Of epigenetics - Publications


Peer-reviewed publications

Below are a list of all peer-reviewed publications.  Please click on any of titles to be directed to the article.

1.    Hoffer P, Ivashuta S, Pontes O, Vitins A, Pikaard CS, Mroczka A and Voelker T. (2010).
Posttranscriptional Gene Silencing in Nuclei. Proc Natl Acad Sci USA. Dec 20. [Epub ahead of print]. (F1000

  1. 2.   Earley KW, Pontvianne F, Wierzbicki AT, Blevins T, Tucker S, Costa-Nunes P, Pontes O, and Pikaard CS
    Mechanisms of HDA6 mediated rRNA gene silencing: suppression of intergenic Pol II transcription and
            differential effects on maintenance versus siRNA directed cytosine methylation
    . Genes Dev 24:1119-32.

3.    Searle IR, Pontes O, Melnyk CW, Smith L, and Baulcombe DC. (2010).
A JmjC domain protein is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in
. Genes Dev 24:986-91.

4.    Gao Z*, Liu H*, Daxinger L*, Pontes O*, He L , Qian W, Xie M, Lorkovic ZJ, Zhang S, Pontier D, Lagrange T,
        Jacobsen SE, Jin H, Matzke A, Matzke M, Pikaard CS, and Zhu JK. (2010).
A novel methyl DNA binding protein interacts with AGO4 and RNA polymerase II and functions in RNA
        directed DNA methylation in Arabidopsis
. Nature 465:106-9. *Equal contribution.

5.    Costa-Nunes P,
Pontes O, Preuss SB, and Pikaard CS.
        RNA-dependent DNA methylation and the establishment of nucleolar dominance in Arabidopsis suecica
        Nucleus 1: 1-6.
(Cover issue).

6.    He XJ, Hsu YF, Zhu S, Liu HL, Pontes O, Zhu J, Cui X, Wang C, and Zhu JK. (2009).
A transcriptional regulator conserved from yeasts to
        humans is required for RNA-directed DNA methylation and plant development
. Genes & Dev 23:2717-22.

7.    Blevins T, Pontes O, Pikaard CS, and Meins F Jr. (2009).
Heterochromatic siRNAs and DDM1 independently silence aberrant 5S rDNA transcripts in Arabidopsis.

        PLoS One 16:e5932.

8.    He XJ, Hsu YF, Zhu S, Wierzbicki AT, Pontes O, Pikaard CS, Wang CS, and Zhu JK. (2009).
An Effector of RNA-Directed DNA Methylation
        in Arabidopsis Is an ARGONAUTE 4- and RNA-Binding Protein
. Cell 37:498-509.

9.    Pontes O*, Costa-Nunes P, Vithayathil P, and Pikaard CS. (2009).
RNA polymerase V functions in Arabidopsis interphase heterochromatin organization independent of the
        siRNA-directed DNA methylation pathway
. Mol Plant 2: 700-710. *Corresponding author. (Cover issue).

10.   He JX, Hsu YF, Pontes O, Zhu J, Lu J, Bressan RA, Pikaard CS, Wang CS, and Zhu JK. (2009).
NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV
        and V and is required for siRNA production, RNA-directed DNA methylation, and transcriptional gene
. Genes Dev 23:318-30.

11.   Haag JR, Pontes O, and Pikaard CS. (2009).
Metal A and Metal B sites of nuclear RNA polymerases Pol IV and Pol V are required for siRNA-dependent
        DNA methylation and gene silencing
. PLoS One. 4(1):e4110.

12.   Preuss S, Costa-Nunes P, Tucker S, Pontes O, Lawrence RJ, Mosher R, Kasschau KC, Carrington JC,
        Baulcombe DC, Viegas W, and Pikaard CS. (2008).
Multi-megabase silencing in nucleolar dominance: evidence for siRNA-directed de novo DNA methylation
        recognized by specific methylcytosine binding proteins
. Mol Cell 32: 673-84.

13.   Zheng X, Pontes O, Zhu Z, Miki D, Iida K, Kapoor A, Pikaard CS, and Zhu JK. (2008).
ROS3, a small RNA-binding protein required for DNA demethylation in Arabidopsis. Nature 455:1259-62.

14.   Pontes O, Lawrence RJ, Silva M, Preuss S, Costa-Nunes P, Earley K, Neves N, Viegas W, and Pikaard CS.

        Postembryonic establishment of megabase-scale gene silencing in nucleolar dominance. PLoS One


15.   Smith LM, Pontes O, Searle I, Yelina N, Yousafzai KF, Herr AJ, Pikaard CS, and Baulcombe DC. (2007).
A SNF2 protein associated with nuclear RNA silencing and spread of a silencing signal between cell in
. Plant Cell 19:1507-21.

16.   Woo HR, Pontes O, Pikaard CS, and Richards EJ. (2007).
VIM1, a non-MBD class methylcytosine binding protein required for centromeric heterochromatinization.
        Genes Dev
21:267-277. (Cover issue).

17.   Li C, Pontes O, El-Shami M, Henderson R, Bernatavichute Y, Chan S, Lagrange T, Pikaard C, and Jacobsen S
An ARGONAUTE4 containing nuclear processing center co-localized with Cajal bodies in Arabidopsis
. Cell 126: 93-106. (Faculty 1000 Exceptional)

18.   Pontes O, Li CF, Costa-Nunes P, Haag JR, Ream T, Vitins A, Jacobsen SJ, and Pikaard C. (2006).
The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center.
        Cell 126: 79-92.
(Faculty 1000 Must read)

19.   Earley K, Lawrence R, Pontes O, Reuther R, Enciso AJ, Silva M, Neves N, Gross M, Viegas W, and Pikaard
        CS. (2006).
Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar
. Genes Dev 20: 1283-1293. (Cover issue, NIH Biomedical Beat Cool Image)

20.   Earley KW, Haag JR, Pontes O, Opper K, Juehne T, Song K, and Pikaard CS. (2006).
Gateway-compatible vectors for plant functional genomics and proteomics. Plant J 45: 616-629.

21.   Onodera Y, Haag JR, Ream T, Costa-Nunes P, Pontes O, and Pikaard CS. (2005).
Plant Nuclear RNA Polymerase IV Mediates siRNA and DNA Methylation-Dependent Heterochromatin
. Cell 120: 613-622. (Faculty 1000 Must read, Science Editor’s choice)

22.   Pontes O, Neves N, Silva M, Lewis M, Madlung A, Comai L, Viegas W, and Pikaard CS. (2004).
Rapid chromosomal locus rearrangements accompany formation of the allotetraploid Arabidopsis suecica
. Proc Natl Acad Sci USA 101: 18210-18245.

23.   Lawrence RJ, Early K, Pontes O, Silva M, Chen ZJ, Neves N, Viegas W, and Pikaard CS. (2004).
A concerted DNA methylation/histone methylation switch controlling rRNA gene dosage and nucleolar
        dominance requires nuclear histone deacetylase, HTD1
. Mol Cell 13; 599-609. (Faculty 1000 Must Read)

24.   Pontes O, Lawrence RJ, Neves N, Silva M, Lee JH, Z. Chen JZ, Viegas, W, and Pikaard CS (2003).
Natural variation in nucleolar dominance reveals the relationship between nucleolus organizer chromatin
        topology and rRNA gene transcription in Arabidopsis
. Proc Natl Acad Sci USA 100:11418-11423.

25.    Pontes O, Cotrim H, Pais S, and Viegas W. (2000).
Physical mapping, expression patterns and interphase organisation of rDNA loci in Portuguese endemic
        Silene cintrana and Silene rothmaleri
. Chrom Res 8: 313-317.