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  



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


2001 and earlier

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.