The past decade has seen an incredible growth of genomic approaches to query gene regulation and the nature of the transcriptome on a global scale. The Kraus Lab has leveraged new genomic methodologies, including global run-on sequencing (GRO-seq), to explore signal-regulated transcription in multiple cell types. We have also annotated new non-coding RNAs, including long non-coding RNAs (lncRNAs), antisense RNAs, and enhancer RNAs, and have begun to explore their functions.
Our recent focus has been on the biological functions and molecular actions of lncRNAs and enhancer RNAs, including short peptides derived from lncRNAs. Our studies on non-coding RNAs are helping to increase our understanding of how the transcriptome is controlled by, as well as regulates, signal-regulated transcription.
Selected Publications
- 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.