Research

The objective of the RNA Bioscience Initiative is to understand the role of RNA in biology, engage in collaborative research, create a fluid pipeline from basic science to clinical diagnostics and therapeutics, and train the next generation of RNA researchers.

Investigators on the CU Anschutz campus have already made important discoveries in the field, covering RNA structure-function, RNA biogenesis, mechanisms of regulation by non-coding RNAs, non-coding RNAs in disease, diagnostics, and therapeutics, cutting-edge RNA technologies and advanced genome-wide computational methods.

The RNA Bioscience Initiative continues to make substantial and sustained contributions to four major research areas:

Highlights

A brief look at the latest discoveries from RBI faculty and trainees.

The pausing zone and control of RNA polymerase II elongation by Spt5: Implications for the pause-release model

October 6, 2022

Nova Fong, Ryan M Sheridan, Srinivas Ramachandran, David L Bentley

The pause-release model of transcription proposes that 40-100 bases from the start site RNA Pol II pauses, followed by release into productive elongation. Pause release is facilitated by the PTEFb phosphorylation of the RNA Pol II elongation factor, Spt5. We mapped paused polymerases by eNET-seq and found frequent pausing in zones that extend ∼0.3-3 kb into genes even when PTEFb is inhibited. The fraction of paused polymerases or pausing propensity declines gradually over several kb and not abruptly as predicted for a discrete pause-release event. Complete Abstract

Single-cell transcriptome mapping identifies a local, innate B cell population driving chronic rejection after lung transplantation

September 22, 2022

Natalia F Smirnova, Kent Riemondy, Marta Bueno, Susan Collins, Pavan Suresh, Xingan Wang, Kapil N Patel, Carlyne Cool, Melanie Königshoff, Nirmal S Sharma, Oliver Eickelberg

Bronchiolitis obliterans syndrome (BOS) is the main reason for poor outcomes after lung transplantation (LTx). We and others have recently identified B cells as major contributors to BOS after LTx. The extent of B cell heterogeneity and the relative contributions of B cell subpopulations to BOS, however, remain unclear. Here, we provide a comprehensive analysis of cell population changes and their gene expression patterns during chronic rejection after...  Complete Abstract

High-throughput identification of RNA localization elements in neuronal cells

September 15, 2022

Ankita Arora, Roberto Castro-Gutierrez, Charlie Moffatt, Davide Eletto, Raquel Becker, Maya Brown, Andreas E Moor, Holger A Russ, J Matthew Taliaferro

Hundreds of RNAs are enriched in the projections of neuronal cells. For the vast majority of them, though, the sequence elements that regulate their localization are unknown. To identify RNA elements capable of directing transcripts to neurites, we deployed a massively parallel reporter assay that tested the localization regulatory ability of thousands of sequence fragments drawn from endogenous mouse 3' UTRs. We identified peaks of regulatory activity within several 3' UTRs and found that sequences derived from these peaks were both necessary… Complete Abstract

Diverse cell-specific patterns of alternative polyadenylation in Drosophila

September 13, 2022

Seungjae Lee, Yen-Chung Chen, FCA Consortium, Austin E Gillen, J Matthew Taliaferro, Bart Deplancke, Hongjie Li, Eric C Lai

Most genes in higher eukaryotes express isoforms with distinct 3' untranslated regions (3' UTRs), generated by alternative polyadenylation (APA). Since 3' UTRs are predominant locations of post-transcriptional regulation, APA can render such programs conditional, and can also alter protein sequences via alternative last exon (ALE) isoforms. We previously used 3'-sequencing from diverse Drosophila samples to define multiple tissue-specific APA landscapes. Here, we exploit comprehensive single nucleus RNA-sequencing data (Fly Cell Atlas) to elucidate cell-type expression of 3' UTRs  across >250 adult Drosophila cell types. We reveal the cellular bases of multiple tissue-specific APA/ALE programs, such as 3' UTR lengthening in differentiated neurons and 3' UTR shortening in spermatocytes and spermatids.  Complete Abstract

Cryo-EM reveals an entangled kinetic trap in the folding of a catalytic RNA

August 26, 2022

Steve L Bonilla, Quentin Vicens, Jeffrey S Kieft

Functional RNAs fold through complex pathways that can contain misfolded "kinetic traps." A complete model of RNA folding requires understanding the formation of these misfolded states, but they are difficult to characterize because of their transient and potentially conformationally dynamic nature. We used cryo-electron microscopy (cryo-EM) to visualize a long-lived misfolded state in the folding pathway of the Tetrahymena thermophila group I intron, a paradigmatic RNA structure-function model system. The structure revealed how this state forms ... Complete Abstract

Transcription factor-nucleosome dynamics from plasma cfDNA identifies ER-driven states in breast cancer

August 26, 2022, 2021

Satyanarayan Rao, Amy L Han, Alexis Zukowski, Etana Kopin, Carol A Sartorius, Peter Kabos, Srinivas Ramachandran

Genome-wide binding profiles of estrogen receptor (ER) and FOXA1 reflect cancer state in ER+ breast cancer. However, routine profiling of tumor transcription factor (TF) binding is impractical in the clinic. Here, we show that plasma cell-free DNA (cfDNA) contains high-resolution ER and FOXA1 tumor binding profiles for breast cancer. Enrichment of TF footprints in plasma reflects the binding strength of the TF in originating tissue. We defined pure in vivo tumor TF signatures in plasma using ER+ breast cancer xenografts, which can distinguish... Complete Abstract

Limited effects of m⁶A modification on mRNA partitioning into stress granules

June 29, 2022

Anthony Khong, Tyler Matheny, Thao Ngoc Huynh, Vincent Babl, Roy Parker

The presence of the m6A modification in mammalian mRNAs is proposed to promote mRNA recruitment to stress granules through the interaction with YTHDF proteins. We test this possibility by examining the accumulation of mRNAs in stress granules in both WT and ∆METTL3 mES cells, which are deficient in m6A modification. A critical observation is that all m6A modified mRNAs partition similarly into stress granules in both wild-type and m6A-deficient cells by single-molecule FISH. Moreover, multiple linear regression analysis indicates m6A modification explains only 6% of the variance in stress granule localization when controlled for length. Finally, the artificial tethering of 25... Complete Abstract

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