From promoter motif to cardiac function: A single DPE motif affects transcription regulation and organ function in vivo.
Sloutskin, A.*, ‡, Itzhak, D.*, Vogler, G., Pozeilov, H., Ideses, D., Alter, H., Adato, O., Shachar, H., Doniger, D., Shohat-Ophir, G., Frasch, M., Bodmer, R., Duttke, S.H. and Juven-Gershon, T.‡ (2024) Development, dev.202355. PubMed
*The first two authors contributed equally to this paper
‡co-corresponding authors
ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements
Adato, O.*, Sloutskin, A.*, Komemi, H., Brabb, I., Duttke, S., Bucher, P., Unger, R. ‡, and Juven-Gershon, T. ‡ (2024) Bioinformatics, btae110. online publication PubMed
*The first two authors contributed equally to this paper
‡co-corresponding authors
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 two 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
‡co-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
‡co-corresponding authors
2019
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.