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Rob Martienssen

Rob Martienssen

Professor & HHMI Investigator
William J. Matheson Professor
Cancer Center Member

Ph.D., Cambridge University, 1986

martiens@cshl.edu | 516-367-8322

Martienssen Lab Website   Faculty Profile

Chromosomes are covered with chemical modifications that help control gene expression. I study this secondary genetic code - the epigenome - and how it is guided by small mobile RNAs in plants and fission yeast. Our discoveries impact plant breeding and human health, and we use this and other genomic information to improve aquatic plants as a source of bioenergy.

Epigenetic mechanisms of gene regulation—chemical and conformational changes to DNA and the chromatin that bundles it—have had an important impact on genome organization and inheritance and on cell fate. These mechanisms are conserved in eukaryotes and provide an additional layer of information superimposed on the genetic code. Robert Martienssen, a pioneer in the study of epigenetics, investigates mechanisms involved in gene regulation and stem cell fate in yeast and model plants including Arabidopsis and maize. He and his colleagues have shed light on a phenomenon called position-effect variegation, caused by inactivation of a gene positioned near densely packed chromosomal material called heterochromatin. They have discovered that small RNA molecules arising from repeating genetic sequences program that heterochromatin. Martienssen and colleagues have described a remarkable process by which “companion cells” to sperm in plant pollen grains provide them with instructions that protect sperm DNA from transposon damage. They found that some of these instructions, or epigenetic marks, could be inherited in the next generation. These marks, and the small RNA responsible that guide them, can sense the number of chromosomes inherited from pollen and may allow Arabidopsis, a flowering plant, to produce egg cells without meiosis, an important step toward a long-time goal of plant breeding: generating clonal offspring to perpetuate hybrid vigor. The lab has also shown that when RNA polymerase II has transcribed a stretch of DNA, the RNA interference mechanism causes the enzyme to release its hold on the DNA and fall away. This allows the replication fork to progress smoothly and the DNA strands to be copied; histone-modifying proteins, which follow right along, establish heterochromatin. Martienssen’s group also continues to work on problems related to the creation of plant-based biofuels. As part of a collaborative project to generate a high-quality full genome map of the oil palm plant, Martienssen and his colleagues identified a transposon whose modification controls the yield of oil palm trees. This discovery will increase yields and should lessen the environmental burden of oil palm production, which often threatens already endangered rainforest lands.

    photo of corn

    Corn’s ancient ancestors are calling

    February 6, 2025

    Cold Spring Harbor Laboratory Professors Thomas Gingeras and Rob Martienssen have launched a new genomic encyclopedia called MaizeCODE.


    image of Arabidopsis pollen

    Big clues emerge in small RNA mystery

    December 16, 2024

    How does the body separate “self” from “nonself?” CSHL Professor Rob Martienssen uncovers fascinating new leads in plant pollen and mouse sperm.


    photo of a North American Bullfrog

    Frog Pond

    November 27, 2024

    These hopping amphibians aren’t the only animals that call the pond home. It’s a living snapshot of our area’s diverse ecosystem.


    image of Cold Spring Harbor campus from across the harbor with At the Lab podcast logo

    At the Lab Season 1 Research Rewind: Genetics

    October 22, 2024

    It’s the code for all life on Earth. This week At the Lab, we’re hacking it with the help of Cold Spring Harbor Laboratory’s geneticists.


    photo of Arabidopsis

    Plants have a backup plan

    October 3, 2024

    CSHL’s Rob Martienssen and his team discovered how plants like Arabidopsis continue to reproduce even when things go wrong in chromosome division.


    image of Cold Spring Harbor campus from across the harbor with At the Lab podcast logo and portrait of Rob Martienssen

    At the Lab Episode 25: How maize became corn

    September 24, 2024

    Cold Spring Harbor Laboratory solves a plant biology mystery some 4,000 years in the making. The implications may go far beyond vegetables.


    image of the pollen-producing part of the maize-teosinte hybrid

    Corn’s ‘missing link’

    August 7, 2024

    CSHL researchers have discovered a biological mechanism that may explain how corn spread so rapidly across the Americas 4,000 years ago.


    image of Barbara McClintock's cornfield behind Carnegie Library

    Barbara McClintock’s corn

    June 16, 2024

    You’ve heard about Barbara McClintock’s Nobel Prize-winning research on corn genetics, but what about the corn itself?


    image of the CSHL SBS convocation booklet

    The CSHL School of Biological Sciences’ class of 2024

    May 5, 2024

    The School of Biological Sciences awarded Ph.D. degrees to 11 students this year. Here are some stories and reflections from their time at CSHL.


    photo of Tom Gingeras

    CSHL’s Thomas Gingeras awarded $2 million NSF grant

    April 3, 2024

    Climate change threatens crops with acidic soils and aluminum toxicity. Gingeras leads an international team tackling this problem head-on.


See all Martienssen news

All Publications

MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication

30 Dec 2024 | Nature Communications | 15(1):10854
Cahn, Jonathan;  Regulski, Michael;  Lynn, Jason;  Ernst, Evan;  de Santis Alves, Cristiane;  Ramakrishnan, Srividya;  Chougule, Kapeel;  Wei, Sharon;  Lu, Zhenyuan;  Xu, Xiaosa;  Ramu, Umamaheswari;  Drenkow, Jorg;  Kramer, Melissa;  Seetharam, Arun;  Hufford, Matthew;  McCombie, W;  Ware, Doreen;  Jackson, David;  Schatz, Michael;  Gingeras, Thomas;  Martienssen, Robert;  

Clr4SUV39H1 ubiquitination and non-coding RNA mediate transcriptional silencing of heterochromatin via Swi6 phase separation

30 Oct 2024 | Nature Communications | 15(1):9384
Kim, Hyun-Soo;  Roche, Benjamin;  Bhattacharjee, Sonali;  Todeschini, Leila;  Chang, An-Yun;  Hammell, Christopher;  Verdel, André;  Martienssen, Robert;  

Pseudouridine guides germline small RNA transport and epigenetic inheritance

6 Sep 2024 | Nature Structural & Molecular Biology
Herridge, Rowan;  Dolata, Jakub;  Migliori, Valentina;  de Santis Alves, Cristiane;  Borges, Filipe;  Schorn, Andrea;  van Ex, Frédéric;  Lin, Ann;  Bajczyk, Mateusz;  Parent, Jean-Sebastien;  Leonardi, Tommaso;  Hendrick, Alan;  Kouzarides, Tony;  Martienssen, Robert;  

Retrotransposon addiction promotes centromere function via epigenetically activated small RNAs

2 Sep 2024 | Nature Plants
Shimada, Atsushi;  Cahn, Jonathan;  Ernst, Evan;  Lynn, Jason;  Grimanelli, Daniel;  Henderson, Ian;  Kakutani, Tetsuji;  Martienssen, Robert;  

Leishmania major telomerase RNA knockout: From altered cell proliferation to decreased parasite infectivity

30 Aug 2024 | International Journal of Biological Macromolecules | :135150
de Oliveira, Beatriz;  Shiburah, Mark;  Assis, Luiz;  Fontes, Veronica;  Bisetegn, Habtye;  de Oliveira Passos, Arthur;  de Oliveira, Leilane;  de Santis Alves, Cristiane;  Ernst, Evan;  Martienssen, Rob;  Gallo-Francisco, Pedro;  Giorgio, Selma;  Batista, Marcos;  de Nazaré Correia Soeiro, Maria;  Menna-Barreto, Rubem;  Aoki, Juliana;  Coelho, Adriano;  Cano, Maria;  

Teosinte Pollen Drive guides maize diversification and domestication by RNAi

7 Aug 2024 | Nature
Berube, Benjamin;  Ernst, Evan;  Cahn, Jonathan;  Roche, Benjamin;  de Santis Alves, Cristiane;  Lynn, Jason;  Scheben, Armin;  Grimanelli, Daniel;  Siepel, Adam;  Ross-Ibarra, Jeffrey;  Kermicle, Jerry;  Martienssen, Robert;  

Mechanisms of metabolic adaptation in the duckweed Lemna gibba: an integrated metabolic, transcriptomic and flux analysis

3 Oct 2023 | BMC Plant Biology | 23(1):458
Shi, Hai;  Ernst, Evan;  Heinzel, Nicolas;  McCorkle, Sean;  Rolletschek, Hardy;  Borisjuk, Ljudmilla;  Ortleb, Stefan;  Martienssen, Robert;  Shanklin, John;  Schwender, Jorg;  

Oncogene-like addiction to aneuploidy in human cancers

25 Aug 2023 | Science | 381(6660):eadg4521
Girish, Vishruth;  Lakhani, Asad;  Thompson, Sarah;  Scaduto, Christine;  Brown, Leanne;  Hagenson, Ryan;  Sausville, Erin;  Mendelson, Brianna;  Kandikuppa, Pranav;  Lukow, Devon;  Yuan, Monet;  Stevens, Eric;  Lee, Sophia;  Schukken, Klaske;  Akalu, Saron;  Vasudevan, Anand;  Zou, Charles;  Salovska, Barbora;  Li, Wenxue;  Smith, Joan;  Taylor, Alison;  Martienssen, Robert;  Liu, Yansheng;  Sun, Ruping;  Sheltzer, Jason;  

Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation

24 Aug 2023 | Cell | 186(19):4100-4116.e15
Lee, Seung;  Adams, Dexter;  Ipsaro, Jonathan;  Cahn, Jonathan;  Lynn, Jason;  Kim, Hyun-Soo;  Berube, Benjamin;  Major, Viktoria;  Calarco, Joseph;  LeBlanc, Chantal;  Bhattacharjee, Sonali;  Ramu, Umamaheswari;  Grimanelli, Daniel;  Jacob, Yannick;  Voigt, Philipp;  Joshua-Tor, Leemor;  Martienssen, Robert;  

The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity

24 Aug 2023 | bioRxiv
Stevenson, Dennis;  Ramakrishnan, Srividya;  Alves, Cristiane;  Coelho, Laís;  Kramer, Melissa;  Goodwin, Sara;  Ramos, Olivia;  Eshel, Gil;  Sondervan, Veronica;  Frangos, Samantha;  Zumajo-Cardona, Cecilia;  Jenike, Katherine;  Ou, Shujun;  Wang, Xiaojin;  Lee, Yin;  Loke, Stella;  Rossetto, Maurizio;  McPherson, Hannah;  Nigris, Sebastiano;  Moschin, Silvia;  Little, Damon;  Katari, Manpreet;  Varala, Kranthi;  Kolokotronis, Sergios-Orestis;  Ambrose, Barbara;  Croft, Larry;  Coruzzi, Gloria;  Schatz, Michael;  McCombie, W;  Martienssen, Robert;  

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