August 2014
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Molecular Biology and Genetics Archives

1. Guo Y, Park JM, Cui B, Humes E, Gangadharan S, Hung S, FitzGerald PC, Hoe K-L, Grewal SIS, Craig NL, Levin HL. Integration profiling of gene function with dense maps of transposon integration. Genetics 2013 Oct; 195(2):599-609.
Key words: Hermes, Schizosaccharomyces pombe, Transposon, integration profile
http://www.genetics.org/content/195/2/599.full.pdf+html
PMID:23893486

2. Wright JA, Smith RC, Li X, Craig NL, Atkinson PW. IPB7 transposase behavior in Drosophila melanogaster and Aedes aegypti. Insect Biochemistry and Molecular Biology 2013; 43:899-906.
Key words: piggyBac, Transposable element, Hyperactive, Drosophila, Aedes http://www.sciencedirect.com/science/article/pii/S096517481300115X
PMID:23835045

1. Rattner A, Yu H, Williams J, Smallwood PM, Nathans J. Endothelin-2 signaling in the neural retina promotes the endothelial tip cell state and inhibits angiogenesis. Proc Natl Acad Sci USA. 2013 Oct 1;110(40)
Key words: endothelin-2, neural retina, angiogenesis
http://www.pnas.org/content/110/40/E3830.long
PMID: 24043815

1. Halper-Stromberg E, Steranka J, Giraldo-Castillo N, Fuller T, Desiderio S, Burns KH. Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies. BMC Genomics. 2013 Aug 19;14(1):565 [Epub ahead of print]
Key words: Lymphocytes, antigen, PCR amplification
http://www.biomedcentral.com/1471-2164/14/565/abstract
PMID: 23957733

2. Lee J, Baldwin WM 3rd, Lee Cy, Desiderio S. Stat3? mitigates development of atherosclerosis in apolipoprotein E-deficient mice. J Mol Med (Berl). 2013 Aug; 91(8):965-76.
Key words: transcription factor, Stat3, pathologic sequelae
http://link.springer.com/article/10.1007%2Fs00109-013-1013-5
PMID: 23619910

1. Choi KY, Li Y, Sarnovsky R, Craig NL. Direction interaction between the TnsA and TnsB subunits controls the heteromeric Tn7 transposase. Proc. Nat'l Acad. Sci. U.S.A. 2013 May 28;110(22):E2038-45.
Key words: protein-protein interaction, transposition, protein-DNA interaction, asymmetric transposon ends
http://www.pnas.org/content/110/22/E2038.long
PMID: 23674682

2. Li X, Burnight ER, Cooney AL, Malani N, Brady T, Sander JD, Staber J, Wheelan S, Joung JK, McCray PB Jr, Bushman FD, Sinn PL, Craig NL. piggyBac transposase tools for genome engineering. Proc. Nat'l Acad. Sci. U.S.A. 2013 Jun 18;110(25):E2279-87.
Key words: GULOP, ROSA26, induced pluripotent stem cell production, protein-DNA interaction
http://www.pnas.org/content/110/25/E2279.long
PMID: 23723351; PMCID: PMC3690869

3. O'Donnell KA, An W, Schrum, CT, Wheelan SJ, Boeke JD. Controlled Insertional mutagenesis using a LINE-1 (ORFeus) gene-trap mouse model. 2013 Jul 16;110(29):E2706-13.
Key words: L1 retrotransposon; mud musculus; tet-promoter; white-spotted phenotype; LINE-1
http://www.ncbi.nlm.nih.gov/pubmed/23818630

4. Rybanska-Spaeder I, Reynolds TL, Chou J, Prakash M, Jefferson T, Husso DL, Desiderio S, Franco S. 53BP1 is limiting for nonhomologous end-joining in ATM-deficient cells subjected to oncogenic stress or radiation. Mol Cancer Res. 2013 Jul 15 (Epub ahead of print)
Key words: Oncogneric translocations, T lineage lymphomas, NHEJ defect, double mutants http://www.ncbi.nlm.nih.gov/pubmed/23858098

1. Huang L, Rattner A, Liu H, Nathans J. How to draw the line in biomedical research. Elife. 2013;2:e00638. doi: 10.7554/eLife.00638
Key words: biomedical research, scatter plot
http://www.ncbi.nlm.nih.gov/pubmed/23538852

2. Lee J, Baldwin WM 3rd, Lee CY, Desiderio S. Stat3? mitigates development of atherosclerosis in apolipoprotein E-deficient mice J Mol Med (Berl). 2013 Apr 26. Epub ahead of print
Key words: transcription factor Stat3, dimerization, DNA binding
http://link.springer.com/article/10.1007%2Fs00109-013-1013-5
PMID: 236119910

3. Newman RH, Hu J, Rho HS, Xie Z, Woodard C, Neiswinger J, Cooper C, Shirley M, Clark HM, Hu S, Hwang W, Seop Jeong J, Wu G, Lin J, Gao X, Ni Q, Goel R, Xia S, Ji H, Dalby KN, Birnbaum MJ, Cole PA, Knapp S, Ryazanov AG, Zack DJ, Blackshaw S, Pawson T, Gingras AC, Desiderio S, Pandey A, Turk BE, Zhang J, Zhu H, Qian J. Construction of human activity-based phosphorylation networks. Mol Syst Biol. 2013 Apr 2:9:655 doi.10.1038/msb.201312.
Key words: human phosphorylation networks, vivo phosphorylated residues, kinase-substrate relationships, CEASAR
http://www.nature.com/msb/journal/v9/n1/full/msb201312.html
PMID: 23549483

4. Shilagardi, K., Li, S., Luo, F., Marikar, F, Duan R., Jin, P., Kim, J., Murnen, K., and Chen, E.H. Actin-propelled invasive membrane protrusions promote fusogenic protein engagement during cell-cell fusion. Science. 2013 Apr 19;340(6130):359-363.
Key words: cell-cell fusion, actin polymerization, invasive membrane protrusion
http://www.sciencemag.org/content/340/6130/359.long
PMID: 23623557

1. Newman RH, Hu J, Rho HS, Xie Z, Woodard C, Neiswinger J, Cooper C, Shirley M, Clark HM, Hu S, Hwang W, Seop Jeong J, Wu G, Lin J, Gao X, Ni Q, Goel R, Xia S, Ji H, Dalby KN, Birnbaum MJ, Cole PA, Knapp S, Ryazanov AG, Zack DJ, Blackshaw S, Pawson T, Gingras AC, Desiderio S, Pandey A, Turk BE, Zhang J, Zhu H, Qian J. Construction of human activity-baed phosphorylation networks. Mol Syst Biol. 2013 Apr 2;9:655. doi: 10.1038/msb.2013.12.
Key words: human phosphorylation, mass spectrometry, upstream kinases, CESAR, KSRs
http://www.ncbi.nlm.nih.gov/pubmed/23549483

2. Thapa P, Das J, McWilliams D, Shapiro M, Sundsbak R, Nelson-Holte M, Tangen S, Anderson J, Desiderio S, Hiebert S, Sant'angelo DB, Shapiro VS. The transcriptional repressor NKAP is required for the development of iNKT cells. Nat Commun. 2013;4:1582. doi: 10.1038/ncomms2580.
Key words: transcriptional repressor, NKAP, T cell, CD4-cre, knockout mice, histone deacetylase 3
http://www.nature.com/ncomms/journal/v4/n3/full/ncomms2580.html
PMID: 23481390

1. Benachenhou F, Sperber GO, Bongcam-Rudloff E, Andersson G, Boeke JD, Blomberg J. Conserved structure and inferred evolutionary history of long terminal repeats (LTRs).Mob DNA. 2013 Feb 1;4(1):5.
Key words: LTRs, U3-R-U5 portions
http://www.mobilednajournal.com/content/4/1/5/abstract
PMID: 23369192

2. Huang CR, Burns KH, Boeke JD. Active transposition in genomes. Annu Rev Genet. 2012;46:651-75. doi: 10.1146/annurev-genet-110711-155616.
Key words: transposons, somatic mutation, retrotransposon, polymorphism, genome dynamics
http://www.annualreviews.org/doi/full/10.1146/annurev-genet-110711-155616?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dpubmed&
PMID:23145912

3. Huang Q, Purzycka KJ, Lusvarghi S, Li D, Legrice SF, Boeke JD. Retrotransposon Ty1 RNA contains a 5'-terminal long-range pseudoknot required for efficient reverse transcription. RNA. 2013 Mar;19(3):320-32.
Key words: Ty1 retrotransposon, RNA structure; retrotransposon; reverse transcription; pseudoknot; SHAPE
http://rnajournal.cshlp.org/content/early/2013/01/15/rna.035535.112.long
PMID: 23329695

4. Li X, Ewis H, Hice RH, Malani N, Parker N, Zhou L, Feschotte C, Bushman FD, Atkinson PW, Craig NL. A resurrected mammalian hAT transposable element and a closely related insect element are highly active in human cell culture. PNAS. 2013; 110(6):E478-87;
Key words: hAT element, target site selection, gene therapy, insertional mutagenesis
www.ncbi.nlm.nih.gov/pubmed/23091042

5. Lu, JY, Lin YY, Boeke JD, Zhu H. Using functional proteome microarrays to study protein lysine acetylation. Methods Mol Biol. 2013;981:151-65. doi: 10.1007/978-1-62703-305-3_12.
Key words: Acetylation, proteome microarrays
http://link.springer.com/protocol/10.1007%2F978-1-62703-305-3_12
PMID: 23381860

6. Mitra R, Li X, Kapusta A, Mayhew D, Mitra RD, Feschotte C, Craig NL. Functional characterization of piggyBat from the bat Myotis lucifugus unveils an active mammalian DNA transposon. Proc. Nat'l Acad. Sci. U.S.A. 2013; 110(1):234-239.
Key words: genome evolution, mobile genetic element
www.ncbi.nlm.nih.gov/pubmed/23248290

7. Woodard LE, Li X, Malani N, Kaja A, Hice RH, Atkinson PW, Bushman FD, Craig
NL, Wilson MH. Comparative analysis of the recently discovered hAT transposon
TcBuster in human cells. PLoS ONE. 2012; 7(11):e42666.
Key words: TcBuster; HEK-293; transposase, transposon
http://dx.plos.org/10.1371/journal.pone.0042666
PMID:23166581

8. Wang JT, Seydoux G. Germ cell specification. Adv Exp Med Biol. 2013;757:17-39.
Key words: germ cell, germ plasm, RNA
http://www.springerlink.com/content/p1270wk447k75012/
PMID:22872473

9. Yu H, Ye X, Guo N, Nathans J. Frizzled 2 and frizzled 7 function redundantly in convergent extension and closure of the ventricular septum and palate: evidence for a network of interacting genes. Development. 2012 Dec;139(23):4383-94.
Key words: frizzled 2, frizzled 7, ventricular septum, ventricular palate
http://dev.biologists.org/content/139/23/4383.long
PMID: 23095888

1. Burnight ER, Staber JM, Korsakov P, Li X, Brett BT, Scheetz TE, Craig NL, McCray PB Jr. A hyperactive transposase promotes persistent gene transfer of a piggyBac DNAtransposon. Molecular Therapy-Nucleic Acids. 2012; 1, e50.
Key words: hepatocyte; liver; mouse; transposase; transposon
http://www.nature.com/mtna/journal/v1/n10/full/mtna201212a.html
no PMID available

2. Huang CR, Burns KH, Boeke JD. Active transposition in genomes. Annu Rev Genet. 2012 Dec 15;46:651-75.
Key words: transposons, somatic mutation, retrotransposon, polymorphism, genome dynamics
http://www.annualreviews.org/doi/full/10.1146/annurev-genet-110711-155616?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dpubmed&
PMID: 23145912

3. Voronina E, Paix A, Seydoux G. The P granule component PGL-1 promotes the localization and silencing activity of the PUF protein FBF-2 in germline stem cells. Development. 2012 Oct;139(20):3732-40.
http://dev.biologists.org/content/139/20/3732.long
PMID: 22991439

4. Wang JT, Seydoux G. Germ cell specification. Adv Exp Med Biol. 2013;757:17-39.
Key words: germ cells
http://www.springerlink.com/content/p1270wk447k75012/
PMID: 22872473

5. Woodard LE, Malani N, Kaja A, Hice RH, Atkinson PW, Bushman FD, Craig NL, Wilson MH. Comparative analysis of the recently discovered hAT transposonTcBuster in human cells. PLoS ONE. 2012; 7(11):e42666.
Key words: TcBuster; HEK-293; transposase, transposon
http://dx.plos.org/10.1371/journal.pone.0042666
PMID: 23166581

6. Yu H, Ye X, Guo N, Nathans J. Frizzled 2 and frizzled 7 function redundantly in convergent extension and closure of the ventricular septum and palate: evidence for a network of interacting genes. Development. 2012 Dec;139(23):4383-94.
Key words: ventricular septum, palate, frizzled 2, frizzled 7
http://dev.biologists.org/content/139/23/4383.long
PMID: 23095888

1. Dancy BM, Crump NT, Peterson DJ, Mukherjee C, Bowers EM, Ahn YH, Yoshida M, Zhang J, Mahadevan LC, Meyers DJ, Boeke JD, Cole PA. Live-cell studies of p300/CBP histone acetyltransferase activity and inhibition. 2012 Sep 24;13(14):2113-21.
Key words: drug design, enzymes; FRET; histone H4; protein modifications
http://onlinelibrary.wiley.com/doi/10.1002/cbic.201200381/abstract;jsessionid=
B1C90EF43380454DBBD67EB932581FFE.d03t02
PMID: 22961914

2. Dai L, Taylor MS, O'Donnell KA, Boeke JD. Poly(A) binding protein C1 is essential for efficient L1 retrotransposition and affects L1 RNP formation. 2012 Aug 20. [Epub ahead of print].
Key words: poly binding proteins, L1 RNP, polyadenylation
http://mcb.asm.org/content/early/2012/08/14/MCB.06785-11.long
PMID: 22907758

3. Lee SJ, Huynh TV, Lee YS, Sebald SM, Wilcox-Adelman SA, Iwamori N, Lepper C, Matzuk MM, Fan CM. Role of satellite cells versus myofibers in muscle hypertrophy induced by inhibition of the myostatin/activin signaling pathway. Proc Natl Acad Sci U S A. 2012 Aug 28;109(35):E2353-60.
Key words: activin receptors, GDF-8, follistatin
http://www.ncbi.nlm.nih.gov/pubmed/22869749

1. Baker RP, Urban S. Architectural and thermodynamic principles underlying intramembrane protease function. Nature Chemical Biology. 2012 Jul 15;8(9):759-68.
Key words: intramembrane protease function
http://www.nature.com/nchembio/journal/vaop/ncurrent/full/nchembio.1021.html
PMID: 22797666

2. Greider CW. Wnt regulates TERT--putting the horse before the cart. Science. 2012 June; 336:1519-20.
Key words: telomeres, telomerase, chromosomes
http://www.sciencemag.org/content/336/6088/1519.full
PMID: 22723405

3. Shoemaker CJ, Green R. Translation drives mRNA quality control. Nat Struct Mol Biol. 2012 Jun 5;19(6):594-601.
Key words: mRNA, translation
http://www.nature.com/nsmb/journal/v19/n6/full/nsmb.2301.html
PMID: 22664987

4. Zhou Y, Moin SM, Urban S, Zhang Y. An internal water-retention site in the rhomboid intramembrane protease GlpG ensures catalytic efficiency. Structure. 2012 Jul 3;20(7):1255-63.
Key words: rhomboid intramembrane protease, catalytic efficiency, GlpG
http://www.cell.com/structure/abstract/S0969-2126(12)00182-7

1. Djuranovic S, Nahvi A, Green R. miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science. 2012 Apr 13;336(6078):237-40.
http://www.sciencemag.org/content/336/6078/237.short
PMID: 22499947

2. Petropoulos AD, Green R. Further in vitro exploration fails to support the allosteric three-site model. J Biol Chem. 2012 Apr 6;287(15):11642-8.
Key words: allosteric model, in vitro
http://www.jbc.org/content/287/15/11642.long
PMID: 22378789

3. Shoemaker CJ, Green R. Translation drives mRNA quality control. Nat Struct Mol Biol. 2012 Jun 5;19(6):594-601.
Key words: translation, mRNA
http://www.ncbi.nlm.nih.gov/pubmed/22664987

4. Strong MA, Vidal-Cardenas SL, Karim B, Yu H, Guo N, Greider CW. Phenotypes in mTERT?/? and mTERT?/? mice are due to short telomeres, not telomere-independent functions of telomerase reverse transcriptase. Mol Cell Biol. 2011 Jun;31(12):2369-79. Epub 2011 Apr 4.
Key words: telomeres, telomerase reverse transcriptase
http://mcb.asm.org/content/31/12/2369.long

1. Cooper CL, Hardy RR, Reth M, Desiderio S. Cell-nonautonomous hedgehod signaling promotes murine B lumphopoiesis from hematopoietic progenitors. Blood. 2012 April 18. [Epub ahead of print].
Key words: hedgehog signaling, lymphopoiesis, hematopoietic progenitors
http://bloodjournal.hematologylibrary.org/content/early/2012/04/18/blood-2011-12-397976.long
PMID: 22517907

1. Urban S, Dickey SW. A decade of rhomboid proteases; charting progress on mechanism and function. Genome Biology. 2011 Oct 27; 12(10): 231-41.
Key words: rhomboid, proteases
http://genomebiology.com/content/12/10/231
PMID:22035660

1. Cai Y, Boeke JD. Genome remodeling. Nat Biotechnol. 2011 Sept 8;29(9):807-8.
Key words: Synthetic Biology, MAGE, CAGE, Genome Engineering
http://www.nature.com/nbt/journal/v29/n9/full/nbt.1964.html
PMID: 21904325

2. Doherty JE, Huye L, Yusa K, Zhou L, Craig NL, Wilson M. Hyperactive piggyBac gene transfer in human cells and in vivo. Hum Gene Ther. 2011 Oct 12 [Epub ahead of print].
Key words: transgenesis, hyperactive piggyBac, Sleeping Beauty, transposon comparison
PMID: 21992617
http://www.liebertonline.com/doi/abs/10.1089/hum.2011.138

3. Dymond JS, Richardson SM, Coombes C, Babatz T, Muller S, Annaluru N, Blake WJ, Schwerzmann JW, Dai J, Lindstrom DL, Boeke A, Gottschling DE, Chandrasegaran S, Bader JS, Boeke JD. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature. 2011 Sep 14;477(7365):471-6
Key words: synthetic biology, yeast, genomics, SCRaMbLE
http://www.nature.com/nature/journal/v477/n7365/full/nature10403.html
PMID: 21918511

4. Griffin EE, Odde DJ, Seydoux G. Regulation of the MEX-5 gradient by a spatially segregated kinase/phosphatase cycle. Cell. 2011 Sep 16;146(6):955-68.
Key words: regulation, MEX-5, kinase/phosphatase
PMID: 21925318
http://www.sciencedirect.com/science/article/pii/S0092867411009354

5. Li MA, Turner D, Ning Z, Yusa K, Liang Q, Eckert S, Rad L, Fitzgerald T, Craig NL, Bradley A. Mobilization of giant piggyBac transposons in the mouse genome. Nucleic Acids Res. 2011 Sept 24 [Epub ahead of print}.
Key words: transgenesis, hyperactive piggyBac, suppression of length-dependent reduction in transposition
PMID: 21948799
http://nar.oxfordjournals.org/content/early/2011/09/24/nar.gkr764.long

6. Li Z, Craig NL, Peters JE Transposon Tn7. In: Bacterial Integrative Mobile Genetic
Elements. 2011 (ed. Roberts AP, Mullany P) Landes Bioscience/Madame Curie Bioscience Database.
Key words: site-specific insertion, attTn7, ATP-control of transposition, two-peptide transposase, targeting by the processivity factor

7. Lu JY, Lin YY, Sheu JC, Wu JT, Lee FJ, Chen Y, Lin MI, Chiang FT, Tai TY, Berger SL, Zhao Y, Tsai KS, Zhu H, Chuang LM, Boeke JD. Acetylation of yeast AMPK controls intrinsic aging independently of caloric restriction. Cell. Sep 16;146(6):969-79.
Key words: Acetylation, AMPK, replicative lifespan, Sip2, Snf1, Sch9, intrinsic aging
http://www.sciencedirect.com/science/article/pii/S0092867411008889
PMID: 21906795

8. Motegi F, Zonies S, Hao Y, Cuenca AA, Griffin E, Seydoux G.Microtubules induce self-organization of polarized PAR domains in Caenorhabditis elegans zygotes. Nat Cell Biol. 2011 Oct 9;13(11):1361-7.
PMID: 21983565
http://www.nature.com/ncb/journal/v13/n11/full/ncb2354.html

9. Zaher HS, Green R. A primary role for release factor 3 in quality control during translation elongation in Escherichia coli. Cell. 2011 Oct 14;147(2):396-408.
Key words: release factor 3, translation, E. coli
PMID: 22000017
http://www.sciencedirect.com/science/article/pii/S009286741101066X

1. Cai Y, Boeke JD. Genome remodeling. Nat Biotechnol. 2011 Sep 8;29(9):807-8.
Key words: genome, remodelin
http://www.nature.com/nbt/journal/v29/n9/full/nbt.1964.html
PMID: 21904325

2. Ortiz-Meoz RF, Green R. Helix 69 is key for uniformity during substrate selection on the ribosome. J Biol Chem. 2011 Jul 22;286(29):25604-10.
Key words: Helix 69, substrate, ribosome
http://www.jbc.org/content/286/29/25604.long
PMID: 21622559

3. Matsuoka RL, Chivatakarn O, Badea TC, Samuels IS, Cahill H, Katayama K, Kumar SR, Suto F, Chédotal A, Peachey NS, Nathans J, Yoshida Y, Giger RJ, Kolodkin AL. Class 5 transmembrane semaphorins control selective Mammalian retinal lamination and function. Neuron. 2011 Aug 11;71(3):460-73.
Key words: semaphorins, retinal lamination
http://www.sciencedirect.com/science/article/pii/S0896627311005137
PMID: 21835343

4. Cahill H, Rattner A, Nathans J. Preclinical assessment of CNS drug action using eye movements in mice. J Clin Invest. 2011 Sep 1;121(9):3528-41. doi: 10.1172/JCI45557. Epub 2011 Aug 8.
Key words: central nervous system, drug action, eye movement, mice
http://www.jci.org/articles/view/45557
PMID:21821912

5. Voronina E, Seydoux G, Sassone-Corsi P, Nagamori I. RNA granules in germ cells. Cold Spring Harb Perspect Biol. 2011 Jul 18.
http://cshperspectives.cshlp.org/content/early/2011/07/18/cshperspect.a002774.long
PMID: 21768607

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