ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements
Orit Adato, Anna Sloutskin, Hodaya Komemi, Ian Brabb, Sascha Duttke, Philipp Bucher, Ron Unger, Tamar Juven-Gershon (2024) Bioinformatics, btae110. online publication PubMed
CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
Critical Assessment of Genome Interpretation Consortium, (2024) Genome Biology, 25(1):53. online publication PubMed
2022
Rapid Biosensing Method for Detecting Protein–DNA Interactions
Roth, S., Ideses, D., Juven-Gershon, T. and Danielli, A. (2022) ACS Sens. online publication PubMed
Changing and stable chromatin accessibility supports transcriptional overhaul during neural stem cell activation and is altered with age
Maybury-Lewis, S.Y., Brown, A.K., Yeary, M., Sloutskin, A., Dhakal, S, Juven-Gershon, T. and Webb, A.E. (2021) Aging Cell, e13499 PubMed
The core promoter is a regulatory hub for developmental gene expression
Sloutskin, A., Shir-Shapira, H., Freiman, R. and Juven-Gershon, T. (2021) Frontiers in Cell and Developmental Biology, 9:666508 PubMed Full Text
Computational identification and experimental characterization of preferred downstream positions in human core promoters
Dreos, R.*, Sloutskin, A.*, Malachi, N.*, Ideses, D., Bucher, P.‡ and Juven-Gershon, T.‡ (2021) PLOS Computational Biology, 17(8):e1009256 PubMed Full Text
*The first three authors contributed equally to this paper
‡ co-corresponding authors
Quantitative analysis of differential expression of HOX genes in multiple cancers
Adato, O., Orenstein, Y., Kopolovic, J., Juven-Gershon, T.‡ and Unger, R.‡ (2020) Cancers (Basel). 12(6):1572 PubMed Full Text
‡ Corresponding authors
Efficient in vivo introduction of point mutations using ssODN and a Co-CRISPR approach
Levi, T.*, Sloutskin, A.*‡, Kalifa, R., Juven-Gershon, T.‡ and Gerlitz, O.‡ (2020) Biol Proced Online. 22:14 PubMed Full Text
‡ Corresponding authors
Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay
Shigaki, D., Adato, O., Adhikari, AN., Dong, S.,Hawkins-Hooker, A., Inoue, F., Juven-Gershon, T., Kenlay, H., Martin, B., Patra, A., Penzar, DD., Schubach, M., Xiong, C., Yan, Z., Boyle, AP., Kreimer, A., Kulakovskiy, IV., Reid, J., Unger, R., Yosef, N., Shendure, J., Ahituv, N., Kircher, M., Beer, MA. (2019) Hum Mutat 40(9): 1280-1291 PubMed
Identification of evolutionarily conserved downstream core promoter elements required for the transcriptional regulation of Fushi tarazu target genes
Shir-Shapira, H.*, Sloutskin, A.*, Adato, O., Ovadia-Shochat, A., Ideses, D., Zehavi, Y., Kassavetis, G., Kadonaga, J.T., Unger, R. and Juven-Gershon, T. (2019) PLoS ONE. 14(4): e0215695 PubMed Full Text
Functional Screening of Core Promoter Activity
Even, D.Y., Kedmi, A., Ideses, D. and Juven-Gershon, T. (2017) Methods Mol Biol. 1651, 77-91 PubMed
Structural and dynamics characterization of the MerR family metalloregulator CueR in its repression and activation states
Sameach, H., Narunsky, A., Azoulay-Ginsburg, S., Gevorkyan-Aiapetov, L., Zehavi, Y., Moskovitz, Y., Juven-Gershon, T., Ben-Tal, N. and Ruthstein, S. (2017) Structure. 25(7), 988-996.e3 PubMed
SELMAP – SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics
Chen, D., Orenstein Y., Golodnitsky R., Pellach M., Avrahami D., Wachtel C., Ovadia-Shochat A., Shir-Shapira H., Kedmi A., Juven-Gershon T., Shamir R., and Gerber D. (2016) Scientific Reports, 6, 33351 PubMed
Engineered Promoters for Potent Transient Overexpression
Even, D.Y.*, Kedmi A.*, Basch-Barzilay, S.*, Ideses, D., Tikotzki, R., Shir-Shapira, H., Shefi, O. and Juven-Gershon, T. (2016) PLOS ONE, 11(2): e0148918 PubMed Full Text
ElemeNT: A Computational Tool for Detecting Core Promoter Elements
Sloutskin, A., Danino, YM., Orenstein, Y., Zehavi, Y., Doniger, T., Shamir, R. and Juven-Gershon, T. (2015) Transcription, 6(3), 41-50 PubMed Full Text
Here you can find the described resources.
Structure-Function Analysis of the Drosophila melanogaster Caudal provides insights into core promoter-preferential activation
Shir-Shapira, H.*, Sharabany,J.*, Filderman, M., Ideses, D., Ovadia-Shochat, A., Mannervik, M. and Juven-Gershon, T. (2015) Journal of Biological Chemistry, 290(28) 17293-305 PubMed Full Text
The core promoter: at the heart of gene expression
Danino,Y.M, Even, D., Ideses, D., and Juven-Gershon,T. (2015) BBA Gene Regulatory Mechanisms, 1849(8), 1116-31 PubMed Full Text
TRF2: TRansForming the view of general transcription factors
Zehavi, Y.*, Kedmi, A.*, Ideses, D., and Juven-Gershon, T. (2015) Transcription, 6(1), 1-6 PubMed Full Text
The FOXO Transcription Factor DAF-16 Bypasses ire-1 Requirement to Promote Endoplasmic Reticulum Homeostasis
Safra M., Fickentscher R., Levi-Ferber M., Danino Y.M., Haviv-Chesner A., Hansen M., Juven-Gershon T., Weiss M., Henis-Korenblit S. (2014) Cell Metabolism, 20, 870-881 PubMed
Drosophila TRF2 Is a Preferential Core Promoter Regulator
Kedmi, A.*, Zehavi, Y*., Glick, Y., Orenstein, Y., Ideses, D., Wachtel, C., Doniger, T., Waldman Ben-Asher, H., Munster, N., Thompson, J., Anderson, S., Avrahami, D., Yates, JR 3rd, Shamir, R., Gerber, D., and Juven-Gershon, T. (2014) Genes & Development, 28, 2163-2174 PubMed Full Text
The core promoter composition establishes a new dimension in developmental gene networks
Zehavi, Y., Sloutskin, A., Kuznetsov, O., and Juven-Gershon, T. (2014) Nucleus, 5:4,298–303 PubMed Full Text
Core promoter functions in the regulation of gene expression of Drosophila Dorsal target genes
Zehavi, Y., Kuznetsov, O., Ovadia-Shochat, A. and Juven-Gershon, T. (2014) Journal of Biological Chemistry, 289, 11993-12004 PubMed Full Text
Human TFIID binds to core promoter DNA in a reorganized structural state
Cianfrocco, M.A., Kassavetis, G.A., Grob, P., Fang, J., Juven-Gershon, T., Kadonaga, J.T. and Nogales, E. (2013) Cell, 152, 120-131 PubMed Full Text
Regulation of gene expression via the core promoter and the basal transcriptional machinery
Juven-Gershon, T. and Kadonaga, J.T. (2010) Developmental Biology, 339, 225-229 PubMed Full Text
-One of the top-five most cited articles published in the journal Developmental
Biology during the period 1/1/2009-31/12/2011
Caudal, a key developmental regulator, is a DPE-specific transcriptional factor
Juven-Gershon, T., Hsu, J.-Y. and Kadonaga, J.T. (2008) Genes & Development, 22, 2823-2830 PubMed Full Text
TBP, Mot1, and NC2 establish a regulatory circuit that controls DPE-dependent versus TATA-dependent transcription
Hsu, J.-Y, Juven-Gershon, T., Marr, M.T. 2nd, Wright, K.J., Tjian, R. and Kadonaga, J.T. (2008) Genes & Development, 22, 2353-2358 PubMed Full Text
The RNA polymerase II core promoter – the gateway to transcription
Juven-Gershon, T., Hsu, J.-Y. Theisen J.W.M. and Kadonaga, J.T. (2008) Current Opinion in Cell Biology, 20, 253-259 PubMed Full Text
Perspectives on the RNA polymerase II core promoter
Juven-Gershon, T., Hsu, J.-Y. and Kadonaga, J.T. (2006) Biochemical Society Transactions 34, 1051-1054 PubMed Full Text
Rational design of a super core promoter that enhances gene expression
Juven-Gershon, T., Cheng, S. and Kadonaga, J.T. (2006) Nature Methods, 3, 917 –922 PubMed
-Potential applications of this study were discussed in: Perkel, J.M. (2007)
Studies you can use. The Scientist, 21,63
Siah-1 binds and regulates the function of Numb
Susini, L.*,Passer, B.J.*,Amzallag-Elbaz, N.*, Juven-Gershon, T.*, Prieur, S., Privat, N., Tuynder, M, Gendron M., Israel, A., Amson, R., Oren, M. and Telerman, A. (2001) Proc. Natl. Acad. Sci. USA, 98, 15067-15072 PubMed Full Text
*The first four authors contributed equally to this paper
Critical role for Ser20 of human p53 in the negative regulation of p53 by Mdm2
Unger, T.*, Juven-Gershon, T.*, Moallem, E.*, Berger, M., Vogt-Sionov, R., Lozano, G., Oren, M. and Haupt, Y. (1999) EMBO J., 18, 1805-1814 PubMed Full Text
*The first three authors contributed equally to this paper
The c-fos proto-oncogene is a target for transactivation by the p53 tumor suppressor
Elkeles, A., Juven-Gershon, T., Israeli, D., Wilder, S., Zalcenstein, A. and Oren, M. (1999) Molecular & Cellular Biology, 19, 2594-2600 PubMed Full Text
Mdm2: the ups and the downs
Juven-Gershon, T. and Oren, M. (1999) Molecular Medicine, 5, 71-83 PubMed Full Text
The Mdm2 oncoprotein interacts with the cell fate regulator Numb
Juven-Gershon, T., Shifman, O., Unger, T., Elkeles, A., Haupt, Y. and Oren, M. (1998) Molecular & Cellular Biology, 18, 3974-3982 PubMed Full Text
Regulation of mdm2 expression by p53: alternative promoters produce transcripts with nonidentical translation potential
Barak, Y., Gottlieb, E., Juven-Gershon, T. and Oren, M. (1994) Genes & Development, 8, 1739-1749 PubMed Full Text
Targets for transcriptional activation by wild-type p53: endogenous retroviral LTR, immunoglobulin-like promoter, and an internal promoter of the mdm2 gene
Barak, Y., Lupo, A., Zauberman, A., Juven, T., Aloni-Grinstein, R., Gottlieb, E., Rotter, V. and Oren, M. (1994) Cold Spring Harb Symp. Quant. Biol., 59, 225-235 PubMed
Antibodies to different isoforms of the heavy neurofilament protein (NF- H) in normal aging and Alzheimer’s disease
Soussan, L., Tchernakov, K., Bachar-Lavi, O., Juven, T., Wertman, E. and Michaelson, D.M. (1994) Molecular Neurobiology, 9, 83-91 PubMed
Wild type p53 can mediate sequence-specific transactivation of an internal promoter within the mdm2 gene
Juven, T., Barak, Y., Zauberman, A., George, D.L. and Oren, M. (1993) Oncogene, 8, 3411-3416 PubMed
mdm2 expression is induced by wild type p53 activity
Barak, Y., Juven, T., Haffner, R. and Oren, M. (1993) EMBO J., 12, 461-468 PubMed Full Text
Optimized core promoters and uses thereof
Kadonaga and Gershon. Patent no. US 7,968,698 B2: 2006.