Publications

Signal-Regulated Transcription

• Kim HB, Nandu T, Kim YJ, Camacho CV, Kraus WL. Dose-dependent hormone actions at estrogen receptor enhancers specify distinct molecular and biological outcomes. Sci Adv. 2026 Jun 5;12(23):eaec2424. doi: 10.1126/sciadv.aec2424. Epub 2026 Jun 3. PMID: 42234735.
• Tripathy S, Nagari A, Chiu SP, Nandu T, Camacho CV, Mahendroo M, Kraus WL. Relaxin Modulates the Genomic Actions and Biological Effects of Estrogen in the Myometrium. Endocrinology. 2024 Sep 26;165(11):bqae123. doi: 10.1210/endocr/bqae123. PMID: 39283953
• Owen DM, Kwon M, Huang X, Nagari A, Nandu T, Kraus WL. Genome-wide identification of transcriptional enhancers during human placental development and association with function, differentiation, and disease. Biol Reprod. 2023 Dec 11;109(6):965-981. doi: 10.1093/biolre/ioad119. PMID: 37694817.
• Hou TY, Kraus WL. Analysis of estrogen-regulated enhancer RNAs identifies a functional motif required for enhancer assembly and gene expression. Cell Rep. 2022 Jun 14;39(11):110944. doi: 10.1016/j.celrep.2022.110944. PMID: 35705040.
• Gupte R, Nandu T, Kraus WL. Nuclear ADP-ribosylation drives IFNγ-dependent STAT1α enhancer formation in macrophages. Nat Commun. 2021 Jun 24;12(1):3931. doi: 10.1038/s41467-021-24225-2. PMID: 34168143.
• Ryu KW., Nandu T, Kim J, Challa S, DeBerardinis RJ, Kraus WL. Metabolic regulation of transcription through compartmentalized NAD+ biosynthesis. Science. 2018 May 11;360(6389):eaan5780. doi: 10.1126/science.aan5780. PMID: 29748257.
• Franco HL, Nagari A, Malladi VS, Li W, Xi Y, Richardson D, Allton KL, Tanaka K, Li J, Murakami S, Keyomarsi K, Bedford MT, Shi X, Li W, Barton MC, Dent SYR, Kraus WL. Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis. Genome Res. 2018 Feb;28(2):159-170. doi: 10.1101/gr.226019.117. Epub 2017 Dec 22. PMID: 29273624.
• Murakami S, Nagari A, Kraus WL. Dynamic assembly and activation of estrogen receptor α enhancers through coregulator switching. Genes Dev. 2017 Aug 1;31(15):1535-1548. doi: 10.1101/gad.302182.117. Epub 2017 Sep 8. PMID: 2888741.
• Franco HL, Nagari A, Kraus WL. TNFα signaling exposes latent estrogen receptor binding sites to alter the breast cancer cell transcriptome. Mol Cell. 2015 Apr 2;58(1):21-34. doi: 10.1016/j.molcel.2015.02.001. Epub 2015 Mar 5. PMID: 25752574.
• Luo X, Chae M, Krishnakumar R, Danko CG, Kraus WL. Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFα signaling revealed by integrated genomic analyses. BMC Genomics. 2014 Feb 24;15:155. doi: 10.1186/1471-2164-15-155. PMID: 24564208.
• Danko CG, Hah N, Luo X, Martins A, Siepel A, Kraus WL. Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol Cell. 2013 Apr 25;50(2):212-22. doi: 10.1016/j.molcel.2013.02.015. Epub 2013 Mar 21. Erratum in: Mol Cell. 2013 Jun 6;50(5):778. PMID: 23523369.
• Hah N, Murakami S, Nagari A, Danko CG, Kraus WL. Enhancer transcripts mark active estrogen receptor binding sites. Genome Res. 2013 Aug;23(8):1210-23. doi: 10.1101/gr.152306.112. Epub 2013 May 1. PMID: 23636943.
• Hah N, Danko CG, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL. A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell. 2011 May 13;145(4):622-34. doi: 10.1016/j.cell.2011.03.042. Epub 2011 May 5. Erratum in: Cell. 2011 Jun 24;145(7):1156. PMID: 21549415.

PARPs and NAD⁺

• Stokes MS, Kim YJ, Kim Y, Koul S, Chiu SP, Liu C, Dasovich M, Zuniga J, Nandu T, Huang D, Mathews TP, Solmonson A, Camacho CV, Kraus WL. NAD+ sensing by PARP7 regulates the C/EBPβ-dependent transcription program during adipogenesis. Cell Rep. 2026 Feb 24;45(2):116929. doi: 10.1016/j.celrep.2026.116929. Epub 2026 Jan 31. PMID: 41621069.
• Challa S, Nandu T, Kim HB, Gong X, Renshaw CW, Li WC, Tan X, Aljardali MW, Camacho CV, Chen J, Kraus WL. RACK1 MARylation regulates translation and stress granules in ovarian cancer cells. J Cell Biol. 2025 Feb 3;224(2):e202401101. doi: 10.1083/jcb.202401101. Epub 2025 Jan 6. PMID: 39760726.
• Chiu SP, Camacho CV, Kraus WL. Development and characterization of recombinant ADP-ribose binding reagents that allow simultaneous detection of mono and poly ADP-ribose. J Biol Chem. 2024 Sep;300(9):107609. doi: 10.1016/j.jbc.2024.107609. Epub 2024 Jul 27. PMID: 39074634.
• Huang D, Edwards AD, Gong X, Kraus WL. Functional Analysis of Histone ADP-Ribosylation In Vitro and in Cells. Methods Mol Biol. 2023;2609:157-192. doi: 10.1007/978-1-0716-2891-1_11. PMID: 36515836.
• Challa S, Whitaker AL, Kraus WL. Detecting Poly (ADP-Ribose) In Vitro and in Cells Using PAR Trackers. Methods Mol Biol. 2023;2609:75-90. doi: 10.1007/978-1-0716-2891-1_5. PMID: 36515830.
• Gupte R, Lin KY, Nandu T, Lea JS, Kraus WL. Combinatorial Treatment with PARP-1 Inhibitors and Cisplatin Attenuates Cervical Cancer Growth through Fos-Driven Changes in Gene Expression. Mol Cancer Res. 2022 Aug 5;20(8):1183-1192. doi: 10.1158/1541-7786.MCR-22-0111. PMID: 35503086.
• Jones A, Kraus WL. Multiomics analysis of the NAD+-PARP1 axis reveals a role for site-specific ADP-ribosylation in splicing in embryonic stem cells. Genes Dev. 2022 May 1;36(9-10):601-617. doi: 10.1101/gad.349335.121. Epub 2022 Jun 2. PMID: 35654456.
• Challa S, Ryu KW, Whitaker AL, Abshier JC, Camacho CV, Kraus WL. Development and characterization of new tools for detecting poly(ADP-ribose) in vitro and in vivo. Elife. 2022 Apr 27;11:e72464. doi: 10.7554/eLife.72464. PMID: 35476036.
• Huang D, Camacho CV, Martire S, Nagari A, Setlem R, Gong X, Edwards AD, Chiu SP, Banaszynski LA, Kraus WL. Oncohistone Mutations Occur at Functional Sites of Regulatory ADP-Ribosylation. Cancer Res. 2022 Jul 5;82(13):2361-2377. doi: 10.1158/0008-5472.CAN-22-0742. PMID: 35472077.
• Challa S, Khulpateea BR, Nandu T, Camacho CV, Ryu KW, Chen H, Peng Y, Lea JS, Kraus WL. Ribosome ADP-ribosylation inhibits translation and maintains proteostasis in cancers. Cell. 2021 Aug 19;184(17):4531-4546.e26. doi: 10.1016/j.cell.2021.07.005. Epub 2021 Jul 26. PMID: 34314702.
• Gupte R, Nandu T, Kraus WL. Nuclear ADP-ribosylation drives IFNγ-dependent STAT1α enhancer formation in macrophages. Nat Commun. 2021 Jun 24;12(1):3931. doi: 10.1038/s41467-021-24225-2. PMID: 34168143.
• Palavalli Parsons LH, Challa S, Gibson BA, Nandu T, Stokes MS, Huang D, Lea JS, Kraus WL. Identification of PARP-7 substrates reveals a role for MARylation in microtubule control in ovarian cancer cells. Elife. 2021 Jan 21;10:e60481. doi: 10.7554/eLife.60481. PMID: 33475085.
• Huang D, Camacho CV, Setlem R, Ryu KW, Parameswaran B, Gupta RK, Kraus WL. Functional Interplay between Histone H2B ADP-Ribosylation and Phosphorylation Controls Adipogenesis. Mol Cell. 2020 Sep 17;79(6):934-949.e14. doi: 10.1016/j.molcel.2020.08.002. Epub 2020 Aug 20. PMID: 32822587.
• Huang D, Kim DS, Kraus WL. Specific binding of snoRNAs to PARP-1 promotes NAD+-dependent catalytic activation. Biochemistry. 2020 Apr 28;59(16):1559-1564. doi: 10.1021/acs.biochem.0c00100. Epub 2020 Apr 17. PMID: 32293172.
• Kim DS, Camacho CV, Nagari A, Malladi VS, Challa S, Kraus WL. Activation of PARP-1 by snoRNAs controls ribosome biogenesis and cell growth via the RNA helicase DDX21. Mol Cell. 2019 Sep 19;75(6):1270-1285.e14. doi: 10.1016/j.molcel.2019.06.020. Epub 2019 Jul 24. PMID: 31351877.
• Ryu KW, Nandu T, Kim J, Challa S, DeBerardinis RJ, Kraus WL. Metabolic regulation of transcription through compartmentalized NAD(+) biosynthesis. Science. 2018 May 11;360(6389):eaan5780. doi: 10.1126/science.aan5780. PMID: 29748257.
• Luo X, Ryu KW, Kim DS, Nandu T, Medina CJ, Gupte R, Gibson BA, Soccio RE, Yu Y, Gupta RK, Kraus WL. PARP-1 controls the adipogenic transcription program by PARylating C/EPBβ and modulating its transcriptional activity. Mol Cell. 2017 Jan 19;65(2):260-271. doi: 10.1016/j.molcel.2016.11.015. PMID: 28107648.
• Liu Z, Kraus WL. Catalytic-independent functions of PARP-1 determine Sox2 pioneer activity at intractable genomic loci. Mol Cell. 2017 Feb 16;65(4):589-603.e9. doi: 10.1016/j.molcel.2017.01.017. PMID: 28212747.
• Gibson BA, Zhang Y, Jiang H, Hussey KM, Shrimp JH, Lin H, Schwede F, Yu Y, Kraus WL. Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation. Science. 2016 Jul 1;353(6294):45-50. doi: 10.1126/science.aaf7865. Epub 2016 Jun 2. PMID: 27256882.
• Krishnakumar R, Kraus WL. PARP-1 Regulates chromatin structure and transcription through a KDM5B-dependent Pathway. Mol Cell. 2010 Sep 10;39(5):736-49. doi: 10.1016/j.molcel.2010.08.014. PMID: 20832725.
• Gamble MJ, Frizzell KM, Yang C, Krishnakumar R, Kraus WL. The histone variant macroH2A1 marks repressed autosomal chromatin, but protects a subset of its target genes from silencing. Genes Dev. 2010 Jan 1;24(1):21-32. doi: 10.1101/gad.1876110. Epub 2009 Dec 15. PMID: 20008927.
• Krishnakumar R, Gamble MJ, Frizzell KM, Berrocal JG, Kininis M, Kraus WL. Reciprocal binding of PARP-1 and histone H1 at promoters specifies transcriptional outcomes. Science. 2008 Feb 8;319(5864):819-21. doi: 10.1126/science.1149250. PMID: 18258916.

Noncoding RNAs

• Gadad SS, Camacho CV, Gong X, Thornton M, Malladi VS, Nagari A, Sundaresan A, Nandu T, Koul S, Peng Y, Kraus WL. X-linked cancer-associated polypeptide (XCP) from lncRNA1456 modulates PHF8 histone demethylase activity to regulate the epigenome, gene expression, and cellular pathways in breast cancer. Oncogene. 2026 May;45(17):1557-1571. doi: 10.1038/s41388-026-03740-w. Epub 2026 Apr 1. PMID: 41922576.
• Kim DS, Camacho CV, Setlem R, Kim K, Malladi S, Hou TY, Nandu T, Gadad SS, Kraus WL. Functional Characterization of lncRNA152 as an Angiogenesis-Inhibiting Tumor Suppressor in Triple-Negative Breast Cancers. Mol Cancer Res. 2022 Nov 3;20(11):1623-1635. doi: 10.1158/1541-7786.MCR-22-0123. PMID: 35997635.
• Hou TY, Kraus WL. Analysis of estrogen-regulated enhancer RNAs identifies a functional motif required for enhancer assembly and gene expression. Cell Rep. 2022 Jun 14;39(11):110944. doi: 10.1016/j.celrep.2022.110944. PMID: 35705040.
• Huang D, Kim DS, Kraus WL. Specific binding of snoRNAs to PARP-1 promotes NAD+-dependent catalytic activation. Biochemistry. 2020 Apr 28;59(16):1559-1564. doi: 10.1021/acs.biochem.0c00100. Epub 2020 Apr 17. PMID: 32293172.
• Kim DS, Camacho CV, Nagari A, Malladi VS, Challa S, Kraus WL. Activation of PARP-1 by snoRNAs controls ribosome biogenesis and cell growth via the RNA helicase DDX21. Mol Cell. 2019 Sep 19;75(6):1270-1285.e14. doi: 10.1016/j.molcel.2019.06.020. Epub 2019 Jul 24. PMID: 31351877.
• Sun M, Gadad SS, Kim DS, Kraus WL. Discovery, annotation, and functional analysis of long noncoding RNAs controlling cell cycle gene expression and growth in breast cancer cells. Mol Cell. 2015 Aug 20;59(4):698-711. doi: 10.1016/j.molcel.2015.06.023. Epub 2015 Jul 30. PMID: 26236012.
• Luo X, Chae M, Krishnakumar R, Danko CG, Kraus WL. Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFα signaling revealed by integrated genomic analyses. BMC Genomics. 2014 Feb 24;15:155. doi: 10.1186/1471-2164-15-155. PMID: 24564208.
• Hah N, Murakami S, Nagari A, Danko CG, Kraus WL. Enhancer transcripts mark active estrogen receptor binding sites. Genome Res. 2013 Aug;23(8):1210-23. doi: 10.1101/gr.152306.112. Epub 2013 May 1. PMID: 23636943.
• Hah N, Danko CG, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL. A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell. 2011 May 13;145(4):622-34. doi: 10.1016/j.cell.2011.03.042. Epub 2011 May 5. Erratum in: Cell. 2011 Jun 24;145(7):1156. PMID: 21549415.

Genomics and Bioinformatics

• Koul S, Kwon M, Tapadar P, Dai Y, Song W, Dasovich M, Nandu T, Huang D, Camacho CV, Kraus WL. Mapping the Subtype-Specific PARP1 ADP-ribosylated Proteome in Breast Cancer Cells. Mol Cancer Res. 2026 May 28. doi: 10.1158/1541-7786.MCR-25-1068. PMID: 42206981.
• Tripathy S, Nagari A, Chiu SP, Nandu T, Camacho CV, Mahendroo M, Kraus WL. Relaxin Modulates the Genomic Actions and Biological Effects of Estrogen in the Myometrium. Endocrinology. 2024 Sep 26;165(11):bqae123. doi: 10.1210/endocr/bqae123. PMID: 39283953.
• Owen DM, Kwon M, Huang X, Nagari A, Nandu T, Kraus WL. Genome-wide identification of transcriptional enhancers during human placental development and association with function, differentiation, and disease. Biol Reprod. 2023 Dec 11;109(6):965-981. doi: 10.1093/biolre/ioad119. PMID: 37694817.
• Huang D, Camacho CV, Martire S, Nagari A, Setlem R, Gong X, Edwards AD, Chiu SP, Banaszynski LA, Kraus WL. Oncohistone Mutations Occur at Functional Sites of Regulatory ADP-Ribosylation. Cancer Res. 2022 Jul 5;82(13):2361-2377. doi: 10.1158/0008-5472.CAN-22-0742. PMID: 35472077.
• Challa S, Khulpateea BR, Nandu T, Camacho CV, Ryu KW, Chen H, Peng Y, Lea JS, Kraus WL. Ribosome ADP-ribosylation inhibits translation and maintains proteostasis in cancers. Cell. 2021 Aug 19;184(17):4531-4546.e26. doi: 10.1016/j.cell.2021.07.005. Epub 2021 Jul 26. PMID: 34314702.
• Gupte R, Nandu T, Kraus WL. Nuclear ADP-ribosylation drives IFNγ-dependent STAT1α enhancer formation in macrophages. Nat Commun. 2021 Jun 24;12(1):3931. doi: 10.1038/s41467-021-24225-2. PMID: 34168143.
• Palavalli Parsons LH, Challa S, Gibson BA, Nandu T, Stokes MS, Huang D, Lea JS, Kraus WL. Identification of PARP-7 substrates reveals a role for MARylation in microtubule control in ovarian cancer cells. Elife. 2021 Jan 21;10:e60481. doi: 10.7554/eLife.60481. PMID: 33475085.
• Huang D, Camacho CV, Setlem R, Ryu KW, Parameswaran B, Gupta RK, Kraus WL. Functional Interplay between Histone H2B ADP-Ribosylation and Phosphorylation Controls Adipogenesis. Mol Cell. 2020 Sep 17;79(6):934-949.e14. doi: 10.1016/j.molcel.2020.08.002. Epub 2020 Aug 20. PMID: 32822587.
• Ryu KW, Nandu T, Kim J, Challa S, DeBerardinis RJ, Kraus WL. Metabolic regulation of transcription through compartmentalized NAD+ biosynthesis. Science. 2018 May 11;360(6389):eaan5780. doi: 10.1126/science.aan5780. PMID: 29748257.
• Franco HL, Nagari A, Malladi VS, Li W, Xi Y, Richardson D, Allton KL, Tanaka K, Li J, Murakami S, Keyomarsi K, Bedford MT, Shi X, Li W, Barton MC, Dent SYR, Kraus WL. Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis. Genome Res. 2018 Feb;28(2):159-170. doi: 10.1101/gr.226019.117. Epub 2017 Dec 22. PMID: 29273624.
• Nagari A, Murakami S, Malladi VS, Kraus WL. Computational approaches for mining GRO-Seq data to identify and characterize active enhancers. Methods Mol Biol. 2017;1468:121-38. doi: 10.1007/978-1-4939-4035-6_10. PMID: 27662874.
• Danko CG, Hyland SL, Core LJ, Martins AL, Waters CT, Lee HW, Cheung VG, Kraus WL, Lis JT, Siepel A. Identification of active transcriptional regulatory elements from GRO-seq data. Nat Methods. 2015 May;12(5):433-8. doi: 10.1038/nmeth.3329. Epub 2015 Mar 23. PMID: 25799441.
• Chae M, Danko CG, Kraus WL. groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data. BMC Bioinformatics. 2015 Jul 16;16:222. doi: 10.1186/s12859-015-0656-3. PMID: 26173492.
• Danko CG, Chae M, Martins A, Kraus WL. groHMM: GRO-seq Analysis Pipeline. R package version 1.0.0. Bioconductor. (Software) www.bioconductor.org/packages/release/bioc/html/groHMM.html

Reviews

• Huang D, Kraus WL. The expanding universe of PARP1-mediated molecular and therapeutic mechanisms. Mol Cell. 2022 Jun 16;82(12):2315-2334. doi: 10.1016/j.molcel.2022.02.021. Epub 2022 Mar 9. PMID: 35271815. (Review)
• Challa S, Stokes MS, Kraus WL. MARTs and MARylation in the Cytosol: Biological Functions, Mechanisms of Action, and Therapeutic Potential. Cells. 2021 Feb 3;10(2):313. doi: 10.3390/cells10020313. PMID: 33546365. (Review)
• Hou TY, Kraus WL. Spirits in the material world: Enhancer RNAs in transcriptional regulation. Trends Biochem Sci. 2021 Feb;46(2):138-153. doi: 10.1016/j.tibs.2020.08.007. Epub 2020 Sep 1. PMID: 32888773. (Review)
• Cambronne XA, Kraus WL. Location, Location, Location: Compartmentalization of NAD⁺ Synthesis and Functions in Mammalian Cells. Trends Biochem Sci. 2020 Oct;45(10):858-873. doi: 10.1016/j.tibs.2020.05.010. Epub 2020 Jun 25. PMID: 32595066. (Review)
• Gupte R, Liu Z, Kraus WL. PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes. Genes Dev. 2017 Jan 15;31(2):101-126. doi: 10.1101/gad.291518.116. PMID: 28202539. (Review)
• Liu X, Kraus WL, Bai X. Ready, pause, go: regulation of RNA polymerase II pausing and release by cellular signaling pathways. Trends Biochem Sci. 2015 Sep;40(9):516-25. doi: 10.1016/j.tibs.2015.07.003. Epub 2015 Aug 4. PMID: 26254229. (Review)
• Ryu KW, Kim DS, Kraus WL. New facets in the regulation of gene expression by ADP-ribosylation and poly(ADP-ribose) polymerases. Chem Rev. 2015 Mar 25;115(6):2453-81. doi: 10.1021/cr5004248. Epub 2015 Jan 9. PMID: 25575290. (Review)
• Sun M, Kraus WL. From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease. Endocr Rev. 2015 Feb;36(1):25-64. doi: 10.1210/er.2014-1034. Epub 2014 Nov 26. PMID: 25426780. (Review)
• Hah N, Kraus WL. Hormone-regulated transcriptomes: lessons learned from estrogen signaling pathways in breast cancer cells. Mol Cell Endocrinol. 2014 Jan 25;382(1):652-664. doi: 10.1016/j.mce.2013.06.021. Epub 2013 Jun 28. PMID: 23810978. (Review)