TALIAFERRO LAB
Subcellular Transcriptomics
University of Colorado Anschutz Medical Campus
Subcellular Transcriptomics
Overview
Welcome to the Taliaferro lab in the Department of Biochemistry and Molecular Genetics at the University of Colorado School of Medicine. We study how the expression of genetic information is spatially regulated within a cell.
Individual mRNA molecules are often trafficked to specific cellular locations which facilitates robust, localized protein production where and when it is needed. Although thousands of mRNAs are asymmetrically distributed in cells, the RNA sequences and protein factors that regulate this process are unknown for the vast majority of messages.
Our lab uses experimental and computational methods to understand mechanisms behind this regulation and how disruption of the process can result in neurological disease.
Research
We study the spatial regulation of gene expression
The key to being efficient and success is having everything you need at the right place at the right time. As it turns out, this is true even on a subcellular level. Our group works toward understanding the sequences within RNA molecules that govern their spatial organization as well as the RNA binding proteins that mediate this process. The effects of RNA localization are most apparent in large, polarized cells.
As such, we use neuronal models and their subcellular fractionation as a system to study localized transcripts. The two main focuses in the lab are devoted to studying cis and trans regulators of RNA localization, respectively.
Cis elements direct RNA molecules to cellular destinations
What elements within the transcriptome have the ability to direct RNAs to subcellular locations? We and many others have shown that most such sequences, termed “zipcodes” for their sorting abilities, reside in the 3’ untranslated regions of mRNAs.
Using high-throughput screening, functional genomics, computational biology, as well as classical molecular and cell biology, we can zero in on sequences within transcripts that drive RNA localization.
Trans factors mediate the movement
Most RNA-based processes are driven through the complex interaction between RNA and proteins. RNA localization is no different. Several RNA binding proteins have been identified as key regulators of RNA localization. Mutations in some of these factors are associated with neurological disease, implicating the misregulation of RNA localization in the development of disease phenotypes.
With a functional genomics approach, we can identify individual transcripts that depend on the activity of specific RNA binding proteins for their proper localization, allowing insights into the mechanisms and specificities that govern RNA localization.
LAB MEMBERS
Matthew Taliaferro, Ph.D.
PrincipAL investigator
Ph.D., University of California, Berkeley
Postdoctoral Fellow, MIT
CV
Hei-yong Lo
MSTP Student
B.A. Washington University in St. Louis
Joelle lo
Graduate Student
B.S. Western Washington University
CHARLIE MOFFATT
GRADUATE STUDENT
B.A. University of California, Santa Barbara
KATIE VAETH
GRADUATE STUDENT
B.S. Saint Louis University
Megan pockalny
graduate student
B.S. University of California, San Diego
We are always looking for interested postdoc applicants! Send an email!
Alumni
Postdoctoral fellows
Amaresh Panda, Ph.D. Ramajuan Faculty Fellow, Institute of Life Sciences, Bhubaneswar, India
Krysta Engel, Ph.D. Assistant Research Professor, CU Anschutz
Ankita Arora, Ph.D. Science Writer, Nucleus Genomics, NYC
GRADUATE STUDENTS
Raeann Goering, Ph.D. Spatial Biology Scientist, Corteva Agriscience
Summer Students
Brandon Titus NIH BRAiN Initiative 2018
Pedro Tirado Velez RNA Bioscience Initiative Summer Intern 2019
Maya Brown RNA Bioscience Initiative Summer Intern 2021
Luis Gonzalez RNA Bioscience Initiative Summer Intern 2022
Nicole Sheptov RNA Bioscience Initiative Summer Intern 2023
NEWS
Charlie Moffatt has received an F31 fellowship from NIGMS! Huge congratulations, Charlie!
Molecular Biology Program student Megan Pockalny has joined our lab. We are very excited to have her!
We have received an equipment supplement from NIGMS for a sorely needed new microscope.
Former graduate student Raeann Goering has accepted a position as a scientist with Corteva Agriscience. Good luck Rae!
We have published a paper which you can find here describing how RNA localization mechanisms operate in predictably similar ways across cell types with vastly different morphologies.
Postdoc Ankita Arora has accepted a position as a science writer with Nucleus Genomics. Good luck Ankita!
2023
A big congratulations to our first graduate student, Raeann Goering, for successfully defending her thesis and graduating!
Molecular Biology Program student Katie Vaeth has joined our lab! She will be a joint student with the lab of Rytis Prekeris. Welcome Katie!
We have published a paper describing the use of massively parallel reporter assays for identifying RNA localization regulatory elements.
Graduate student Charlie Moffatt was awarded a T32 fellowship!
We have published 4 papers! A review on connections between alternative polyadenylation and RNA localization which you can find here, a review on the use of transcriptome-scale methods for studying RNA localization that can be found here, a paper on the use of single molecule FISH for visualizing RNA molecules in cells which you can find here, and a methods paper describing the use of Halo-seq, that can be found here.
2022
2021
We have published a paper describing an RNA proximity labeling method we call Halo-seq. You can read the paper here. Additionally, there was a nice write up about this approach which you can find here.
In collaboration with the lab of Chad Pearson, we have been awarded a grant by the Keck Foundation to study connections between RNA localization and control of cell division.
Graduate student Hei-Yong Lo has been awarded a place on the Molecular Biology Program’s T32 Training Grant and has been named an RNA Scholar by the RNA Bioscience Initiative!
Welcome a new graduate student, Charlie Moffatt! Charlie is a member of the Molecular Biology Graduate Program.
We have published a paper describing LABRAT, our software for quantifying alternative polyadenylation. You can read the paper here, and download LABRAT here. Additionally, we have published a methods paper describing the use of LABRAT here.
Maya Brown will be joining us this summer from Howard University as part of the RNA Bioscience Initiative Summer Internship Program. Welcome Maya!
We have published a paper describing a protocol we have developed for the separation of neuronal cells into soma and neurite fractions for further analysis, particularly of RNA localization. You can read all about it here.
2020
Postdoctoral fellow Krysta Engel has accepted a position as an Assistant Research Professor in the laboratory of Craig Jordan at CU Anschutz. Good luck Krysta!
Graduate student Raeann Goering has been named an RNA Scholar by the RNA Bioscience Initiative!
Welcome a new graduate student, Joelle Lo! Joelle is a member of the Molecular Biology Graduate Program.
Graduate students Raeann Goering and Hei-Yong Lo have both been awarded places on the Molecular Biology Program’s T32 Training Grant!
A team led by Raeann Goering has published a study on how FMRP regulates RNA localization in neuronal cells. Read about it here!
The lab has published a review on the mechanisms and consequences of subcellular RNA localization in a variety of cell types. Read all about it here.
2019
The lab is honored to have received an R35 MIRA Award from the NIH! We will use these funds to study mechanisms that govern RNA localization in a variety of cell types.
Welcome a new graduate student, Hei-Yong Lo! Hei-Yong is an MSTP student at CU Anschutz.
Graduate student Raeann Goering has been awarded a place on the Molecular Biology Graduate Program’s T32 training grant!
Pedro Tirado Velez will be joining us this summer from Colorado College as part of the RNA Bioscience Initiative Summer Internship Program. Welcome Pedro!
Lab members Ankita Arora, Krysta Engel, and Raeann Goering have received travel grants to attend the FASEB RNA localization conference this summer!
Postdoctoral fellow Krysta Engel has received a postdoctoral fellowship from cureSMA! This will fund her work seeking to understand how SMN regulates RNA transport in neurons and how this contributes to SMA phenotypes.
Brandon Titus from the University of Colorado, Colorado Springs has joined the lab as a summer intern as part of the NIH BRAiN program!
The lab is honored to have received a Boettcher Foundation Webb-Waring Biomedical Research Award for 2018! We will use these funds to study RNA mislocalization in the context of genetic neurological diseases.
Raeann Goering has joined the lab from the Molecular Biology program. She is the lab's first graduate student!
Krysta Engel has joined the lab as a postdoctoral fellow! She joins us after completing her Ph.D. at the University of Alabama, Birmingham and a postdoctoral position at Hudson Alpha Institute for Biotechnology.
Ankita Arora has joined the lab as a postdoctoral fellow. The size of the lab has now doubled! She joins us after completing her Ph.D. at Heidelberg University and a postdoctoral position at the University of California, San Francisco.
2018
Software
LABRAT
Lightweight Alignment-Based Reckoning of Alternative Three-prime ends
We have written software to investigate alternative polyadenylation using RNAseq or 3’ end sequencing data. LABRAT will quantify the relative usage of alternative polyadenylation sites in a dataset and then compare that usage across conditions to identify genes whose alternative polyadenylation status has changed.
It is freely available for download here. You can find the rest of our software on GitHub.
FeatureReachR
Feature extraction and analysis from biological sequence sets
The FeatureReachR packages enables users to take a deep dive into human or mouse data sets to extract biologically relevant sequence features in experimental versus control genes. FeatureReachR allows analysis of a diverse set of features with the convenience of R/RStudio. Biological insight is streamlined with this package, and prevents users from the tasks of wrangling public data sets themselves, such as RNA binding protein occupancy (e.g. CLIP-seq), conservation (phastcons), and protein binding motif databases. The package makes use of a variety of custom functions and existing tools. Our goal was not to reinvent the wheel, but rather provide a convenient platform to query sequence data in a thorough manner.
It is available for download here.
Teaching
MOLB 7900 - Practical Computational Biology for Biologists
This is an interactive course taught in conjunction with Srinivas Ramachandran. It serves as an introduction to Python programming in the context of large biological datasets. All material for the course can be found in the form of interactive Jupyter notebooks here.
MOLB 7950 - Informatics and Statistics for Molecular Biology
This is an interactive course taught in conjunction with Jay Hesselberth, Neel Mukherjee, Suja Jagannathan, and Srinivas Ramachandran. It is designed as an introduction to the computational and statistical techniques common in modern molecular biology. Links to lectures on using RNA sequencing to study gene expression and alternative splicing can be found below:
Quality control of RNA sequencing datasets (takes a bit to load, be patient)
Transcript features associated with post-transcriptional regulation
More material for this course can be found here.
IDPT 7810: Core Topics in Biomed Science -- Gene Expression
This survey and literature-based course gives graduate students and introduction to transcriptional and post-transcriptional regulatory mechanisms that impact gene expression. Lectures on alternative splicing and RNA localization can be found here.
Molecules to Medicine
This is a course for medical students designed to give them a foundation in molecular techniques and their application to modern medicine. Lectures on the use of diagnostic techniques that make use of nucleic acid and protein quantification can be found here.
Contact
Email:
matthew <dot> taliaferro <at> cuanschutz <dot> edu
Office mailing address:
12801 E 17th Ave
Research 1 South 10114
University of Colorado School of Medicine
Aurora, CO 80045
(303) 724-3274
Lab mailing address:
12801 E 17th Ave
Research 1 South 10403D
University of Colorado School of Medicine
Aurora, CO 80045