press) In : Current Topics in Developmental Biology.

Research output: Contribution to journalArticle

Frizzled Receptors
Cell Polarity
Central Nervous System
Wnt Receptors
Ventricular Septum

How scientists can reduce their carbon footprint

Nathans, J. & Sterling, P., Mar 31 2016, In : eLife. 5, MARCH2016, e15928.

Research output: Contribution to journalArticle

Carbon Footprint
Air Travel
Carbon footprint
Greenhouse gases
Gases

Inhibition of Eukaryotic Translation by the Antitumor Natural Product Agelastatin A

McClary, B., Zinshteyn, B., Meyer, M., Jouanneau, M., Pellegrino, S., Yusupova, G., Schuller, A., Reyes, J. C. P., Lu, J., Guo, Z., Ayinde, S., Luo, C., Dang, Y., Romo, D., Yusupov, M., Green, R. & Liu, J. O., Dec 18 2016, (Accepted/In press) In : Cell Chemical Biology.

Research output: Contribution to journalArticle

Biological Products
Ribosomes
agelastatin A
Chemotherapy
Cell proliferation

Patterning of papillae on the mouse tongue: A system for the quantitative assessment of planar cell polarity signaling

Wang, Y., Williams, J., Rattner, A., Wu, S., Bassuk, A. G., Goffinet, A. M. & Nathans, J., Nov 15 2016, In : Developmental Biology. 419, 2, p. 298-310 13 p.

Research output: Contribution to journalArticle

Cell Polarity
Tongue
Alleles
Phenotype
Genes

Regressive phenomena: Refining connections

Agnew-Svoboda, W., Kolodkin, A. L. & Riccomagno, M. M., Jan 1 2016, Neuroscience in the 21st Century: From Basic to Clinical, Second Edition. Springer New York, p. 265-294 30 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

refining
nervous system
Nervous System
neurons
Neurons

Ryk controls remapping of motor cortex during functional recovery after spinal cord injury

Hollis, E. R., Ishiko, N., Yu, T., Lu, C. C., Haimovich, A., Tolentino, K., Richman, A., Tury, A., Wang, S. H., Pessian, M., Jo, E., Kolodkin, A. L. & Zou, Y., May 1 2016, In : Nature Neuroscience. 19, 5, p. 697-705 9 p.

Research output: Contribution to journalArticle

Forelimb
Motor Cortex
Spinal Cord Injuries
Knockout Mice
Rehabilitation

The cellular compass

Adler, P. N. & Nathans, J., Feb 16 2016, In : Scientific American. 314, 3, p. 67-71 5 p.

Research output: Contribution to journalArticle

Body Patterning
Frizzled Receptors
Cell Physiological Phenomena
Drosophila melanogaster
Cell Communication

The cellular compass

Adler, P. N. & Nathans, J., Feb 16 2016, In : Scientific American. 314, 3, p. 67-71 5 p.

Research output: Contribution to journalArticle

The DEAD-Box Protein Dhh1p Couples mRNA Decay and Translation by Monitoring Codon Optimality

Radhakrishnan, A., Chen, Y. H., Martin, S., Alhusaini, N., Green, R. & Coller, J., Sep 22 2016, In : Cell. 167, 1, p. 122-132.e9

Research output: Contribution to journalArticle

RNA Stability
Protein Biosynthesis
Codon
Ribosomes
Messenger RNA

The fail-safe mechanism of post-transcriptional silencing of unspliced HAC1 mRNA

Di Santo, R., Aboulhouda, S., Weinberg, D. E. & Green, R., Oct 1 2016, In : eLife. 5, OCTOBER2016, e20069.

Research output: Contribution to journalArticle

Unfolded Protein Response
Introns
Messenger RNA
Proteins
Stored Messenger RNA

When stop makes sense

Zinshteyn, B. & Green, R., Dec 2 2016, In : Science. 354, 6316, p. 1106 1 p.

Research output: Contribution to journalShort survey

Translational Peptide Chain Termination
Euplotes
Ciliophora
Terminator Codon
RNA Stability
2015

Avoiding the ends: Internal epitope tagging of proteins using transposon Tn7

Zordan, R. E., Beliveau, B. J., Trow, J. A., Craig, N. L. & Cormack, B. P., Jan 1 2015, In : Genetics. 200, 1, p. 47-58 12 p.

Research output: Contribution to journalArticle

Epitopes
Proteins
Peptides
GPI-Linked Proteins
Saccharomyces cerevisiae Proteins

Axon Dynamics during Neocortical Laminar Innervation

Hand, R. A., Khalid, S., Tam, E. & Kolodkin, A. L., Jul 14 2015, In : Cell Reports. 12, 2, p. 172-182 11 p.

Research output: Contribution to journalArticle

Pyramidal Cells
Cerebral Cortex
Neurons
Axons
Networks (circuits)

Endothelial microRNA-150 is an intrinsic suppressor of pathologic ocular neovascularization

Liu, C. H., Sun, Y., Li, J., Gong, Y., Tian, K. T., Evans, L. P., Morss, P. C., Fredrick, T. W., Saba, N. J., Chen, J. & Nathans, J., Sep 29 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 39, p. 12163-12168 6 p.

Research output: Contribution to journalArticle

Pathologic Neovascularization
MicroRNAs
Endothelial Cells
Physiologic Neovascularization
Retinal Neovascularization

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

Mo, A., Mukamel, E. A., Davis, F. P., Luo, C., Henry, G. L., Picard, S., Urich, M. A., Nery, J. R., Sejnowski, T. J., Lister, R., Eddy, S. R., Ecker, J. R. & Nathans, J., Jun 17 2015, In : Neuron. 86, 6, p. 1369-1384 16 p.

Research output: Contribution to journalArticle

Epigenomics
DNA Methylation
Brain
Neurons
Chromatin

Functional Assembly of Accessory Optic System Circuitry Critical for Compensatory Eye Movements

Sun, L. O., Brady, C. M., Cahill, H., Al-Khindi, T., Sakuta, H., Dhande, O. S., Noda, M., Huberman, A. D., Nathans, J. & Kolodkin, A. L., May 20 2015, In : Neuron. 86, 4, p. 971-984 14 p.

Research output: Contribution to journalArticle

Semaphorins
Eye Movements
Visual Fields
varespladib methyl
Retinal Ganglion Cells

High-Precision analysis of translational pausing by ribosome profiling in bacteria lacking EFP

Woolstenhulme, C., Guydosh, N. R., Green, R. & Buskirk, A., Apr 7 2015, In : Cell Reports. 11, 1, p. 13-21 9 p.

Research output: Contribution to journalArticle

Peptide Elongation Factors
Ribosomes
Proline
Escherichia coli
Elongation

Identification of Astrotactin2 as a Genetic Modifier That Regulates the Global Orientation of Mammalian Hair Follicles

Chang, H., Cahill, H., Smallwood, P. M., Wang, Y. & Nathans, J., 2015, In : PLoS Genetics. 11, 9, e1005532.

Research output: Contribution to journalArticle

hair follicles
modifiers (genes)
Hair Follicle
hair
Hair

Large-scale clinical validation of a lateral flow immunoassay for detection of cryptococcal antigen in serum and cerebrospinal fluid specimens

Suwantarat, N., Dalton, J. B., Lee, R., Green, R., Memon, W., Carroll, K. C., Riedel, S. & Zhang, S. X., May 1 2015, In : Diagnostic Microbiology and Infectious Disease. 82, 1, p. 54-56 3 p.

Research output: Contribution to journalArticle

Immunoassay
Cerebrospinal Fluid
Antigens
Serum
Cryptococcosis

MIR retrotransposon sequences provide insulators to the human genome

Wang, J., Vicente-García, C., Seruggia, D., Moltó, E., Fernandez-Miñán, A., Neto, A., Lee, E., Gómez-Skarmeta, J. L., Montoliu, L., Lunyak, V. V., Jordan, I. K. & Craig, N. L., Aug 11 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 32, p. E4428-E4437

Research output: Contribution to journalArticle

Retroelements
Human Genome
Chromatin
T-Lymphocytes
DNA Transposable Elements

Rac1 plays an essential role in axon growth and guidance and in neuronal survival in the central and peripheral nervous systems

Hua, Z. L., Emiliani, F. E. & Nathans, J., Sep 23 2015, In : Neural Development. 10, 1, 21.

Research output: Contribution to journalArticle

Peripheral Nervous System
Axons
Central Nervous System
Motor Neurons
Growth

Ribosomes slide on lysine-encoding homopolymeric A stretches

Koutmou, K. S., Schuller, A. P., Brunelle, J. L., Radhakrishnan, A., Djuranovic, S. & Green, R., Feb 19 2015, In : eLife. 2015, 4

Research output: Contribution to journalArticle

Ribosomes
Codon
Lysine
Proteins
Messenger RNA