Many extracellular and intracellular signals culminate at signal-regulated transcription factors in the nuclei of cells. The Kraus Lab is interested in how these signals control transcription factor activity, enhancer formation, and target gene expression in a broad array of biological systems. We are particularly interested in pathways controlled by estrogen receptor alpha (ERα), NF-kβ, and Stat1α. We are also interested in the kinetics of the signal-regulated transcriptional response, and the detailed molecular mechanisms of transcription complex assembly and function. We use a wide range of methodological approaches, from biochemistry to genomics, to study fundamental questions related to normal physiology and disease. The Kraus Lab has leveraged new genomic methodologies, including global run-on sequencing (GRO-seq), to explore signal-regulated transcription in multiple cell types.
Current projects are focused on: (1) enhancer assembly and function, (2) mechanisms of target gene expression in response to cellular signals, and (3) downstream biological outcomes related to cancer, stem cells, inflammation, metabolism, and reproduction.
Our studies are revealing the molecular mechanisms and biological outcomes of various cellular signaling patterns.
Selected Publications
- 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.