Andrew Nelson

Assistant Professor
Andrew Nelson
an425@cornell.edu
Office/Lab: 231
Office/Lab: 231
Email: an425@cornell.edu
 
Research Overview

Plants respond to changes in their environment in a myriad of ways – some deeply conserved, and others more specific adaptations to a particularly harsh local environment. These responses to environmental stress can be complex, with copious interconnected regulatory mechanisms that contribute (hopefully) to a successful outcome. Work into understanding these regulatory mechanisms has largely focused on their protein components, and for good reason; functional and evolutionary analysis of proteins and the genes that encode them is relatively straightforward and these analyses have greatly expanded our understanding of how plants perceive and cope with stress.

Diagram of RNA-mediated regulationHowever, perception and regulation of stress occurs at the RNA level as well. This RNA-mediated regulation can occur through direct action of an RNA (micro and long non-coding RNA) on a target RNA/protein/DNA locus, or through chemical modification of RNAs (both mRNAs and ncRNAs) that change the target RNA’s structure, localization, or stability. These RNA-based regulatory mechanisms have the potential for both high specificity and sensitivity and therefore would be promising breeding targets in developing more stress-resilient crops. While promising, the who, where, when, and how of these RNA regulatory mechanisms are still poorly understood, particularly outside of Arabidopsis thaliana.

The Nelson lab uses comparative genomic, bioinformatic, and molecular approaches to better understand how plants regulate their stress responses at the RNA level and the degree to which these responses are conserved.

 

Current projects include:

 

The systematic identification and annotation of long non-coding RNAs in plants.

LncRNAs genomic sequence The technology necessary to monitor gene expression in a single cell, within a tissue, or across an entire organism has developed tremendously over the past decade. As a direct result, there are now tens of thousands of publicly available data sets providing snapshots of how plants modulate the transcription of their genetic material to produce a phenotype. In order to appreciate the transcriptional complexity leading to phenotype, it is first necessary to understand the full composition of the transcriptome itself. Aside from protein-coding RNAs and small RNAs, a third class of transcript has recently been uncovered: long non-coding RNAs (lncRNAs). LncRNAs are emerging as key regulatory molecules impacting how plants respond to changes in their environment such as temperature and water abundance. Despite the their many important roles, lncRNAs remain poorly annotated in plants. LncRNAs are difficult to predict from genomic sequence alone and often require extensive transcriptional information, and the capacity to process that data, to confidently annotate. To overcome difficulties in lncRNA annotation and functional classification, this NSF-funded project is repurposing all (> 100 Tb) publicly available transcriptomic data for the top fifteen most studied model and agriculturally significant plant species (NSF-IOS PGRP 1758532). LncRNAs are being identified, cross-species conservation determined, and putative functional pathways inferred in each of the fifteen focal species.

 

Identification and characterization of stress-responsive and conserved base modifications
(aka the epitranscriptome) in plants.

Across prokaryotes and eukaryotes, RNA chemical modifications are diverse, occur on all classes of RNA molecules, and are physiologically relevant. In plants, just two of the > 150 known RNA modifications have been studied in depth, and primarily in Arabidopsis, where they have been shown to have an impact at both the organismal and cellular levels. Little else is known about the role of the epitranscriptome in plants.  This gap in knowledge is in large part due to the cost and technical difficulties of the biochemical assays used to measure abundance of specific RNA modifications. In light of these difficulties, in silico methods have been developed that facilitate high-throughput identification and prediction of these chemical additions. This NSF-funded collaborative project aims to address challenges in identifying modifications and placing them into a biological context by: 1) developing an exhaustive, annotated plant epitranscriptomic resource of over 47 unique modifications using approximately 1 petabase of publicly available RNA-seq data, and 2) provide a biological and evolutionary context for each of these modifications and the RNAs they are found to modify (NSF-IOS PGRP 2023310). To process the wealth of publicly available RNA-seq data and present the resulting information in a manner that will drive hypothesis generation, this project is developing novel computational workflows and data visualization tools. In sum, this project aims to provide the research community with an innovative plant epitranscriptome resource that is supplemented with sufficient biological and evolutionary context to facilitate in vivo functional analyses. This project is a collaboration with Drs. Brian Gregory (University of Pennsylvania), Eric Lyons (University of Arizona), and Rebecca Murphy (Centenary College of Louisiana).

RNA Chemical Modifications

 

Comparative analysis of stress-induced RNA modifications in the mustard (Brassicaceae) lineage.

Comparative analysis of stress-induced RNA modifications in the mustard (Brassicaceae) lineage.RNA sequencing has advanced dramatically in the past few years, with some platforms allowing researchers the ability to directly sequence RNA without the prior conversion to cDNA (what is sequenced by Illumina). Nanopore’s direct RNA sequencing captures not only an entire transcript but can also reveal if that transcript contains certain base modifications (i.e., m6A and m5C). We are applying this technology to address how these modifications influence transcriptional responses to heat and salt stress in four Brassicaceae: Arabidopsis thaliana, Camelina sativa, Brassica rapa, and Eutrema salsugineum. These four species represent an ideal comparative system. They reflect both diploid and recent polyploids (i.e., differing genomic influences on gene retention and function), as well as different levels of tolerance to these two stresses (e.g., Eutrema is highly salt tolerant whereas Arabidopsis is not). Finally, their evolutionary relationships to one another are well-described; Arabidopsis and Camelina reside in Lineage I of the family, whereas Brassica and Eutrema are in Lineage II, with the two lineages diverging from one another ~43 MYA. We are using this comparative system to better understand the degree to which m6A and m5C deposition during stress is conserved – especially between recently duplicated genes. In addition, we hope to understand how the evolution of RNA modifications influence stress tolerance or resilience in plants.

 

Understanding Mechanisms of Plant Resilience (alongside Magda Julkowska).

The Nelson and Julkowska labs make up the Mechanisms of Plant Resilience (MoPR) Cluster at BTI. The goal of the MoPR Cluster is to combine the strengths of the two labs (Julkowska = phenomics and stress physiology; Nelson = genomics and RNA biology) to develop a more complete understanding of the genetic and molecular factors associated with tolerance and acclimation to abiotic stress in domesticated plants and their wild relatives (primarily Solanaceae and Brassicaceae). Phenomics approaches will utilize both small scale but high temporal resolution Raspberry Pi imaging as well as large-scale high throughput phenotyping (HTP) platforms. Genomics approaches will span from single-cell RNA-seq to transcriptome-wide association studies (TWAS). Check back soon for more details!

The Nelson and Julkowska labs are looking for personnel. Apply here.

  • NSF Backs Bioinformatics Approach to Understanding Plant RNA Modifications

    RNA perform a variety of functions in cells, helping with everything from regulating genes to building proteins. In recent years, it has become clear that chemical modifications to RNA help guide these functions, but only a handful of these modifications have been identified in plants. On July 24, Andrew Nelson, a faculty member at the […] Read more »
  • Cluster Hire Yields Three New Faculty Members

    Boyce Thompson Institute is pleased to announce the hiring of three faculty members as part of its new and innovative “cluster hire” approach. Out of 113 applicants, the three people who will join BTI over the next year are: Magdalena (Magda) Julkowska, a postdoctoral fellow at King Abdullah University of Science and Technology in Saudi […] Read more »
N6-methyladenosine and RNA secondary structure affect transcript stability and protein abundance during systemic salt stress in Arabidopsis
2020.
Kramer, M.C., Janssen, K.A., Palos, K., Nelson, Andrew D.L., Vandivier, L.E., Garcia, B.A., Lyons, E…
Plant Direct..
4
:
e00239
Read Mapping and Transcript Assembly: A Scalable and High-Throughput Workflow for the Processing and Analysis of Ribonucleic Acid Sequencing Data
2020.
Peri, S., Roberts, S., Kreko, I.R., McHan, L.B., Naron, A., Ram, A., Murphy, R.L., Lyons, E., Gregor…
Front Genet..
10
:
1361
Transcriptomic and evolutionary analysis of the mechanisms by which P. argentatum, a rubber producing perennial, responds to drought
2019.
Nelson, Andrew D.L., Ponciano, G., McMahan, C., Ilut, D.C., Pugh, N.A., Elshikha, D.E., Hunsaker, D.…
BMC plant biology.
19
:
1–13
Recent emergence and extinction of the protection of telomeres 1c gene in Arabidopsis thaliana
2019.
Kobayashi, C.R., Castillo-González, C., Survotseva, Y., Canal, E., Nelson, Andrew D.L., Shippen, D.…
Plant cell reports.
:
1–17
Origin and evolution of the octoploid strawberry genome
2019.
Edger, P.P., Poorten, T.J., VanBuren, R., Hardigan, M.A., Colle, M., McKain, M.R., Smith, R.D., Tere…
Nature genetics.
51
:
541
Tail Wags the Dog? Functional Gene Classes Driving Genome-Wide GC Content in Plasmodium spp.
2019.
Castillo, A.I., Nelson, Andrew D.L., Lyons, E.
Genome biology and evolution.
11
:
497–507
N6-methyladenosine inhibits local ribonucleolytic cleavage to stabilize mRNAs in Arabidopsis
2018.
Anderson, S.J., Kramer, M.C., Gosai, S.J., Yu, X., Vandivier, L.E., Nelson, Andrew D.L., Anderson, Z…
Cell reports.
25
:
1146–1157
A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B)
2018.
François-Moutal, L., Jahanbakhsh, S., Nelson, Andrew D.L., Ray, D., Scott, D.D., Hennefarth, M.R., …
ACS chemical biology.
13
:
3000–3010
EPIC-CoGe: managing and analyzing genomic data
2018.
Nelson, Andrew D.L., Haug-Baltzell, A.K., Davey, S., Gregory, B.D., Lyons, E.
Bioinformatics.
34
:
2651–2653
A tutorial of diverse genome analysis tools found in the CoGe web-platform using Plasmodium spp. as a model
2018.
Castillo, A.I., Nelson, Andrew D.L., Haug-Baltzell, A.K., Lyons, E.
Database.
2018
:
Evolinc: A tool for the identification and evolutionary comparison of long intergenic non-coding RNAs
2017.
Nelson, Andrew D.L., Devisetty, U.K., Palos, K., Haug-Baltzell, A.K., Lyons, E., Beilstein, M.A.
Frontiers in genetics.
8
:
52
A genomic analysis of factors driving lincRNA diversification: lessons from plants
2016.
Nelson, Andrew D.L., Forsythe, E.S., Devisetty, U.K., Clausen, D.S., Haug-Batzell, A.K., Meldrum, A.…
G3: Genes, Genomes, Genetics.
6
:
2881–2891
Algicidal effect of hybrid peptides as potential inhibitors of harmful algal blooms
2016.
Park, S.C., Moon, J.C., Kim, N.H., Kim, E.J., Jeong, J.E., Nelson, Andrew D.L., Jo, B.H., Jang, M.K.…
Biotechnology letters.
38
:
847–854
Evolution of TERT-interacting lncRNAs: expanding the regulatory landscape of telomerase
2015.
Nelson, Andrew D.L., Shippen, D.
Frontiers in genetics.
6
:
277
A transposable element within the non-canonical telomerase RNA of arabidopsis thaliana modulates telomerase in response to DNA damage
2015.
Xu, H., Nelson, Andrew D.L., Shippen, D.E.
PLoS genetics.
11
:
e1005281
Single-Cell Telomere-Length Quantification Couples Telomere Length to Meristem Activity and Stem Cell Development in Arabidopsis
2015.
González-García, M.P., Pavelescu, I., Canela, A., Sevillano, X., Leehy, K.A., Nelson, Andrew D.L.,…
Cell reports.
11
:
977–989
Global Analysis of the RNA-Protein Interaction and RNA Secondary Structure Landscapes of the Arabidopsis Nucleus
2015.
Gosai, S.J., Foley, S.W., Wang, D., Silverman, I.M., Selamoglu, N., Nelson, Andrew D.L., Beilstein, …
Molecular cell.
57
:
376–388
Nucleus and Genome: Telomeres
2015.
Nelson, Andrew D.L., Beilstein, M.A., Shippen, D.E.
Molecular Biology.
:
1–21
Extending the model of Arabidopsis telomere length and composition across Brassicaceae
2014.
Nelson, Andrew D.L., Forsythe, E.S., Gan, X., Tsiantis, M., Beilstein, M.A.
Chromosome research.
22
:
153–166
Plant telomeres and telomerase
2014.
Nelson, Andrew D.L., Beilstein, M.S., Shippen, D.E.
Molecular Biology.
:
25–49
An alternative telomerase RNA in Arabidopsis modulates enzyme activity in response to DNA damage
2012.
Cifuentes-Rojas, C., Nelson, Andrew D.L., Boltz, K.A., Kannan, K., She, X., Shippen, D.E.
Genes & development.
26
:
2512–2523
Blunt-ended telomeres: an alternative ending to the replication and end protection stories
2012.
Nelson, Andrew D.L., Shippen, D.E.
Genes & development.
26
:
1648–1652
ATR cooperates with CTC1 and STN1 to maintain telomeres and genome integrity in Arabidopsis
2012.
Boltz, K.A., Leehy, K., Song, X., Nelson, Andrew D.L., Shippen, D.E.
Molecular biology of the cell.
23
:
1558–1568
Parameters affecting telomere-mediated chromosomal truncation in Arabidopsis
2011.
Nelson, Andrew D.L., Lamb, J.C., Kobrossly, P.S., Shippen, D.E.
The Plant Cell.
23
:
2263–2272
Protection of Telomeres 1 is required for telomere integrity in the moss Physcomitrella patens
2010.
Shakirov, E.V., Perroud, P.F., Nelson, Andrew D.L., Cannell, M.E., Quatrano, R.S., Shippen, D.E.
The Plant Cell.
22
:
1838–1848
 

Contact:

Boyce Thompson Institute
533 Tower Rd.
Ithaca, NY 14853
607.254.1234
contact@btiscience.org