Andrew Nelson

Assistant Professor
Andrew Nelson
an425@cornell.edu
Office/Lab: 231
Office/Lab: 231
Cornell Affiliations: Adjunct Assistant Professor, Plant Biology Section, School of Integrative Plant Science, Cornell University
Graduate Fields: Plant Biology
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!

LncRNA FLAIL affects alternative splicing and represses flowering in Arabidopsis
2023.
Jin, Y., Ivanov, M., Nelson Dittrich, A., Nelson, Andrew D.L., Marquardt, S.
The EMBO Journal.
42
:
Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long non-coding RNAs
2023.
Palos, K., Yu, L., Railey, C.E., Nelson Dittrich, A.C., Nelson, Andrew D.L.
Plant Cell.
35
:
1762–1786
Telomerase RNA in Hymenoptera (Insecta) switched to plant/ciliate-like biogenesis
2022.
Fajkus, P., Adámik, M., Nelson, Andrew D.L., Kilar, A.M., Franek, M., Bubeník, M., Frydrychová, R.Č., Votavová, A., Sýkorová, E., Fajkus, J., Peška, V.
Nucleic Acids Res..
51
:
420–433
Composition and function of stress granules and P-bodies in plants
2022.
Kearly, A., Nelson, Andrew D.L., Skirycz, Aleksandra, Chodasiewicz, M.
Semin Cell Dev Biol..
:
Evolutionary analysis of the LORELEI gene family in plants reveals regulatory subfunctionalization.
2022.
Noble, J.A., Bielski, N.V., Liu, M.J., DeFalco, T.A., Stegmann, M., Nelson, Andrew D.L., McNamara, K., Sullivan, B., Dinh, K.K., Khuu, N., Hancock, S., Shiu, S.H., Zipfel, C., Cheung, A.Y., Beilstein, M.A., Palanivelu, R.
Plant Physiol..
190
:
2539–2556
High-Throughput Evolutionary Comparative Analysis of Long Intergenic Noncoding RNAs in Multiple Organisms
2022.
Nelson Dittrich, A.C., Nelson, Andrew D.L.
Methods Mol Biol..
2512
:
45–60
A Conserved Long Intergenic Non-coding RNA Containing snoRNA Sequences, lncCOBRA1, Affects Arabidopsis Germination and Development.
2022.
Kramer, M.C., Kim, H.J., Palos, K.R., Garcia, B.A., Lyons, E., Beilstein, M.A., Nelson, Andrew D.L., Gregory, B.D.
Front Plant Sci..
13
:
Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae.
2022.
Palos, K., Nelson Dittrich, A.C., Yu, L., Brock, J.R., Railey, C.E., Wu, H.L., Sokolowska, E., Skirycz, Aleksandra, Hsu, P.Y., Gregory, B.D., Lyons, E., Beilstein, M.A., Nelson, Andrew D.L.
Plant Cell..
:
2′,3′-cAMP treatment mimics the stress molecular response in Arabidopsis thaliana
2022.
Chodasiewicz, M., Kerber, O., Gorka, M., Moreno, J.C., Maruri-Lopez, I., Minen, R.I., Sampathkumar, A., Nelson, Andrew D.L., Skirycz, Aleksandra
Plant Physiol..
:
Overcoming the Challenges to Enhancing Experimental Plant Biology With Computational Modeling.
2021.
Dale, R., Oswald, S., Jalihal, A., LaPorte, M.F., Fletcher, D.M., Hubbard, A., Shiu, S.H., Nelson, Andrew D.L., Bucksch, A.
Front Plant Sci..
12
:
Evolution of plant telomerase RNAs: farther to the past, deeper to the roots
2021.
Fajkus, P., Kilar, A., Nelson, Andrew D.L., Holá, M., Peška, V., Goffová, I., Fojtová, M., Zachová, D., Fulnečková, J., Fajkus, J.
Nucleic Acids Research.
49
:
7680–694
Chloroplast quality control pathways are dependent on plastid DNA synthesis and nucleotides provided by cytidine triphosphate synthase two
2021.
Alamdari, K., Fisher, K.E., Tano, D.W., Rai, S., Palos, K., Nelson, Andrew D.L., Woodson, J.D.
New Phytologist.
231
:
1431–1448
EDC3 phosphorylation regulates growth and invasion through controlling P-body formation and dynamics
2021.
Bearss, J.J., Padi, S.K., Singh, N., Cardo-Vila, M., Song, J.H., Mouneimne, G., Fernandes, N., Li, Y., Harter, M.R., Gard, J.M., Cress, A.E., Peti, W., Nelson, Andrew D.L., Buchan, J.R., Kraft, A.S., Okumura, K.
EMBO Rep..
:
Identification and Characterization of the Heat-Induced Plastidial Stress Granules Reveal New Insight Into Arabidopsis Stress Response
2020.
Chodasiewicz, M., Sokolowska, E.M., Nelson-Dittrich, Anna C., Masiuk, A., Beltran, J.C.M., Nelson, Andrew D.L., Skirycz, Aleksandra
Front Plant Sci..
11
:
Biased Gene Retention in the Face of Introgression Obscures Species Relationships
2020.
Forsythe, E.S., Nelson, Andrew D.L., Beilstein, M.A.
Genome Biol Evol.
12
:
1646–1663
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., Beilstein, M.A., Gregory, B.D.
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., Gregory, B.D., Devisetty, U.K., Nelson, Andrew D.L.
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.J., Pauli, 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.E.
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., Teresi, S.J., Nelson, Andrew D.L., Wai, C.M., Alger, E.I., Bird, K.A., Yocca, A.E., Pumplin, N., Ou, S., Ben-Zvi, G., Brodt, A., Baruch, K., Swale, T., Shiue, L., Acharya, C.B., Cole, G.S., Mower, J.P., Childs, K.L., Jiang, N., Lyons, E., Freeling, M., Puzey, J.R., Knapp, S.J.
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.D., Beilstein, M.A., Fray, R.G., Lyons, E., Gregory, B.
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., Moutal, A., Perez-Miller, S., Ambrose, A.J., Al-Shamari, A., Coursodon, P., Meechoovet, B., Reiman, R., Lyons, E., Beilstein, M., Chapman, E., Morris, Q.D., Van Keuren-Jensen, K., Hughes, T.R., Khanna, R., Koehler, C., Jen, J., Gokhale, V., Khanna, M.
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.M.R., Frank, M.R., Lyons, E., Beilstein, M.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., Lee, J.R.
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

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