Katherine Jones

Professor Emerita

Salk Institute for Biological Studies - Publications

all Publications


Choi, S.H., Kim, S., Jones, K.A. Gene expression regulation by CDK12: a versatile kinase in cancer with functions beyond CTD phosphorylation. (2020) Experimental & Molecular Medicine. DOI: 10.1038/s12276-020-0442-9

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Choi, S.H., Martinez, T.F., Kim, S., Donaldson, C., Shokhirev, M.N., Saghatelian, A., Jones, K.A. CDK12 phosphorylates 4E-BP1 to enable mTORC1-dependent translation and mitotic genome stability. (2019) Genes & Development. 33(7-8):418-435. DOI: 10.1101/gad.322339.118

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Hsu, H.T., Estarás, C., Huang, L., Jones, K.A. Specifying the Anterior Primitive Streak by Modulating YAP1 Levels in Human Pluripotent Stem Cells. (2018) Stem Cell Reports. 11(6):1357-1364. DOI: 10.1016/j.stemcr.2018.10.013

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Xu, M., Moresco, J.J., Chang, M., Mukim, A., Smith, D., Diedrich, J.K., Yates, J.R., Jones, K.A. SHMT2 and the BRCC36/BRISC deubiquitinase regulate HIV-1 Tat K63-ubiquitylation and destruction by autophagy. (2018) PLOS pathogens. 14(5):e1007071. DOI: 10.1371/journal.ppat.1007071

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Estarás, C., Hsu, H.T., Huang, L., Jones, K.A. YAP repression of the WNT3 gene controls hESC differentiation along the cardiac mesoderm lineage. (2017) Genes & Development. 31(22):2250-2263. DOI: 10.1101/gad.307512.117

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Estarás, C., Benner, C., Jones, K.A. SMADs and YAP compete to control elongation of β-catenin:LEF-1-recruited RNAPII during hESC differentiation. (2015) Molecular Cell. 58(5):780-93. DOI: 10.1016/j.molcel.2015.04.001

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Chen, Y., Zhang, L., Estarás, C., Choi, S.H., Moreno, L., Karn, J., Moresco, J.J., Yates, J.R., Jones, K.A. A gene-specific role for the Ssu72 RNAPII CTD phosphatase in HIV-1 Tat transactivation. (2014) Genes & Development. 28(20):2261-75. DOI: 10.1101/gad.250449.114

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Jones, K.A. Changing the core of transcription. (2014) Elife. 3:e03575.

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Choi, S.H., Estarás, C., Moresco, J.J., Yates, J.R., Jones, K.A. α-Catenin interacts with APC to regulate β-catenin proteolysis and transcriptional repression of Wnt target genes. (2013) Genes & Development. 27(22):2473-88. DOI: 10.1101/gad.229062.113

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Türbachova, I., Schwachula, T., Vasconcelos, I., Mustea, A., Baldinger, T., Jones, K.A., Bujard, H., Olek, A., Olek, K., Gellhaus, K., Braicu, I., Könsgen, D., Fryer, C., Ravot, E., Hellwag, A., Westerfeld, N., Gruss, O.J., Meissner, M., Hasan, M.T., Weber, M., Hoffmüller, U., Zimmermann, S., Loddenkemper, C., Mahner, S., Babel, N., Berns, E., Adams, R., Zeilinger, R., Baron, U., Vergote, I., Maughan, T., Marme, F., Dickhaus, T., Sehouli, J., Olek, S. The cellular ratio of immune tolerance (immunoCRIT) is a definite marker for aggressiveness of solid tumors and may explain tumor dissemination patterns. (2013) Epigenetics. 8(11):1226-35. DOI: 10.4161/epi.26334

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Jones, K.A. A SirT'N repression for Notch. (2011) Molecular Cell. 42(5):559-60. DOI: 10.1016/j.molcel.2011.05.017

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Chen, Y., Zhang, L., Jones, K.A. SKIP counteracts p53-mediated apoptosis via selective regulation of p21Cip1 mRNA splicing. (2011) Genes & Development. 25(7):701-16. DOI: 10.1101/gad.2002611

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Jones, K.A. Outsmarting a mastermind. (2009) Developmental Cell. 17(6):750-2. DOI: 10.1016/j.devcel.2009.12.002

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Brès, V., Yoshida, T., Pickle, L., Jones, K.A. SKIP interacts with c-Myc and Menin to promote HIV-1 Tat transactivation. (2009) Molecular Cell. 36(1):75-87. DOI: 10.1016/j.molcel.2009.08.015

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Yoh, S.M., Lucas, J.S., Jones, K.A. The Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation. (2008) Genes & Development. 22(24):3422-34. DOI: 10.1101/gad.1720008

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Jones, K.A., Kemp, C.R. Wnt-induced proteolytic targeting. (2008) Genes & Development. 22(22):3077-81. DOI: 10.1101/gad.1741008

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Brès, V., Yoh, S.M., Jones, K.A. The multi-tasking P-TEFb complex. (2008) Current Opinion in Cell Biology. 20(3):334-40. DOI: 10.1016/j.ceb.2008.04.008

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Jones, K.A. Transcription strategies in terminally differentiated cells: shaken to the core. (2007) Genes & Development. 21(17):2113-7. DOI: 10.1101/gad.1598007


Yoh, S.M., Cho, H., Pickle, L., Evans, R.M., Jones, K.A. The Spt6 SH2 domain binds Ser2-P RNAPII to direct Iws1-dependent mRNA splicing and export. (2007) Genes & Development. 21(2):160-74. DOI: 10.1101/gad.1503107

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Wang, S., Jones, K.A. CK2 controls the recruitment of Wnt regulators to target genes in vivo. (2006) Current Biology. 16(22):2239-44. DOI: 10.1016/j.cub.2006.09.034

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Willert, K., Jones, K.A. Wnt signaling: is the party in the nucleus? (2006) Genes & Development. 20(11):1394-404. DOI: 10.1101/gad.1424006

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Sierra, J., Yoshida, T., Joazeiro, C.A., Jones, K.A. The APC tumor suppressor counteracts beta-catenin activation and H3K4 methylation at Wnt target genes. (2006) Genes & Development. 20(5):586-600. DOI: 10.1101/gad.1385806

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Brès, V., Gomes, N., Pickle, L., Jones, K.A. A human splicing factor, SKIP, associates with P-TEFb and enhances transcription elongation by HIV-1 Tat. (2005) Genes & Development. 19(10):1211-26. DOI: 10.1101/gad.1291705

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Fryer, C.J., White, J.B., Jones, K.A. Mastermind recruits CycC:CDK8 to phosphorylate the Notch ICD and coordinate activation with turnover. (2004) Molecular Cell. 16(4):509-20. DOI: 10.1016/j.molcel.2004.10.014

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Gomes, N., Garber, M.E., Jones, K.A. Techniques to analyze the HIV-1 Tat and TAR RNA-dependent recruitment and activation of the cyclin T1: CDK9 (P-TEFb) transcription elongation factor. (2003) Methods in Enzymology. 371:324-36. DOI: 10.1016/S0076-6879(03)71024-6


Orlando, V., Jones, K.A. Wild chromatin: regulation of eukaryotic genes in their natural chromatin context. (2002) Genes & Development. 16(16):2039-44. DOI: 10.1101/gad.1017402


Fryer, C.J., Lamar, E., Turbachova, I., Kintner, C., Jones, K.A. Mastermind mediates chromatin-specific transcription and turnover of the Notch enhancer complex. (2002) Genes & Development. 16(11):1397-411. DOI: 10.1101/gad.991602

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Tutter, A.V., Fryer, C.J., Jones, K.A. Chromatin-specific regulation of LEF-1-beta-catenin transcription activation and inhibition in vitro. (2001) Genes & Development. 15(24):3342-54. DOI: 10.1101/gad.946501

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Zhang, J., Tamilarasu, N., Hwang, S., Garber, M.E., Huq, I., Jones, K.A., Rana, T.M. HIV-1 TAR RNA enhances the interaction between Tat and cyclin T1. (2000) Journal of Biological Chemistry. 275(44):34314-9. DOI: 10.1074/jbc.M006804200

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Kadam, S., McAlpine, G.S., Phelan, M.L., Kingston, R.E., Jones, K.A., Emerson, B.M. Functional selectivity of recombinant mammalian SWI/SNF subunits. (2000) Genes & Development. 14(19):2441-51.

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Garber, M.E., Mayall, T.P., Suess, E.M., Meisenhelder, J., Thompson, N.E., Jones, K.A. CDK9 autophosphorylation regulates high-affinity binding of the human immunodeficiency virus type 1 tat-P-TEFb complex to TAR RNA. (2000) Molecular and Cellular Biology. 20(18):6958-69.

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Jones, K.A., Kadonaga, J.T. Exploring the transcription-chromatin interface. (2000) Genes & Development. 14(16):1992-6.


Garber, M.E., Jones, K.A. HIV-1 Tat: coping with negative elongation factors. (1999) Current Opinion in Immunology. 11(4):460-5. DOI: 10.1016/S0952-7915(99)80077-6

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Tutter, A., McAlpine, G.S., Jones, K.A. Mechanism of chromatin recognition and transcriptional regulation by LEF-1 and the Wnt/Wg-responsive LEF-1:beta-catenin complex. (1999) Cold Spring Harbor Symposia on Quantitative Biology. 64:445-52.


Garber, M.E., Wei, P., Caderas, G., Jones, K.A. Protein and RNA affinity selection techniques using HIV-1 Tat. (1999) Methods in Enzymology. 306:352-64.


Herrmann, C.H., Carroll, R.G., Wei, P., Jones, K.A., Rice, A.P. Tat-associated kinase, TAK, activity is regulated by distinct mechanisms in peripheral blood lymphocytes and promonocytic cell lines. (1998) Journal of Virology. 72(12):9881-8.

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Garber, M.E., Wei, P., KewalRamani, V.N., Mayall, T.P., Herrmann, C.H., Rice, A.P., Littman, D.R., Jones, K.A. The interaction between HIV-1 Tat and human cyclin T1 requires zinc and a critical cysteine residue that is not conserved in the murine CycT1 protein. (1998) Genes & Development. 12(22):3512-27.

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Tutter, A., Jones, K.A. Chemicals that footprint DNA: hitting HIV-1 in the minor groove. (1998) Proceedings of the National Academy of Sciences of the United States of America. 95(22):12739-41.


Garber, M.E., Wei, P., Jones, K.A. HIV-1 Tat interacts with cyclin T1 to direct the P-TEFb CTD kinase complex to TAR RNA. (1998) Cold Spring Harbor Symposia on Quantitative Biology. 63:371-80.


Wei, P., Garber, M.E., Fang, S.M., Fischer, W.H., Jones, K.A. A novel CDK9-associated C-type cyclin interacts directly with HIV-1 Tat and mediates its high-affinity, loop-specific binding to TAR RNA. (1998) Cell. 92(4):451-62.

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Sheridan, P.L., Mayall, T.P., Verdin, E., Jones, K.A. Histone acetyltransferases regulate HIV-1 enhancer activity in vitro. (1997) Genes & Development. 11(24):3327-40.

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Jones, K.A. Taking a new TAK on tat transactivation. (1997) Genes & Development. 11(20):2593-9.


Mayall, T.P., Sheridan, P.L., Montminy, M.R., Jones, K.A. Distinct roles for P-CREB and LEF-1 in TCR alpha enhancer assembly and activation on chromatin templates in vitro. (1997) Genes & Development. 11(7):887-99.

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Jones, K.A. Taking out Tat. (1996) Nature Biotechnology. 14(11):1542-3. DOI: 10.1038/nbt1196-1542


Okamoto, H., Sheline, C.T., Corden, J.L., Jones, K.A., Peterlin, B.M. Trans-activation by human immunodeficiency virus Tat protein requires the C-terminal domain of RNA polymerase II. (1996) Proceedings of the National Academy of Sciences of the United States of America. 93(21):11575-9.

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Pazin, M.J., Sheridan, P.L., Cannon, K., Cao, Z., Keck, J.G., Kadonaga, J.T., Jones, K.A. NF-kappa B-mediated chromatin reconfiguration and transcriptional activation of the HIV-1 enhancer in vitro. (1996) Genes & Development. 10(1):37-49.

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Sheridan, P.L., Sheline, C.T., Cannon, K., Voz, M.L., Pazin, M.J., Kadonaga, J.T., Jones, K.A. Activation of the HIV-1 enhancer by the LEF-1 HMG protein on nucleosome-assembled DNA in vitro. (1995) Genes & Development. 9(17):2090-104.

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Lin, Y., Sheridan, P.L., Jones, K.A., Evans, G.A. The HIP116 SNF2/SW12-related transcription factor gene (SNF2L3) is located on human chromosome 3q25.1-q26.1. (1995) Genomics. 27(2):381-2. DOI: 10.1006/geno.1995.1064


Sheridan, P.L., Schorpp, M., Voz, M.L., Jones, K.A. Cloning of an SNF2/SWI2-related protein that binds specifically to the SPH motifs of the SV40 enhancer and to the HIV-1 promoter. (1995) Journal of Biological Chemistry. 270(9):4575-87.

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Jones, K.A., Peterlin, B.M. Control of RNA initiation and elongation at the HIV-1 promoter. (1994) Annual Review of Biochemistry. 63:717-43. DOI: 10.1146/annurev.bi.63.070194.003441


Carlsson, P., Waterman, M.L., Jones, K.A. The hLEF/TCF-1 alpha HMG protein contains a context-dependent transcriptional activation domain that induces the TCR alpha enhancer in T cells. (1993) Genes & Development. 7(12A):2418-30.

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Zenzie-Gregory, B., Sheridan, P., Jones, K.A., Smale, S.T. HIV-1 core promoter lacks a simple initiator element but contains a bipartite activator at the transcription start site. (1993) Journal of Biological Chemistry. 268(21):15823-32.

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Jones, K.A. Tat and the HIV-1 promoter. (1993) Current Opinion in Cell Biology. 5(3):461-8.

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Sheridan, P.L., Sheline, C.T., Milocco, L.H., Jones, K.A. Tat and the HIV-1 promoter: A model for RNA-mediated regulation of transcription (1993) Seminars in Virology. 4(1):690808. DOI: 10.1016/1044-5773(93)80010-L

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Sheline, C.T., Milocco, L.H., Jones, K.A. Two distinct nuclear transcription factors recognize loop and bulge residues of the HIV-1 TAR RNA hairpin. (1991) Genes & Development. 5(12B):2508-20.

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Waterman, M.L., Fischer, W.H., Jones, K.A. A thymus-specific member of the HMG protein family regulates the human T cell receptor C alpha enhancer. (1991) Genes & Development. 5(4):656-69.

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Waterman, M.L., Jones, K.A. Purification of TCF-1 alpha, a T-cell-specific transcription factor that activates the T-cell receptor C alpha gene enhancer in a context-dependent manner. (1990) New Biologist. 2(7):621-36.

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Jones, K.A. HIV trans-activation and transcription control mechanisms. (1989) New Biologist. 1(2):127-35.

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Toohey, M.G., Jones, K.A. In vitro formation of short RNA polymerase II transcripts that terminate within the HIV-1 and HIV-2 promoter-proximal downstream regions. (1989) Genes & Development. 3(3):265-82.

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Jones, K.A., Luciw, P.A., Duchange, N. Structural arrangements of transcription control domains within the 5'-untranslated leader regions of the HIV-1 and HIV-2 promoters. (1988) Genes & Development. 2(9):1101-14.

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Dinter, H., Chiu, R., Imagawa, M., Karin, M., Jones, K.A. In vitro activation of the HIV-1 enhancer in extracts from cells treated with a phorbol ester tumor promoter. (1987) EMBO Journal. 6(13):4067-71.

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Jones, K.A., Kadonaga, J.T., Rosenfeld, P.J., Kelly, T.J., Tjian, R. A cellular DNA-binding protein that activates eukaryotic transcription and DNA replication. (1987) Cell. 48(1):79-89.

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Jones, K.A., Kadonaga, J.T., Luciw, P.A., Tjian, R. Activation of the AIDS retrovirus promoter by the cellular transcription factor, Sp1. (1986) Science. 232(4751):755-9.

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Kadonaga, J.T., Jones, K.A., Tjian, R. Promoter-specific activation of RNA polymerase II transcription by Sp1 (1986) Trends in Biochemical Sciences. 11(1):20-23. DOI: 10.1016/0968-0004(86)90226-4

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Jones, K.A., Tjian, R. Sp1 binds to promoter sequences and activates herpes simplex virus 'immediate-early' gene transcription in vitro. (1985) Nature. 317(6033):179-82.

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Jones, K.A., Yamamoto, K.R., Tjian, R. Two distinct transcription factors bind to the HSV thymidine kinase promoter in vitro. (1985) Cell. 42(2):559-72.

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Jones, K.A., Myers, R.M., Tjian, R. Mutational analysis of simian virus 40 large T antigen DNA binding sites. (1984) EMBO Journal. 3(13):3247-55.

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Jones, K.A., Tjian, R. Essential contact residues within SV40 large T antigen binding sites I and II identified by alkylation-interference. (1984) Cell. 36(1):155-62.

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Education

PhD, Biochemistry, University of California, Riverside
Postdoctoral Research, University of California, Berkeley