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.
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. Molecular 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