Publications

Signal-Regulated Transcription

• Hah N., Danko C.G., Core L., Waterfall J.J., Siepel A., Lis J.T., Kraus W.L. (2011) A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell 145:622-634. PMID: 21549415
• Hah N., Murakami S., Nagari A., Danko C.G., Kraus W.L. (2013) Enhancer transcripts mark active estrogen receptor binding sites. Genome Research 23:1210-1223. PMID: 23636943
• Danko C.G., Hah N., Luo X., Martins A., Siepel A., Kraus W.L. (2013) Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Molecular Cell 0:212-222. PMCID: PMC3640649
• Luo X., Chae M., Krishnakumar R., Danko C.G., Kraus W.L. (2014) Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFα signaling revealed by integrated genomic analyses. BMC Genomics. 15:155. PMID: 24564208
• Franco H.L., Nagari A., Kraus W.L. (2015) TNFα signaling exposes latent estrogen receptor binding sites to alter the breast cancer cell transcriptome. Molecular Cell. 58:21-34. PMCID: PMC25752574
• Murakami S., Nagari A., Kraus W.L. (2017) Dynamic assembly and activation of estrogen receptor α enhancers through coregulator switching. Genes Dev. 31:1535-1548. PMID: 28887413
• Franco H.L., Nagari A., Malladi V.S., Li W., Xi Y., Richardson D., Allton K.L., Tanaka K., Li J., Murakami S., Keyomarsi K., Bedford M.T., Shi X., Li W., Barton M.C., Dent S.Y.R., Kraus W.L. (2018) Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis. Genome Res. 28(2):159-170. PMID: 29273624
• Ryu K.W., Nandu T., Kim J., Challa S., DeBerardinis R.J., Kraus W.L. (2018) Metabolic regulation of transcription through compartmentalized NAD+ biosynthesis. Science. 360(6389):eaan5780. PMID: 29748257
• Gupte R., Nandu T., Kraus W.L. (2021) Nuclear ADP-ribosylation drives IFNγ-dependent STAT1α enhancer formation in macrophages. Nat Commun. 12(1):3931. PMID: 34168143
• Hou T.Y., Kraus W.L. (2022) Analysis of estrogen-regulated enhancer RNAs identifies a functional motif required for enhancer assembly and gene expression. Cell Reports. 39:110944. PMCID: PMC9246336

PARPs and NAD⁺

• Krishnakumar R., Gamble M.J., Frizzell K.M., Berrocal J.G., Kininis M., Kraus W.L. (2008) Reciprocal binding of PARP-1 and histone H1 at promoters specifies transcriptional outcomes. Science. 319:819-821. PMID: 18258916
• Gamble M.J., Frizzell K.M., Yang C., Krishnakumar R., Kraus W.L. (2010) The histone variant macroH2A1 marks repressed autosomal chromatin, but protects a subset of its target genes from silencing. Genes Dev. 24(1), 21-32. PMCID: PMC2802188
• Krishnakumar R., Kraus W.L. (2010) PARP-1 Regulates chromatin structure and transcription through a KDM5B-dependent Pathway. Molecular Cell. 39:736-749. PMCID: PMC2939044
• Gibson B.A., Zhang Y., Jiang H., Hussey K.M., Shrimp J.H., Lin H., Schwede F., Yu Y., Kraus W.L. (2016) Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation. Science. 353:45-50. PMID: 27256882
• Liu Z., Kraus W.L. (2017) Catalytic-independent functions of PARP-1 determine Sox2 pioneer activity at intractable genomic loci. Molecular Cell. 65: 589-603. PMID: 28212747
• Luo X., Ryu K.W., Kim D.K., Nandu T., Medina C.J., Gupte R., Gibson B.A., Soccio R.E., Yu Y., Gupta R., Kraus W.L. (2017) PARP-1 controls the adipogenic transcription program by PARylating C/EPBβ and modulating its transcriptional activity. Molecular Cell. 65:260-271. PMID: 28107648
• Ryu K.W., Nandu T., Kim ;J., Challa S., DeBerardinis R.J., Kraus W.L. (2018) Metabolic regulation of transcription through compartmentalized NAD(+) biosynthesis. Science. 360(6389):eaan5780. PMID: 29748257
• Kim D.S., Camacho C.V., Nagari A., Malladi V.S., Challa S., Kraus W.L. (2019) Activation of PARP-1 by snoRNAs controls ribosome biogenesis and cell growth via the RNA helicase DDX21. Mol Cell. 75(6):1270-1285. PMID: 31351877
• Huang D., Kim D.S., Kraus W.L. (2020) Specific binding of snoRNAs to PARP-1 promotes NAD+-dependent catalytic activation. Biochemistry. 59(16):1559-1564. PMID: 32293172
• Huang D., Camacho V.C., Setlem R., Ryu K.W., Parameswaran B., Gupta R.K., Kraus W.L. (2020) Functional Interplay between Histone H2B ADP-Ribosylation and Phosphorylation Controls Adipogenesis. Mol Cell. 79(6):934-939. PMID: 32822587
• Palavalli Parsons L.H., Challa S., Gibson B.A., Nandu T., Stokes M.S., Huang D., Lea J.S., Kraus W.L. (2021) Identification of PARP-7 substrates reveals a role for MARylation in microtubule control in ovarian cancer cells. Elife. 10:e60481. PMID: 33475085
• Gupte R., Nandu T., Kraus W.L. (2021) Nuclear ADP-ribosylation drives IFNγ-dependent STAT1α enhancer formation in macrophages. Nat Commun. 12(1):3931. PMID: 34168143
• Challa S., Khulpateea B.R., Nandu T., Camacho C.V., Ryu K.W., Chen H., Peng Y., Lea J.S., Kraus W.L. (2021) Ribosome ADP-ribosylation inhibits translation and maintains proteostasis in cancers. Cell. 184:4531-4546.e26. PMCID: PMC8380725
• Huang D., Camacho C.V., Martire S., Nagari A., Setlem R., Gong X., Edwards A.D., Chiu S.P., Banaszynski L.A., Kraus W.L. (2022) Oncohistone Mutations Occur at Functional Sites of Regulatory ADP-Ribosylation. Cancer Res. 82(13):2361-2377. PMID 35472077
• Challa S., Ryu K.W., Whitaker A.L., Abshier J.C., Camacho C.V., Kraus W.L. (2022) Development and characterization of new tools for detecting poly(ADP-ribose) in vitro and in vivo. Elife. 11:e72464. PMID: 35476036
• Jones A., Kraus W.L. (2022) Multiomics analysis of the NAD+-PARP1 axis reveals a role for site-specific ADP-ribosylation in splicing in embryonic stem cells. Cell Rep. 36(9-10):601-617. PMID 35654456

Noncoding RNAs

• Hah N., Danko C.G., Core L., Waterfall J.J., Siepel A., Lis J.T., Kraus W.L. (2011) A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell. 145:622-634. PMCID: PMC3099127
• Hah N., Murakami S., Nagari A., Danko C.G., Kraus W.L. (2013) Enhancer transcripts mark active estrogen receptor binding sites. Genome Research. 23:1210-1223. PMCID: PMC3730096
• Luo X., Chae M., Krishnakumar R., Danko C.G., Kraus W.L. (2014) Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFα signaling revealed by integrated genomic analyses. BMC Genomics. 15:155. PMCID: PMC3945043
• Sun M., Gadad S.S., Kraus W.L. (2015) Discovery, annotation, and functional analysis of long noncoding RNAs controlling cell cycle gene expression and growth in breast cancer cells. Molecular Cell. 59:698-711. PMCID: PMC4546522
• Kim D.S., Camacho C.V., Nagari A., Malladi V.S., Challa S., Kraus W.L. (2019) Activation of PARP-1 by snoRNAs controls ribosome biogenesis and cell growth via the RNA helicase DDX21. Mol Cell. 75(6):1270-1285. PMID: 31351877
• Huang D., Kim D.S., Kraus W.L. (2020) Specific binding of snoRNAs to PARP-1 promotes NAD+-dependent catalytic activation. Biochemistry. 59(16):1559-1564. PMID: 32293172
• Hou T.Y., Kraus W.L. (2022) Analysis of estrogen-regulated enhancer RNAs identifies a functional motif required for enhancer assembly and gene expression. Cell Reports. 39:110944. PMCID: PMC9246336

Genomics and Bioinformatics

• Danko C.G., Chae M., Martins A., Kraus W.L. (2014) groHMM: GRO-seq Analysis Pipeline. R package version 1.0.0.  Bioconductor. (Software) www.bioconductor.org/packages/release/bioc/html/groHMM.html
• Chae M., Danko C.G., Kraus W.L. (2015) groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data. BMC Bioinformatics. 16:222. PMCID: PMC4502638
• Danko C.G., Hyland S.L., Core L.J., Martins A.L., Waters C.T., Lee H.W., Cheung V.G., Kraus W.L., Lis J.T., Siepel A. (2015) Identification of active transcriptional regulatory elements from GRO-seq data. Nat Methods. 12(5): 433-438. PMCID: 4507281
• Nagari A., Murakami S., Malladi V. S., Kraus W. L. (2017) Computational approaches for mining GRO-Seq data to identify and characterize active enhancers. Methods Mol Biol. 1468: 121-138. PMCID: PMC5522910
• Franco H.L., Nagari A., Malladi V. S., Li W., Xi Y., Richardson D., Allton K.L., Tanaka K., Li J., Murakami S., Keyomarsi K., Bedford M.T., Shi X., Li W., Barton M.C., Dent S.Y.R., Kraus W. L. (2018) Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis. Genome Res. 28(2): 159-170. PMID: 29273624 
• Ryu K.W., Nandu T., Kim J., Challa S., DeBerardinis R.J., Kraus W.L. (2018) Metabolic regulation of transcription through compartmentalized NAD+ biosynthesis. Science. 360(6389):eaan5780. PMID: 29748257
• Huang D., Camacho V.C., Setlem R., Ryu K.W., Parameswaran B., Gupta R.K., Kraus W.L. (2020) Functional Interplay between Histone H2B ADP-Ribosylation and Phosphorylation Controls Adipogenesis. Mol Cell. 79(6):934-939. PMID: 32822587
• Palavalli Parsons L.H., Challa S., Gibson B.A., Nandu T., Stokes M.S., Huang D., Lea J.S., Kraus W.L. (2021) Identification of PARP-7 substrates reveals a role for MARylation in microtubule control in ovarian cancer cells. Elife. 10:e60481. PMID: 33475085
• Gupte R., Nandu T., Kraus W.L. (2021) Nuclear ADP-ribosylation drives IFNγ-dependent STAT1α enhancer formation in macrophages. Nat Commun. 12(1):3931. PMID: 34168143
• Challa S., Khulpateea B.R., Nandu T., Camacho C.V., Ryu K.W., Chen H., Peng Y., Lea J.S., Kraus W.L. (2021) Ribosome ADP-ribosylation inhibits translation and maintains proteostasis in cancers. Cell. 184:4531-4546.e26. PMCID: PMC8380725
• Huang D., Camacho C.V., Martire S., Nagari A., Setlem R., Gong X., Edwards A.D., Chiu S.P., Banaszynski L.A., Kraus W.L. (2022) Oncohistone Mutations Occur at Functional Sites of Regulatory ADP-Ribosylation. Cancer Res. 82(13):2361-2377. PMID 35472077

Current Reviews

• Huang D., Kraus W.L. (2022) The expanding universe of PARP1-mediated molecular and therapeutic mechanisms. Mol Cell. 82(12):2315-2334. PMID: 35271815 (Review)
• Hou T.Y., Kraus W.L. (2021) Spirits in the material world: Enhancer RNAs in transcriptional regulation. Trends in Biochem Sci. 46(2):138-153. PMID: 32888773 (Review)
• Cambronne X.A., Kraus W.L. (2020) Location, Location, Location: Compartmentalization of NAD⁺ Synthesis and Functions in Mammalian Cells. Trends Biochem Sci. 45(10):858-873. PMID: 32595066 (Review)
• Gupte R., Liu Z., Kraus W.L. (2017) PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes.  Genes Dev. 31(2): 101-126. PMID: 28202539. (Review)
• Liu X., Kraus W.L., Bai X. (2015) Ready, pause, go: regulation of RNA polymerase II pausing and release by cellular signaling pathways. Biochem Sci. 40(9): 516-25. PMID: 26254229. (Review)
• Ryu K.W., Kim D.S., Kraus W.L. (2015) New Facets in the regulation of gene expression by ADP-ribosylation and poly(ADP-ribose) polymerases. Chem Rev. 115(6): 2453-81. PMID: 25575290. (Review)
• Sun M., Kraus W.L. (2015) From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease. Endocr Rev. 36(1): 25-64. PMID: 25426780. (Review)
• Hah N., Kraus W.L. (2014) Hormone-regulated transcriptomes: lessons learned from estrogen signaling pathways in breast cancer cells. Mol Cell Endocrinol. 382(1): 652-664. PMID: 23810978. (Review)