Korennykh Lab Research

Immune & Stress Response Mediated by RNA

We seek a precise molecular understanding of how coding and non-coding RNAs facilitate mammalian stress responses. In particular, we focus on stress-activated RNA cleavage mechanisms, which regulate gene expression and control cell fate to eliminate damaged/overwhelmed cells.

Human cells activate these mechanisms in response to a strong mammalian immunogen - double-stranded RNA (dsRNA). We study the molecular machinery involved in this cellular program by X-ray crystallography, biochemistry and biophysics. This work goes hand in hand with cell biology and genomics projects in the laboratory, which employ RNA-seq and custom RNA-seq methods.

Our ultimate goal is to gain fundamental knowledge with clear biomedical implications, which would elucidate the roles of coding and non-coding RNAs in pathogen defense, interferon and inflammatory signaling and autoimmune diseases.

Keywords: Interferon, inflammation, dsRNA, tRNA, Y-RNA, t-RNA fragments, tRFs, Y-RNA fragments, YRFs, autoantigen, RNase L, oligoadenylate, 2-5A, OAS1, OAS3, microRNA, adhesion, apoptosis, lupus, metastasis, EMT.

Structural biology

Receptors of dsRNA. Our work is providing structural and biochemical insights into double-stranded RNA (dsRNA) sensors, which activate mRNA decay by producing a signaling RNA-like molecule "2-5A" with unusual 2',5'-linkages. The dsRNAs molecules are not abundant in normal cells, but they become abundant upon viral infections or DNA damage that presumably strips off repressive DNA methylation marks from endogenous retrovirus sites. The endogenous dsRNA production, surveillance and physiologic roles are very intriguing and not fully understood.

STRUCTURE OF HUMAN OAS1 WITH dsRNA 

Donovan J, Dufner M, Korennykh A.
PNAS 2013 Jan 29;110(5):1652-7.

HUMAN OAS3 IS A SENSOR OF LONG dsRNA

pic-3Human cells express three related but different sensors of dsRNA that synthesize 2-5A. Using X-ray crystallography and biochemistry we determined that the largest OAS family member, OAS3, is a selective sensor of long dsRNA. OAS3 contains three duplicated domains. The C-terminal domain (DIII) is catalytically active and makes 2-5A, whereas the N-terminal domain (DI) is catalytically inactive and serves for high-affinity dsRNA recruitment and for measurement of minimal dsRNA length.

PNAS 2015 Mar 31;112(13):3949-54.

DsRNA-induced mRNA decay. We are also learning about the 2-5A receptor, RNase L. RNase L contains a protein kinase domain and belongs to the family of more than 500 mammalian protein kinases. RNase L does not phosphorylate any known proteins, which makes it different from most kinases. Uniquely, RNase L cleaves cellular RNAs during the interferon response, which protects the cells from viruses and bacteria, and blocks cell proliferation. We solved the crystal structure of human RNase L with bound 2-5A and RNA substrate, which explains how this enzyme is regulated.

 STRUCTURE OF HUMAN RNASE L WITH 2-5A AND RNA SUBSTRATE

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Structure of human RNase L reveals the basis for regulated RNA decay in the IFN response.
Han Y, Donovan J, Rath S, Whitney G, Chitrakar A, Korennykh A.
Science. 2014 Mar 14;343(6176):1244-8.
 
Cell Reports 2012 Oct 25;2(4):902-13.
pic-6Leading Edge Select: The Fantastic RNase L
Cell 157, 2014
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Cell biology & RNA-seq

Another area of our work is understanding the precise mechanism and roles of mRNA cleavage by RNase L and by other immune proteins. It has been long known that RNase L is activated during the IFN response and that it can inhibit viral and bacterial infections, and cell proliferation. However, mapping the cellular mRNA targets that RNase L cleaves to achieve these effects proved challenging. We used a combination of RNA-seq strategies to identify the mRNA targets of RNase L and map its cellular program.

We found that RNase L cleaves the same mRNAs as are targeted by the microRNA miR-200. MiR-200 is a remarkable microRNA because it is a master regulator of cell adhesion, proliferation and is one of the key modulators of epithelial-to-mesenchymal transition (EMT) during metastasis. Thus, RNase L is functionally a mimic of miR-200. RNase L is unique in that unlike miR-200, it is activated downstream of IFN and dsRNA signaling. RNase L could be approximately described as an "on-demand miR-200 in the innate immune system".

As expected from our analogy, RNase L and miR-200 have many similar effects on human cells. Both block proliferation, both block adhesion and both target ZEB1 transcription factor and regulate cadherins.

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Human cells
KO = knockout

RNA-SEQ OF RNASE L TARGETS IN T47D HUMAN BREAST CANCER CELLS

FDR = false discovery rate (<0.25% is significant; <0.05% is excellent)
RNase L cleaves common mRNA targets of select microRNAs and avoids ribosomal and mitochondrial protein mRNAs
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GSEA and Rath-Korennykh gene signatures

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TargetScan 6 gene signatures

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THE EMERGING PATHWAY OF RNASE L

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KO = knockouts

PNAS 2015 Dec 29;112(52). 

Some of our main  techniques

X-ray crystallography
High-throughput RNA sequencing
Mammalian tissue culture
Biochemistry
Biophysics
Computational biology

Our work is funded by Princeton University, Sidney Kimmel Foundation, Burroughs Wellcome Foundation, and NIH.