 |
Molecular Biology and Genetics Archives 1. Ma Y, Greider
CW. Kinase-independent functions of TEL1 in telomere maintenance. Mol
Cell Biol. 2009 Sep;29(18):5193-202. 1. An W,
Davis ES, Thompson TL, O'Donnell KA, Lee CY, Boeke JD. Plug and play
modular strategies for synthetic retrotransposons. Methods. 2009 May
28. [Epub ahead of print] 2. Ivics
Z, Li MA, Mátés L, Boeke JD, Nagy A, Bradley A, Izsvák
Z. Transposon-mediated genome manipulation in vertebrates. Nat Methods.
2009 Jun;6(6):415-22. 1. Jacobs
GH, Nathans J. The evolution of primate color vision.: A database for
histone mutations and their phenotypes. Sci Am. 2009 Apr;300(4):56-63. 2. Lin YY, Lu JY, Zhang J, Walter W, Dang
W, Wan J, Tao SC, Qian J, Zhao Y, Boeke JD, Berger SL, Zhu H. Protein
acetylation microarray reveals that NuA4 controls key metabolic target
regulating gluconeogenesis. Cell. 2009 Mar 20;136(6):1073-84. 1. Huang
H, Maertens AM, Hyland EM, Dai J, Norris A, Boeke JD, Bader JS. HistoneHits:
A database for histone mutations and their phenotypes. Genome Res. 2009
Feb 13 2. Morrish
TA, Greider CW. Short telomeres initiate telomere recombination in primary
and tumor cells. PLoS Genet. 2009 Jan;5(1):e1000357. Epub 2009 Jan 30.
3. Zaher
HS, Green R. Fidelity at the molecular level: lessons from protein synthesis.
Cell. 2009 Feb 20;136(4):746-62. 4. Zaher
HS, Green R. Quality control by the ribosome following peptide bond
formation. Nature. 2009 Jan 8;457(7226):161-6. Epub 2008 Dec 17. 1. Rotolo T, Smallwood
PM, Williams J, Nathans J. Genetically-directed, cell type-specific sparse
labeling for the analysis of neuronal morphology. : PLoS ONE. 2008;3(12):e4099.
Epub 2008 Dec 31.
Key words: neuronal development, sparse labeling http://www.ncbi.nlm.nih.gov/pubmed/19116659?ordinalpos=1&itool=EntrezSystem2. PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel. Pubmed_RVDocSum
1. Corden
JL. Yeast Pol II start-site selection: the long and the short of it. EMBO
Rep. 2008 Nov; 9(11):1084-6. 2. Dymond
J, Scheifele L, Richardson S, Lee P, Chandrasegaran S, Bader J, Boeke
J. Teaching synthetic biology, bioinformatics, and engineering to undergraduates:
the interdisciplinary build-a-genome course. Genetics. 2008 Nov 17. [Epub
ahead of print] 3. Nakamura
A, Seydoux G. Less is more: specification of the germline by transcriptional
repression. Development. 2008 Dec;135(23):3817-27. 1. Dai J,
Hyland EM, Yuan DS, Huang H, Bader JS, Boeke JD. Probing nucleosome function:
a highly versatile library of synthetic histone H3 and H4 mutants. Cell.
2008 Sep 19;134(6):1066-78. 2. Qi Y, Suhail
Y, Lin YY, Boeke JD, Bader JS. Finding friends and enemies in an enemies-only
network: A graph diffusion kernel for predicting novel genetic interactions
and co-complex membership from yeast genetic interactions. Genome Res.
2008 Oct 2. [Epub ahead of print] 3. Liu C,
Nathans J. An essential role for frizzled 5 in mammalian ocular development.
Development. 2008 Nov;135(21):3567-76. 4. Rattner
A, Toulabi L, Williams J, Yu H, Nathans J. The genomic response of the
retinal pigment epithelium to light damage and retinal detachment. J Neurosci.
2008 Sep 24;28(39):9880-9. 1. Celic I,
Verreault A, Boeke JD. Histone H3 K56 hyperacetylation perturbs replisomes
and causes DNA damange. Genetics 2008 Aug; 179:1769-84. 2. Lin YY,
Qi Y, Lu JY, Pan X, Yuan DS, Zhao Y, Bader JS, Boeke JD. A comprehensive
synthetic genetic interaction network governing yeast histone acetylation
and deacetylation. Genes Dev. 2008 Aug 1;22(15):2062-74. 3. O'Donnell
KA, Burns KH, Boeke JD. A descent into the nuage: the maelstrom of transposon
control. Dev Cell. 2008 Aug;15(2):179-81. 4. Han Y,
Lin YB, An W, Xu J, Yang HC, O'Connell K, Dordai D, Boeke JD, Siliciano
JD, Siliciano RF. Orientation-dependent regulation of integrated HIV-1
expression by host gene transcriptional readthrough. Cell Host Microbe.
2008 Aug 14;4(2):134-46. 5. Scheifele
LZ, Boeke JD. From the shards of a shattered genome, diversity. Proc Natl
Acad Sci U S A. 2008 Aug 19;105(33):11593-4. 1. An W, Han
JS, Schrum CM, Maitra A, Koentgen F, Boeke JD. Conditional activation
of a single-copy L1 transgene in mice by Cre. Genesis 2008 Jul; 46(7):373-83. 2. Wheelan
SJ, Martinez Murillo F, Boeke JD. The incredible shrinking world of DNA
microarrays. Mol Biosyst. 2008 Jul; 4(7):726-32. 1. Cahill
H, Nathans J. The optokinetic reflex as a tool for quantitative analyses
of nervous system function in mice: application to genetic and drug-induced
variation. PLoS ONE 2008 Apr 30;3(4):e2055. 2. Liu C,
Wang Y, Smallwood PM, Nathans J. An essential role for Frizzled5 in neuronal
survival in the parafascicular nucleus of the thalamus. J Neurosci. 2008
May 28;28(22):5641-53. 1. Ben-Aroya
S, Coombes C, Kwok T, O'Donnell KA, Boeke JD, Hieter P. Toward a comprehensive
temperture-sensitive mutant respository of the essential genes of Saccharomyces
cerevisiae. Mol Cell. 2008 Apr 25; 30(2):248-58. 2. Li F, Dong
J, Pan X, Oum JH, Boeke JD, Lee SE. Microarray-based genetic screen defines
SAW1, a gene required for Rad1/Rad10-dependent processing of recombination
inermediates. Mol Cell. 2008 May 9; 30(3):325-35 3. Mitra R.
Fain-Thornton J, Craig NL. piggyBac can bypass DNA synthesis during cut
and paste transposition. EMBO J 2008 27(7):1097-1109. 4. Pan X,
Yuan D, Ye P, Bader J, Boeke JD. Response to Dr. Stephen Cooper's "On
the use of metaphor to understand, explain, or rationalize redundant genes
in yeast". FEMS Yeast Res. 2008 May; 8(3):349-350. 5. Urban S,
Shi Y. Core principles of intramembrane proteolysis: comparison of rhomboid
and site-2 family proteases. Curr Opin Struct Biol. 2008 Apr 25. [Epub
ahead of print] doi:10.1016/j.sbi.2008.03.005 1. O'Donnell KA,
Boeke JD. Domesticated DNA transposon proteins mediate retrotransposon
control. Cell Res. 2008 Mar; 18(3):331-3
Key words: DNA transposon proteins, retrotransposition, gene structure, gene expression http://www.ncbi.nlm.nih.gov/pubmed/18311163?ordinalpos=1&itool=EntrezSystem2. PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 1. Burns,
KH, Boeke JD. Great exaptations. J Biol 2008 Feb 15; 7(2):5. 2. Ghosh D, Seydoux G. Inhibition of transcription
by the Caenorhabditis elegans germline protein PIE-1: genetic evidence
for distinct mechanisms targeting initiation and elongation. Genetics.
2008 Jan;178(1):235-43. 3. Huang Z, Sucgang RS, Lin YY, Shi X, Boeke
JD, Pan X. Plasmid-chromosome shuffling for non-deletion alleles in yeast.
Nat Methods 2008 Feb; 5(2):167-9. 4. Marton
HA, Desiderio S. The Paf1 complex promotes displacement of histones upon
rapid induction of transcription by RNA polymerase II. BMC Mol Biol. 2008
Jan 14;9(1):4 1. Chen J,
Nathans J. Estrogen-related receptor beta/NR3B2 controls epithelial cell
fate and endolymph production by the stria vascularis. Dev Cell. 2007
Sep;13(3):325-37. 2. Sulek M, Yarrington R, McGibbon G, Boeke JD,
Junop M. A critical role for the C-terminus of Nej1 protein in Lif1p assocation,
DNA binding and non-homologous end-joining. DNA Repair (Amst). 2007 Dec
1;6(12):1805-18. 1. Dong J,
Feldman G, Huang J, Wu S, Zhang N, Comerford SA, Gayyed MF, Anders RA,
Maitra A, Pan D. Elucidation of a universal size-control mechanism in
Drosophila and mammals. Cell 2007 Sept 21; 130: 1120-1133. 2. Urban S. Rhomboid intramembrane serine proteases.
In: Proteases in Disease Volume 6: Intramembrane-Cleaving Proteases, Pages
51-78 (eds. Hooper, N.M. & Lendeckel, U.), Springer Press, New York,
2007. 3. Zurita-Martinez SA, Puria R, Pan X, Boeke
JD, Cardenas ME. Efficient Tor signaling requires a functional class C
Vps protein complex in Saccharomyces cerevisiae. Genetics 2007 Aug; 176(4):2139-2150.
1. Chen J,
Nathans J. Genetic ablation of cone photoreceptors eliminates retinal
folds in the retinal degeneration 7 (rd7) mouse. Invest Ophthalmol Vis
Sci. 2007 Jun;48(6):2799-805. 2. Zurita-Martinez SA, Puria R, Pan X, Boeke JD,
Cardenas ME. Efficient Tor signaling requires a functional Class C Vps
protein complex in saccharomyces cerevisiae. Genetics 2007 Aug;176(4):2139-50. 1. Stitzel ML, Seydoux
G. Regulation of the oocyte-to-zygote transition. Science. 2007 Apr 20;316(5823):407-8.
2. Yarrington RM, Chen J, Bolton EC, Boeke
JD. Mn2+ suppressor mutations and biochemical communication between Ty1
reverse transcriptase and RNase H domains. J Virol 2007 May 30; [Epub
ahead of print] 1. Baker RP, Young K, Feng L, Shi Y, Urban S. Enzymatic
analysis of a rhomboid intramembrane protease implicates transmembrane
helix 5 as the lateral substrate gate. Proc Natl Acad Sci U S A. 2007
May 15;104(20):8257-62. Epub 2007 Apr 26. 2. Chen EH, Grote E, Mohler W, Vignery A. Cell-cell
fusion. FEBS Lett 2007 May 29;581(11):2181-93. 3. Kim S, Shilagardi K, Zhang S, Hong SN, Sens KL,
Bo J, Gonzalez GA, Chen EH. A critical function for the actin cytoskeleton
in targeted exocytosis of prefusion vesicles during myoblast fusion. Dev.
Cell 2007;12, 571-86. 4. O'Donnell KA, Boeke JD. Mighty Piwis defend the
germline against genome intruders. Cell 2007; 129:37-44. 5. Pan D. Hippo signaling in organ size control.
Genes Dev. 2007; 21: 886-897. 6. Yin F, Pan D. Fat flies expanded the hippo pathway:
a matter of size control. Sci STKE. 2007 Apr 3;2007(380):pe12. 1. Pan X, Yuan DS, Ooi SL, Wang X, Sookhai-Mahadeo
S, Meluh P, Boeke JD. dSLAM analysis of genome-wide genetic interactions
in Saccharomyces cerevisiae. Methods Feb; 41(2):206-21. 2. Jacobs GH, Williams GA, Cahill H, Nathans J.
Emergence of novel color vision in mice engineered to express a human
cone photopigment. Science 2007 Mar 23; 315(5819): 1723-7125. 3. Wang Y, Nathans J. Tissue/planar cell polarity
in vertebrates: new insights and new questions. 1. An W, Han JS, Wheelan
SJ, Davis ES, Coombes CE, Ye P, Triplett C, Boeke JD. Active retrotransposition
by a synthetic L1 element in mice. Proc Natl Acad Sci U S A. 2006 Dec
5;103(49):18662-7 2. Smallwood PM, Williams J, Xu Q, Leahy DJ, Nathans
J. Mutational analysis of Norrin-frizzled4 recognition. J Biol Chem. 2007
Feb 9;282(6):4057-68. 3. Wang Y, Badea T, Nathans J. Order from
disorder: Self-organization in mammalian hair patterning. PNAS 2006 Dec;
103:52 1. An W, Han JS, Wheelan SJ, Davis ES, Coombes CE,
Ye P, Triplett C, Boeke JD. Active retrotransposition by a synthetic L1
element in mice. Proc Natl Acad Sci U S A. 2006 Dec 5;103(49):18662-7. 2. Feldser D, Strong M, Greider CW. Ataxia telangiectasia
mutated (Atm) is not required for telomerase-mediated elongation of short
telomeres. Proc. Natl. Acad. Sci. U.S.A. (2006) 103: 2249-2251. 3. Frank CJ, Hyde M., Greider CW. Regulation of
telomere elongation by the cyclin-dependent kinase CDK1. Mol Cell, (2006)
24, 423-432. 4. Smallwood PM, Williams J, Xu Q, Leahy DJ, Nathans
J. Mutational analysis of Norrin-frizzled4 recognition. J Biol Chem. 2006
Dec 6; [Epub ahead of print] 5. Wang Y, Badea T, Nathans J. Order from disorder:
Self-organization in mammalian hair patterning. PNAS 2006 Dec 26;103(52):19800-5.
1. Urban S. Rhomboid
proteins: conserved membrane proteases with divergent biological functions.
Genes Dev. 2006 Nov 15;20(22):3054-68. 2. Wu Z, Yan N, Feng L, Oberstein A, Yan H,
Baker RP, Gu L, Jeffrey PD, Urban S, Shi Y. Structural analysis of a rhomboid
family intramembrane protease reveals a gating mechanism for substrate
entry. Nature Structural and Molecular Biology 2006 Dec;13(12):1084-91. 1. Baker RP, Wijetilaka R., Urban S. Two Plasmodium
rhomboid proteases preferentially cleave different adhesins implicated
in all invasive stages of malaria. PLoS Pathogens
2006; 2(8): e113. 2. Caraveo G, van Rossum DB, Patterson RL, Snyder
SH, Desiderio S. Action of TFII-I outside the nucleus as an inhibitor
of agonist-induced calcium entry. Science. 2006 Oct 6;314(5796):122-5.
3. Frank CJ, Hyde M, Greider CW. Regulation of telomere
elongation by the cyclin-dependent kinase CDK1. Molecular Cell 2006; 24(3)
423-432. 4. Rattner A, Nathans J. Macular degeneration: recent
advances and therapeutic opportunities. Nat Rev Neurosci. 2006 Nov;7(11):860-72.
Epub 2006 Oct 11. 5. Wheelan SJ, Martinez-Murillo F, Irizarry RA,
Boeke JD. Stacking the deck: double-tiled DNA microarrays. Nat. Methods
2006 Nov; 3(11):903-907. 1. Arigo JT, Eyler DE,
Carroll KL and Corden JL. Termination of cryptic unstable transcripts
is directed by yeast RNA-binding proteins Nrd1 and Nab3. Mol Cell. 2006
Sep 15;23(6):841-51. 2. Blackburn EH, Greider CW, Szostak JW. Telomeres
and telomerase: the path from maize, Tetrahymena and yeast to human cancer
and aging. Nat Med. 2006 Oct;12(10):1133-8. 3. Echeverri CJ, Beachy PA, Baum B, Boutros M, Buchholz
F, Chanda SK, Downward J, Ellenberg J, Fraser AG, Hacohen N, Hahn WC,
Jackson AL, Kiger A, Linsley PS, Lum L, Ma Y, Mathey-Prevot B, Root DE,
Sabatini DM, Taipale J, Perrimon N, Bernards R. Minimizing the risk of
reporting false positives in large-scale RNAi screens. Nature Methods
2006 October 3; 777-779. 4. Fry CJ, Norris A, Cosgrove M, Boeke JD, Peterson
CL. The LRS and SIN domains: Two structurally equivalent but functionally
distinct nucleosomal surfaces required for transcriptional silencing.
Mol Cell Biol. 2006 Oct 2; [Epub ahead of print] 5. Gallo CM, Seydoux G. Toti "potent"
repressors. Bioessays. 2006 Sep;28(9):865-7. 6. Ma Y, Creanga A, Lum L, Beachy PA. Prevalence
of off-target effects in Drosophila RNA interference screens. Nature 2006;
443, 359-363. 1. Dorner S, Lum L, Kim M, Paro R, Beachy PA, Green
R. A genomewide screen for components of the RNAi pathway in Drosophila
cultured cells. Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):11880-5.
Epub 2006 Aug 1. 1. Celic I, Masumoto H, Griffith WP, Meluh P, Cotter
RJ, Boeke JD, Verreault A. The sirtuins Hst3
and Hst4 preserve genome integrity by controlling histone H3 lysine 56
deacetylation. 2006; [Epub ahead of print] 2. Chen J, Rattner A, Nathans J. Effects of L1 retrotransposon
insertion on transcript processing, localization and accumulation: lessons
from the retinal degeneration 7 mouse and implications for the genomic
ecology of L1 elements. Hum Mol Genet. 2006 Jul 1;15(13):2146-56. Epub
2006 May 24. 3. Suave AA, Wolberger C, Schramm VL, Boeke JD.
The biochemistry of sirtuins. Annu Rev Biochem. 2006; 75: 435-465. 4. Tsunenari T, Nathans J, Yau K-W. Ca2+-activated
Cl- current from human bestrophin-4 in excised membrane patches. J Gen
Physiol. 2006 Jun;127(6):749-54. Epub 2006 May 15. 1. McKenzie GJ, Craig NL. Fast, easy
and efficient: site-specific insertion of transgenes into Enterobacterial
chromosomes using Tn7without need for selection of the insertion event.
BMC Microbiol. 2006 Apr 28;6(1):39 [Epub ahead of print]. 2. Arigo JT, Carroll KL, Ames JM, Corden JL Regulation
of yeast NRD1 expression by premature transcription termination. Mol Cell.
2006 Mar 3;21(5):641-51. 3. D'Agostino I, Merritt C, Chen PL, Seydoux G,
Subramaniam K. Translational repression restricts expression of the C.
elegans Nanos homolog NOS-2 to the embryonic germline. Dev Biol. 2006
Apr 1;292(1):244-52. 1. Richardson SM, Wheelan SJ, Yarrington RM, Boeke
JD. GeneDesign: Rapid, automated design of multikilobase synthetic genes.
Genome Res 2006 Apr; 16(4):550-6. 1. Rattner A, Nathans J. An evolutionary perspective
on the photoreceptor damage response . Am J
Ophthalmol 2006 Mar;141(3):558-562. 2. Arigo JT, Carroll KL, Ames JM, Corden JL. Regulation
of yeast NRD1 expression by premature transcription termination. Mol Cell.
2006 Mar 3;21(5):641-51. 3. D'Agostino I, Merritt C, Chen PL, Seydoux G,
Subramaniam K. Translational repression restricts expression of the C.
elegans Nanos homolog NOS-2 to the embryonic germline. Dev Biol. 2006
Feb 22; [Epub ahead of print] 4. Dorner S, Brunelle JL, Sharma D, Green R. The
hybrid state of tRNA binding is an authentic translation elongation intermediate.
Nat Struct Mol Biol. 2006 Mar;13(3):234-41. Epub 2006 Feb 26. 5. Gandhi TK, Zhong J, Mathivanan S, Karthick L,
Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nargaraju S, Periaswamy B,
Mishra G, Nandakumar K, Shen B, Deshpande N, Nayak R, Sarker M, Boeke
JD, Parmigiani G, Schultz J, Bader JS, Pandey A. Analysis of the human
protein interactome and comparison with yeast, worm and fly interaction
datasets. Nat Genet. 6. Pan X, Xe P, Yuan DS, Wang X, Bader JS, Boeke
JD. A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell.
2006 Mar 10;124(5):1069-81. Epub 2006 Feb 16. 7. Richardson SM, Wheelan SJ, Yarrington RM, Boeke
JD. GeneDesign: rapid, automated design of multikilobase synthetic genes.
Genome Res. 2006 Feb 15; [Epub ahead of print] 8. Wang Y, Guo N, Nathans J. The role of Frizzled3
and Frizzled6 in neural tube closure and in the planar polarity of inner-ear
sensory hair cells. J Neurosci. 2006 Feb 22;26(8):2147-56. 9. Seydoux G. The 2006 Genetics Society of America
medal. Genetics. 2006 Feb;172(2):721-2. 1. Feldser D, Strong
MA, Greider CW. Ataxia telangiectasia mutated (Atm) is not required for
telomerase-mediated elongation of short telomeres. Proc Natl Acad Sci
U S A. 2006 Feb 7; [Epub ahead of print] 2. Valdivia RH, Cormack BP, Falkow S. The uses of
green fluorescent protein in prokaryotes. Methods Biochem Anal. 2006;47:163-78. 3. Hao Y, Boyd Lynn, Seydoux G. Stabilization
of cell polarity by the C. elegans RING protein PAR-2. Developmental Cell
2006; Feb;10(2):199-208. 1. Brunelle JL, Youngman EM, Sharma D, Green R.
The interaction between C75 of tRNA and the A loop of the ribosome stimulates
peptidyl transferase activity. RNA. 2006 Jan;12(1):33-9. 2. Stitzel ML, Pellettieri J, Seydoux G. The C.
elegans DYRK kinase MBK-2 marks oocyte proteins for degradation in response
to meiotic maturation. Curr Biol. 2006 Jan 10;16(1):56-62. Epub 2005 Dec
15. 3. Stultz BG, Jackson DG, Mortin MA, Yang X, Beachy
PA, Hursh DA. Transcriptional activation by extradenticle in the Drosophila
visceral mesoderm. Dev Biol. 2006 Jan 2; [Epub ahead of print] 4. Wang Y, Zhang J, Mori S, Nathans J.Axonal
growth and guidance defects in Frizzled3 knock-out mice: a comparison
of diffusion tensor magnetic resonance imaging, neurofilament staining,
and genetically directed cell labeling. J Neurosci. 2006 Jan 11;26(2):355-64
1. Ooi SL, Pan X, Peyser BD, Meluh PB, Yuan
DS, Irizarry RA, Bader JS, Spencer FA, Boeke JD. Global synthetic-lethality
analysis and yeast functional profiling. Trends in Genetics 2005 Nov 22;
[Epub ahead of print] 2. Hyland EM, Cosgrove MS, Molina H, Wang
D, Pandey A, Cottee RJ, Boeke JD. Insights into the role of histone H3
and histone H4 core modifiable residues in Saccharomyces cerevisiae. Mol
Cell Biol. 2005; 25:10060-70. 1. Armanios M, Chen JL, Chang YP, Brodsky RA, Hawkins
A, Griffin CA, Eshleman JR, Cohen AR, Chakravarti A, Hamosh A, Greider
CW. Haploinsufficiency of telomerase reverse transcriptase leads to anticipation
in autosomal dominant dyskeratosis congenita.
Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15960-4. Epub 2005 Oct 24.
2. Hyland EM, Cosgrove MS, Molina H, Wang D, Pandey
A, Cottee RJ, Boeke JD. Insights into the role of histone H3 and histone
H4 core modifiable residues in Saccharomyces cerevisiae. Mol Cell Biol.
2005 Nov;25(22):10060-70. 3. Maity T, Fuse N, Beachy PA. Molecular mechanisms
of Sonic hedgehog mutant effects in holoprosencephaly. Proc Natl Acad
Sci U S A. 2005 Nov 10 1. Peyser BD, Irizarry RA, Tiffany CW, Chen O, Yuan
DS, Boeke JD, Spencer FA. Improved statistical analysis of budding yeast
TAG microarrays revealed by defined spike-in pools. 2. Jackson TA, Taylor
HE, Sharma D, Desiderio S, Danoff SK. Vascular endothelial growth factor
receptor-2: counter-regulation by the transcription factors, TFII-I and
TFII-IRD1. 3. Segall AM, Craig NL. New wrinkles and folds
in site-specific recombination. 4. Wheelan SJ, Aizawa Y, Han JS, Boeke JD. Gene-breaking:
a new paradigm for human retrotransposon-mediated gene evolution. Genome
Res. 2005 Aug;15(8):1073-8. Epub 2005 Jul 15. Key words: transcription, polyadenylation, splicing, L1 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt= Abstract&list_uids=16015595 2. Hickman AB, Perez ZN, Zhou L, Musingarimi P,
Ghirlando R, Hinshaw JE, Craig NL, Dyda F. Molecular architecture of a
eukaryotic DNA transposase. Nat Struct Mol Biol. 2005 Aug;12(8):715-21.
Epub 2005 Jul 24. 3. Huang J, Wu S, Barrera J, Matthews K, Pan D.
The Hippo signaling pathway coordinately regulates cell proliferation
and apoptosis by inactivating Yorkie, the Drosophila Homolog of YAP. Cell.
2005 Aug 12;122(3):421-34. 4. Jiang H, Chang FC, Ross AE, Lee J, Nakayama K,
Nakayama K, Desiderio S. Ubiquitylation of RAG-2 by Skp2-SCF links destruction
of the V(D)J recombinase to the cell cycle. Mol Cell. 2005 Jun 10;18(6):699-709. 5. Kaur R, Domergue R, Zupancic ML, Cormack BP.
A yeast by any other name: Candida glabrata and its interaction with the
host. Curr Opin Microbiol. 2005 Aug;8(4):378-84. 6. Qi L, Strong MA, Karim BO, Huso DL, Greider CW.
Telomere fusion to chromosome breaks reduces oncogenic translocations
and tumour formation. Nat Cell Biol. 2005 Jul;7(7):706-11. Epub 2005 Jun
19. 7. Segall AM, Craig NL. New wrinkles and folds in
site-specific recombination. Mol Cell. 2005 Aug 19;19(4):433-5. 8. Wheelan SJ, Aizawa Y, Han JS, Boeke JD. Gene-breaking:
a new paradigm for human retrotransposon-mediated gene evolution. Genome
Res. 2005 Aug;15(8):1073-8. Epub 2005 Jul 15. 9. Youngman EM, Green R. Affinity purification of
in vivo-assembled ribosomes for in vitro biochemical analysis. Methods.
2005 Jul;36(3):305-12. 10. Yuan DS, Pan X, Ooi SL, Peyser BD, Spencer FA,
Irizarry RA, Boeke JD. Improved microarray methods for profiling the Yeast
Knockout strain collection. Nucleic Acids Res 2005 Jul 1;33(12):e103. 1. Bachman N, Gelbart ME, Tsukiyama T, Boeke JD.
TFIIIB subunit Bdp1p is required for periodic integration of the Ty1 retrotransposon
and targeting of Isw2p to S. cerevisiae tDNAs. Genes Dev. 2005 Apr 15;19(8):955-64. 2. Chen EH, Olson EN. Unveiling the mechanisms of
cell-cell fusion. Science. 2005 Apr 15;308(5720):369-73. Review. 3. Chen JL, Greider CW. Functional analysis of the
pseudoknot structure in human telomerase RNA. Proc Natl Acad Sci U S A.
2005 Apr 22; [Epub ahead of print] 4. Cukras AR, Green R. Multiple effects of s13 in
modulating the strength of intersubunit interactions in the ribosome during
translation. J Mol Biol. 2005 May 27;349(1):47-59. Epub 2005 Apr 12. 5. Domergue R, Castano I, De Las Penas A, Zupancic
M, Lockatell V, Hebel JR, Johnson D, Cormack BP. Nicotinic acid limitation
regulates silencing of Candida adhesins during UTI. Science. 2005 May
6;308(5723):866-70. Epub 2005 Mar 17. 6. Gelbart ME, Bachman N, Delrow J, Boeke JD, Tsukiyama
T. Genome-wide identification of Isw2 chromatin-remodeling targets by
localization of a catalytically inactive mutant. Genes Dev. 2005 Apr 15;19(8):942-54. 7. Rattner A, Nathans J. The genomic response to
retinal disease and injury: evidence for endothelin signaling from photoreceptors
to glia. J Neurosci. 2005 May 4;25(18):4540-9. 1. Bolton EC, Coombes C, Eby Y, Cardell M, Boeke
JD. Identification and characterization of critical cis-acting sequences
within the yeast Ty1 retrotransposon. RNA. 2005 Mar;11(3):308-22. 2. Brannon AR, Maresca JA, Boeke JD, Basrai MA,
McBride AA. Reconstitution of papillomavirus E2-mediated plasmid maintenance
in Saccharomyces cerevisiae by the Brd4 bromodomain protein. Proc Natl
Acad Sci U S A. 2005 Feb 22;102(8):2998-3003. 3. Coombes CE, Boeke JD. An evaluation of detection
methods for large lariat RNAs.RNA. 2005 Mar;11(3):323-31. 1. Castano I, Pan SJ, Zupancic M, Hennequin C, Dujon
B, Cormack BP. Telomere length control and transcriptional regulation
of subtelomeric adhesins in Candida glabrata.
Mol Microbiol. 2005 Feb;55(4):1246-1258. 2. Chen J, Rattner A, Nathans J. The rod photoreceptor-specific
nuclear receptor Nr2e3 represses transcription of multiple cone-specific
genes. J Neurosci. 2005 Jan 5;25(1):118-29. 3. Chen W, Ren XR, Nelson CD, Barak LS, Chen JK,
Beachy PA, de Sauvage F, Lefkowitz RJ. Activity-dependent internalization
of smoothened mediated by beta-arrestin 2 and GRK2. Science. 2004 Dec
24;306(5705):2257-60. 4. Kuduvalli PN, Mitra R, Craig NL. Site-specific
Tn7 transposition into the human genome. Nucleic Acids Res. 2005 Feb 08;33(3):857-63. 5. Zhang C, Williams EH, Guo Y, Lum L, Beachy PA.
Extensive phosphorylation of Smoothened in Hedgehog pathway activation.
Proc Natl Acad Sci U S A. 2004 Dec 28;101(52):17900-7. 6. Zhou L, Mitra R, Atkinson PW, Hickman AB, Dyda
F, Craig NL. Transposition of hAT elements links transposable elements
and V(D)J recombination. Nature. 2004 Dec 23;432(7020):995-1001. 1. Badea TC, Nathans
J. Quantitative analysis of neuronal morphologies in the mouse retina
visualized by using a genetically directed reporter. J Comp Neurol. 2004
Dec 20;480(4):331-51. 2. Beachy PA, Karhadkar SS, Berman DM. Tissue repair
and stem cell renewal in carcinogenesis. Nature. 2004 Nov 18;432(7015):324-31. 3. Cochella L, Green R. Wobble during decoding:
more than third-position promiscuity. Nat Struct Mol Biol. 2004 Dec;11(12):1160-2. 4. Cosgrove MS, Boeke JD, Wolberger C. Regulated
nucleosome mobility and the histone code. Nat Struct Mol Biol. 2004 Nov;11(11):1037-43.
5. Ferguson SB, Anderson ES, Harshaw RB, Thate T,
Craig NL, Nelson HC. Protein kinase A regulates constitutive expression
of small heat shock genes in an Msn2p/4p-independent and Hsf1p-dependent
manner in Saccharomyces cerevisiae. Genetics. 2004 Nov 15; [Epub ahead
of print] 6. Maxwell PH, Coombes C, Kenny AE, Lawler JF, Boeke
JD, Curcio MJ. Ty1 mobilizes subtelomeric Y' elements in telomerase-negative
Saccharomyces cerevisiae survivors. Mol Cell Biol. 2004 Nov;24(22):9887-98. 7. Pan X, Yuan DS, Xiang D, Wang X, Sookhai-Mahadeo
S, Bader JS, Hieter P, Spencer F, Boeke JD. A robust toolkit for functional
profiling of the yeast genome. Mol Cell. 2004 Nov 5;16(3):487-96. 1. Bachman N, Eby Y, Boeke JD. Local definition
of Ty1 target preference by long terminal repeats and clustered tRNA genes.
Genome Res. 2004 Jul;14(7):1232-47. 2. Carroll KL, Pradhan DA, Granek JA, Clarke ND,
Corden JL. Identification of cis elements directing termination of yeast
nonpolyadenylated snoRNA transcripts. Mol Cell Biol. 2004 Jul;24(14):6241-52. 3. DeRenzo C, Seydoux G. A clean start: degradation
of maternal proteins at the oocyte-to-embryo transition. Trends Cell Biol.
2004 Aug;14(8):420-6. 4. Hao LY, Greider CW. Genomic instability in both
wild-type and telomerase null MEFs. Chromosoma. 2004 Sep;113(2):62-8. 5. Hao LY, Strong MA, Greider CW. Phosphorylation
of H2AX at short telomeres in T cells and fibroblasts. J Biol Chem. 2004
Aug 17 [Epub ahead of print] 6. Karhadkar SS, Bova SG, Abdallah N, Dhara S, Gardner
D, Maitra A, Isaacs JT, Berman DM, Beachy PA. Hedgehog signalling in prostate
regeneration, neoplasia and metastasis. Nature. 2004 Sep 12 [Epub ahead
of print] 7. Kulaga HM, Leitch CC, Eichers ER, Badano JL,
Lesemann A, Hoskins BE, Lupski JR, Beales PL, Reed RR, Katsanis N. Loss
of BBS proteins causes anosmia in humans and defects in olfactory cilia
structure and function in the mouse. Nat Genet. 2004 Sep;36(9):994-8.
Epub 2004 Aug 22 8. Rattner A, Chen J, Nathans J. Proteolytic shedding
of the extracellular domain of photoreceptor cadherin: implications for
outer segment assembly. J Biol Chem. 2004 Jul 28 [Epub ahead of print] 9. Ronning DR, Li Y, Perez ZN, Ross PD, Hickman
AB, Craig NL, Dyda F. The carboxy-terminal portion of TnsC activates the
Tn7 transposase through a specific interaction with TnsA. EMBO J. 2004
Aug 4;23(15):2972-81. 10. Seydoux G. Surfing the actomyosin wave; polarization
of the C. elegans zygote. Dev Cell. 2004 Sep;7(3):285-6. Key words: olfaction, spontaneous activity, sensory map http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db= pubmed&dopt=Abstract&list_uids=15157412 2. Guo N, Hawkins C,
Nathans J. Frizzled6 controls hair patterning in mice. Proc Natl Acad
Sci U S A. 2004 May 28 [Epub ahead of print] 3. Han JS, Boeke JD.
A highly active synthetic mammalian retrotransposon. Nature. 2004 May
20;429(6989):314-8. 4. Han JS, Szak ST, Boeke
JD. Transcriptional disruption by the L1 retrotransposon and implications
for mammalian transcriptomes. Nature. 2004 May 20;429(6989):268-74. 5. Kaur R, Castano I,
Cormack BP. Functional genomic analysis of fluconazole susceptibility
in the pathogenic yeast Candida glabrata: roles of calcium signaling and
mitochondria. Antimicrob Agents Chemother. 2004 May;48(5):1600-13. 6. Mann RK, Beachy PA. Novel lipid modifications
of secreted protein signals. Annu Rev Biochem. 2004;73:891-923. 7. Youngman EM, Brunelle JL, Kochaniak AB, Green
R. The active site of the ribosome is composed of two layers of conserved
nucleotides with distinct roles in peptide bond formation and peptide
release. Cell. 2004 May 28;117(5):589-99. Key words: rhodopsin promotor, UV cone expression http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db= pubmed&dopt=Abstract&list_uids=14966125 1. Avalos JL, Boeke JD, Wolberger C. Structural
basis for the mechanism and regulation of Sir2 enzymes. Mol Cell. 2004
Mar 12;13(5):639-48. 2. Berman DM, Desai N, Wang X, Karhadkar SS, Reynon
M, Abate-Shen C, Beachy PA, Shen MM. Roles for Hedgehog signaling in androgen
production and prostate ductal morphogenesis. Dev Biol. 2004 Mar 15;267(2):387-98. 3. Chen JL, Greider CW. Telomerase RNA structure
and function: implications for dyskeratosis congenita. Trends Biochem
Sci. 2004 Apr;29(4):183-92. 4. Cochella L, Green R. Isolation of antibiotic
resistance mutations in the rRNA by using an in vitro selection system.
Proc Natl Acad Sci U S A. 2004 Mar 16;101(11):3786-91. Epub 2004 Mar 04. 5. Cormack B. Can you adhere me now? Good. Cell.
2004 Feb 6;116(3):353-4. Review. 6. Danoff SK, Taylor HE, Blackshaw S, Desiderio
S. TFII-I, a candidate gene for Williams syndrome cognitive profile: parallels
between regional expression in mouse brain and human phenotype. Neuroscience.
2004;123(4):931-8. 7. Luo W, Marsh-Armstrong N, Rattner A, Nathans
J. An outer segment localization signal at the C terminus of the photoreceptor-specific
retinol dehydrogenase. J Neurosci. 2004 Mar 17;24(11):2623-32. 8. Luo W, Williams J, Smallwood PM, Touchman JW,
Roman LM, Nathans J. Proximal and distal sequences control UV cone pigment
gene expression in transgenic zebrafish. J Biol Chem. 2004 Feb 13 [Epub
ahead of print] 9. Reed RR. After the holy grail: establishing a
molecular basis for Mammalian olfaction. Cell. 2004 Jan 23;116(2):329-36.
Review. 10. Starai VJ, Takahashi H, Boeke JD, Escalante-Semerena
JC. A link between transcription and intermediary metabolism: a role for
Sir2 in the control of acetyl-coenzyme A synthetase. Curr Opin Microbiol.
2004 Apr;7(2):115-9. 11. Wang SS, Lewcock JW, Feinstein P, Mombaerts
P, Reed RR. Genetic disruptions of O/E2 and O/E3 genes reveal involvement
in olfactory receptor neuron projection. Development. 2004 Mar;131(6):1377-88.
12. Xu Q, Wang Y, Dabdoub A, Smallwood PM, Williams
J, Woods C, Kelley MW, Jiang L, Tasman W, Zhang K, Nathans J. Vascular
development in the retina and inner ear: control by Norrin and Frizzled-4,
a high-affinity ligand-receptor pair. Cell. 2004 Mar 19;116(6):883-95.
1. Chen JL, Greider CW. Determinants in mammalian
telomerase RNA that mediate enzyme processivity and cross species incompatability.
Embo J. 22, 304-14. 2. Frieman MB, Cormack BP. The omega-site sequence
of glycosylphosphatidylinositol-anchored proteins in Saccharomyces cerevisiae
can determine distribution between the membrane and the cell wall. Mol
Microbiol. 2003 Nov;50(3):883-96. 3. Hackett JA, Greider CW. End resection initiates
genomic instability in the absence of telomerase. Mol Cell Biol. 2003
Dec;23(23):8450-61. 4. Lum L, Zhang C, Oh S, Mann RK, von Kessler DP,
Taipale J, Weis-Garcia F, Gong R, Wang B, Beachy PA. Hedgehog signal transduction
via Smoothened association with a cytoplasmic complex scaffolded by the
atypical kinesin, Costal-2. Mol Cell. 2003 Nov;12(5):1261-74. 5. Lyuksyutova AI, Lu CC, Milanesio N, King
LA, Guo N, Wang Y, Nathans J, Tessier-Lavigne M, Zou Y. Anterior-posterior
guidance of commissural axons by Wnt-frizzled signaling. Science. 2003
Dec 12;302(5652):1984-8. 1. Ooi SL, Shoemaker
DD, Boeke JD. DNA helicase gene interaction network defined using synthetic
lethality analyzed by microarray. Nat Genet. 2003 Nov; 35(3):277-86. 2. Skelding Z, Queen-Baker J, Craig NL. Alternative
interactions between the Tn7 transposase and the Tn7 target DNA binding
protein regulate target immunity and transposition. EMBO J. 2003 Nov 3;
22(21):5904-17. 1. Berman DM, Karhadkar SS, Maitra A,
Montes De Oca R, Gerstenblith MR, Briggs K, Parker AR, Shimada Y, Eshleman
JR, Watkins DN, Beachy PA. Widespread requirement for Hedgehog ligand
stimulation in growth of digestive tract tumours. Nature. 2003 Sep 14
[Epub ahead of print] 2. Parikh V, Shugart YY, Doheny KF, Zhang J, Li
L, Williams J, Hayden D, Craig B, Capo H, Chamblee D, Chen C, Collins
M, Dankner S, Fiergang D, Guyton D, Hunter D, Hutcheon M, Keys M, Morrison
N, Munoz M, Parks M, Plotsky D, Protzko E, Repka MX, Sarubbi M, Schnall
B, Siatkowski RM, Traboulsi E, Waeltermann J, Nathans J. A strabismus
susceptibility locus on chromosome 7p. Proc Natl Acad Sci U S A. 2003
Sep 30 [Epub ahead of print] 3. Smallwood PM, Olveczky BP, Williams GL, Jacobs
GH, Reese BE, Meister M, Nathans J. Genetically engineered mice with an
additional class of cone photoreceptors: implications for the evolution
of color vision. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11706-11. 1. Boeke JD. The unusual
phylogenetic distribution of retrotransposons: a hypothesis. Genome Res.
2003 Sep;13(9):1975-83. 2. Cukras AR, Southworth DR, Brunelle JL, Culver
GM and Green R. Ribosomal Proteins S12 and S13 Function as Control Elements
for Translocation of the mRNA:tRNA Complex. Mol. Cell 2003 12:321-8. 3. De Las Peñas A, Pan S, Castaño
I, Alder J, Cregg R, Cormack BP. Virulence-related surface glycoproteins
in the yeast pathogen Candida glabrata are encoded in subtelomeric clusters
and subject to RAP1- and SIR-dependent transcriptional silencing. Genes
Devel 2003 Sep 2. 4. Pellettieri J, Reinke V, Kim SK, Seydoux G. Coordinate
activation of maternal protein degradation during the egg-to-embryo transition
in C. elegans. Dev Cell. 2003 Sep;5(3):451-62. 5. Reed RR. The contribution of signaling pathways
to olfactory organization and development. 6. Southworth DR, Green R. Ribosomal translocation:
sparsomycin pushes the button. Curr Biol. 2003 Aug 19;13(16):R652-4. 7. Tsunenari T, Sun H, Williams J, Cahill H, Smallwood
P, Yau KW, Nathans J. Structure-function analysis of the bestrophin family
of anion channels. J Biol Chem. 2003 Aug 7: (Epub ahead of print). 1. DeRenzo C, Reese KJ,
Seydoux G. Exclusion of germ plasm proteins from somatic lineages by cullin-dependent
degradation. Nature. 2003 Aug 7;424(6949):685-9. 2. Feldser DM, Hackett JA, Greider CW. Opinion:
Telomere dysfunction and the initiation of genome instability. Nat Rev
Cancer. 2003 Aug;3(8):623-7. 3. Mason DX, Goneska E, Greider CW. Stem-loop IV
of tetrahymena telomerase RNA stimulates processivity in trans. Mol Cell
Biol. 2003 Aug;23(16):5606-13. 1. Ross AE, Tretter T,
Vuica M, Desiderio S. Overlapping signals for protein degradation and
nuclear localization define a role for intrinsic RAG-2 nuclear uptake
in dividing cells. Mol Cell Biol. 2003 Aug;23(15):5308-5319. 2. Uhl MA, Biery M, Craig N, Johnson AD. Haploinsufficiency-based
large-scale forward genetic analysis of filamentous growth in the diploid
human fungal pathogen C.albicans. EMBO J. 2003 Jun 2;22(11):2668-2678. 1. Castano I, Kaur R, Pan S, Cregg R, Penas Ade
L, Guo N, Biery MC, Craig NL, Cormack BP. Tn7-based genome-wide random
insertional mutagenesis of candida glabrata.
Genome Res. 2003 May;13(5):905-15. 2. Szak ST, Pickeral OK, Landsman D, Boeke JD. Identifying
related L1 retrotransposons by analyzing 3' transduced sequences. Genome
Biol. 2003;4(5) 1. Cooper MK, Wassif
CA, Krakowiak PA, Taipale J, Gong R, Kelley RI, Porter FD, Beachy PA.
Corrigendum: A defective response to Hedgehog signaling in disorders of
cholesterol biosynthesis. Nat Genet 2003 May; 34(1):113. 2. Desiderio S, Yoo JY. A Genome-Wide Analysis of
the Acute-Phase Response and Its Regulation by Stat3beta. Ann N Y Acad
Sci 2003 Apr; 987:280-284. 1. IJpma A, Greider CW.
Short telomeres induce a DNA damage response in Saccharomyces cerevisiae.
Mol Biol Cell 2003;14: 987-1001. 2. Kelliher KR, Ziesmann J, Munger SD, Reed RR,
Zufall F. Importance of the CNGA4 channel gene for odor discrimination
and adaptation in behaving mice. Proc Natl Acad Sci USA 2003; 100(7):4299-304. 1. Cuenca A, Schetter A, Aceto D, Kemphues K, Seydoux,
G. Polarization of the C. elegans zygote proceeds via distinct establishment
and maintenance phases. Development. 2003; 130, 1255-1265 2. Subramaniam K, Seydoux G. Dedifferentiation of
primary spermatocytes into germ cell tumors in C. elegans lacking the
Pumilio-like protein PUF-8. Current Biology. 2003;13, 134-139
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