SENSING RNA

Research

Our lab aims to address fundamental questions in RNA recognition at the molecular and cellular level. Current focus includes microRNA biogenesis and RNA sensing in innate immunity. We employ a variety of tools including molecular biology, biochemistry, functional genomics, imaging, and mass spectrometry, and are eager to develop new methods to tackle existing challenges.

1. Good and bad hairpins: How does the cell make microRNAs?

MicroRNAs (miRNAs) are ~22 nt RNAs that play key roles in post-transcriptional gene regulation. They are first transcribed from the genome as hairpin-containing transcripts known as primary miRNAs (pri-miRNAs). These hairpin-like structures are then processed by the Microprocessor complex, consisting Drosha and DGCR8. How the Microprocessor discriminates bona fide miRNA hairpins in comparison to the numerous other hairpins transcribed from the genome has been a mystery. Our work and that of others have identified pri-miRNA features that are recognized by the Microprocessor complex and associated factors, providing a unifying model of miRNA biogenesis. Using this model, we achieved the first de novo design of miRNA genes.

Our pri-miRNA model also revealed some natural, well-expressed miRNAs with apparent structural defects—how are they able to still enter the miRNA pathway? We showed that the processing of these suboptimal hairpins is made possible by their proximity to another, optimal miRNA hairpin, a phenomenon we call “cluster assistance”. We further discovered that Enhancer of Rudimentary Homolog (ERH), a protein not yet known to associate with the Microprocessor complex, was required for this assistance. Cluster assistance substantially increases the spectrum of miRNA hairpins that can be efficiently processed, and helps explain why miRNA preferentially reside in clusters. Moving forward, we are interested in addressing the following questions:

• What is the molecular mechanism of cluster assistance?

• What is the scope of cluster assistance?

• What is the function of cluster assistance?

2. Self and non-self RNAs: How does the cell tell friends from foe?

Self/non-self RNA discrimination by the innate immune system protects the host against RNA viruses while ensuring proper cell function. Compared to the recognition of pri-miRNA substrates by Microprocessor, the distinction between self and non-self RNAs in the cell is much more complex. Endogenous RNAs may come in different forms with a variety of end chemistry, modification status, and associated protein repertoire. Meanwhile, exogenous RNAs that the cells need to recognize may share many of these features and only differ in a few. In addition, endogenous RNA metabolism is a delicate process. Accumulating evidence suggests that self RNAs can become immunogenic, for example, when they are mis-processed, mis-localized, or not properly bound to partner proteins. We are particularly interested in understanding how cells avoid unwanted self recognition. Specifically, we want to ask:

• How do cells maintain RNA homeostasis to prevent hyperactive innate immune response?

• Are there unknown RNA sensors?

• Does RNA self-recognition contribute to autoimmune diseases and how?

We employ an integrated approach to address fundamental questions in RNA sensing in innate immunity, and by doing so we aim to bring new insights into autoimmunity, virus–­­host interactions, immuno-oncology, and RNA therapeutics.

Publications

Exploration of Nuclear Proteomes in the Ciliate Oxytricha trifallax

Lu MW, Beh LY, Yerlici VT, Fang W, Kulej K, Garcia BA, Landweber LF

Microorganisms 11(2) (2023) PMID: 36838311

Degradation of host translational machinery drives tRNA acquisition in viruses

Yang JY, Fang W, Miranda-Sanchez F, Brown JM, Kauffman KM, Acevero CM, Bartel DP, Polz MF, Kelly L

Cell Systems 12:771–779 (2021) PMID 34143976

MicroRNA clustering assists processing of suboptimal microRNA hairpins through the action of the ERH protein

Fang W and Bartel DP

Molecular Cell 78: 289–302 (2020) PMID 32302541

The menu of features that define primary microRNAs and enable de novo design of microRNA genes

Fang W and Bartel DP

Molecular Cell 60: 131–145 (2015) PMID 26412306

Editorial: The Long, the Short, and the Unstructured: A Unifying Model of miRNA Biogenesis

Denzler R and Stoffel M, Molecular Cell 60: 4–6 (2015) PMID 26431024

RNA-mediated genome rearrangement: hypotheses and evidence

Fang W and Landweber LF

BioEssays 35: 84–87 (2013) PMID 23281134

Genomes on the edge: programmed genome instability in ciliates

Bracht JR, Fang W, Goldman AD, Dolzhenko E, Stein EM, Landweber LF

Cell 152: 406–416 (2013) PMID 23374338

Piwi-interacting RNAs protect DNA against loss during Oxytricha genome rearrangement

Fang W, Wang X, Bracht JR, Nowacki M, Landweber LF

Cell 151: 1243–1255 (2012) PMID 23217708

Editorial: Small RNAs of opposite sign… but same absolute value

Sontheimer E, Cell 151: 1157–1158 (2012) PMID 23217700

Detection of a common chimeric transcript between human chromosome 7 and 16

Fang W, Wei Y, Kang Y, Landweber LF

Biology Direct 7: 49 (2012) PMID 23273016 

RNA-mediated epigenetic regulation of DNA copy number

Nowacki M, Haye J, Fang W, Vijayan V, Landweber LF

Proceedings of the National Academy of Sciences 107: 22140–22144 (2010) PMID 21078984