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Publications

2021

1.

Kumar, S; Zeng, Z; Bagati, A; Tay, R E; Sanz, L A; Hartono, S R; Ito, Y; Abderazzaq, F; Hatchi, E; Jiang, P; Cartwright, A N R; Olawoyin, O; Mathewson, N D; Pyrdol, J W; Li, M Z; Doench, J G; Booker, M A; Tolstorukov, M Y; Elledge, S J; Chedin, F; Liu, X S; Wucherpfennig, K W

CARM1 Inhibition Enables Immunotherapy of Resistant Tumors by Dual Action on Tumor cells and T cells Journal Article

In: Cancer Discov, 2021.

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2.

Chédin, F; Hartono, S R; Sanz, L A; Vanoosthuyse, V

Best practices for the visualization, mapping, and manipulation of R-loops Journal Article

In: EMBO J, 40 (4), pp. e106394, 2021.

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2020

3.

Richard, P; Feng, S; Tsai, Y L; Li, W; Rinchetti, P; Muhith, U; Irizarry-Cole, J; Stolz, K; Sanz, L A; Hartono, S; Hoque, M; Tadesse, S; Seitz, H; Lotti, F; Hirano, M; Chédin, F; Tian, B; Manley, J L

SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation Journal Article

In: Autophagy, pp. 1–18, 2020.

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4.

Shah, S S; Hartono, S; Piazza, A; Som, V; Wright, W; Chédin, F; Heyer, W D

Rdh54/Tid1 inhibits Rad51-Rad54-mediated D-loop formation and limits D-loop length Journal Article

In: Elife, 9 , 2020.

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5.

Shah, S S; Hartono, S R; Chédin, F; Heyer, W D

Bisulfite treatment and single-molecule real-time sequencing reveal D-loop length, position, and distribution Journal Article

In: Elife, 9 , 2020.

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6.

Promonet, A; Padioleau, I; Liu, Y; Sanz, L; Biernacka, A; Schmitz, A L; Skrzypczak, M; Sarrazin, A; Mettling, C; Rowicka, M; Ginalski, K; Chedin, F; Chen, C L; Lin, Y L; Pasero, P

Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites Journal Article

In: Nat Commun, 11 (1), pp. 3940, 2020.

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7.

Malig, M; Chedin, F

Characterization of R-Loop Structures Using Single-Molecule R-Loop Footprinting and Sequencing Journal Article

In: Methods Mol Biol, 2161 , pp. 209–228, 2020.

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8.

Alecki, C; Chiwara, V; Sanz, L A; Grau, D; Pérez, Arias O; Boulier, E L; Armache, K J; Chédin, F; Francis, N J

RNA-DNA strand exchange by the Drosophila Polycomb complex PRC2 Journal Article

In: Nat Commun, 11 (1), pp. 1781, 2020.

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9.

Chedin, F; Benham, C J

Emerging roles for R-loop structures in the management of topological stress Journal Article

In: J Biol Chem, 295 (14), pp. 4684–4695, 2020.

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10.

Malig, M; Hartono, S R; Giafaglione, J M; Sanz, L A; Chedin, F

Ultra-deep Coverage Single-molecule R-loop Footprinting Reveals Principles of R-loop Formation Journal Article

In: J Mol Biol, 432 (7), pp. 2271–2288, 2020.

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2019

11.

Jasoliya, M; Sacca, F; Sahdeo, S; Chedin, F; Pane, C; Morra, Brescia V; Filla, A; Pook, M; Cortopassi, G

Dimethyl fumarate dosing in humans increases frataxin expression: A potential therapy for Friedreich's Ataxia Journal Article

In: PLoS One, 14 (6), pp. e0217776, 2019.

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12.

Carrasco-Salas, Y; Malapert, A; Sulthana, S; Molcrette, B; Chazot-Franguiadakis, L; Bernard, P; Chédin, F; Faivre-Moskalenko, C; Vanoosthuyse, V

The extruded non-template strand determines the architecture of R-loops Journal Article

In: Nucleic Acids Res, 47 (13), pp. 6783–6795, 2019.

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13.

Sanz, L A; Chédin, F

High-resolution, strand-specific R-loop mapping via S9.6-based DNA-RNA immunoprecipitation and high-throughput sequencing Journal Article

In: Nat Protoc, 14 (6), pp. 1734–1755, 2019.

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14.

Stolz, R; Sulthana, S; Hartono, S R; Malig, M; Benham, C J; Chedin, F

Interplay between DNA sequence and negative superhelicity drives R-loop structures Journal Article

In: Proc Natl Acad Sci U S A, 116 (13), pp. 6260–6269, 2019.

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2018

15.

Manzo, S G; Hartono, S R; Sanz, L A; Marinello, J; Biasi, De S; Cossarizza, A; Capranico, G; Chedin, F

DNA Topoisomerase I differentially modulates R-loops across the human genome Journal Article

In: Genome Biol, 19 (1), pp. 100, 2018.

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16.

Zhang, X; Chiang, H C; Wang, Y; Zhang, C; Smith, S; Zhao, X; Nair, S J; Michalek, J; Jatoi, I; Lautner, M; Oliver, B; Wang, H; Petit, A; Soler, T; Brunet, J; Mateo, F; Pujana, Angel M; Poggi, E; Chaldekas, K; Isaacs, C; Peshkin, B N; Ochoa, O; Chedin, F; Theoharis, C; Sun, L Z; Curiel, T J; Elledge, R; Jin, V X; Hu, Y; Li, R

Author Correction: Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis Journal Article

In: Nat Commun, 9 , pp. 16211, 2018.

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17.

Hartono, S R; Malapert, A; Legros, P; Bernard, P; Chédin, F; Vanoosthuyse, V

The Affinity of the S9.6 Antibody for Double-Stranded RNAs Impacts the Accurate Mapping of R-Loops in Fission Yeast Journal Article

In: J Mol Biol, 430 (3), pp. 272–284, 2018.

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2017

18.

Chédin, F

Hybrids in the chromatin Journal Article

In: Nat Plants, 3 (9), pp. 692–693, 2017.

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19.

Zhang, X; Chiang, H C; Wang, Y; Zhang, C; Smith, S; Zhao, X; Nair, S J; Michalek, J; Jatoi, I; Lautner, M; Oliver, B; Wang, H; Petit, A; Soler, T; Brunet, J; Mateo, F; Pujana, Angel M; Poggi, E; Chaldekas, K; Isaacs, C; Peshkin, B N; Ochoa, O; Chedin, F; Theoharis, C; Sun, L Z; Curiel, T J; Elledge, R; Jin, V X; Hu, Y; Li, R

Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis Journal Article

In: Nat Commun, 8 , pp. 15908, 2017.

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20.

Sagie, S; Toubiana, S; Hartono, S R; Katzir, H; Tzur-Gilat, A; Havazelet, S; Francastel, C; Velasco, G; Chédin, F; Selig, S

Telomeres in ICF syndrome cells are vulnerable to DNA damage due to elevated DNA:RNA hybrids Journal Article

In: Nat Commun, 8 , pp. 14015, 2017.

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2016

21.

Anderson, J D; Johansson, H J; Graham, C S; Vesterlund, M; Pham, M T; Bramlett, C S; Montgomery, E N; Mellema, M S; Bardini, R L; Contreras, Z; Hoon, M; Bauer, G; Fink, K D; Fury, B; Hendrix, K J; Chedin, F; El-Andaloussi, S; Hwang, B; Mulligan, M S; Lehtiö, J; Nolta, J A

Comprehensive Proteomic Analysis of Mesenchymal Stem Cell Exosomes Reveals Modulation of Angiogenesis via Nuclear Factor-KappaB Signaling Journal Article

In: Stem Cells, 34 (3), pp. 601–613, 2016.

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22.

Chédin, F

Nascent Connections: R-Loops and Chromatin Patterning Journal Article

In: Trends Genet, 32 (12), pp. 828–838, 2016.

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23.

Stork, C T; Bocek, M; Crossley, M P; Sollier, J; Sanz, L A; Chédin, F; Swigut, T; Cimprich, K A

Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage Journal Article

In: Elife, 5 , 2016.

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24.

Sanz, L A; Hartono, S R; Lim, Y W; Steyaert, S; Rajpurkar, A; Ginno, P A; Xu, X; Chédin, F

Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals Journal Article

In: Mol Cell, 63 (1), pp. 167–178, 2016.

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2015

25.

Hartono, S R; Korf, I F; Chédin, F

GC skew is a conserved property of unmethylated CpG island promoters across vertebrates Journal Article

In: Nucleic Acids Res, 43 (20), pp. 9729–9741, 2015.

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26.

Lim, Y W; Sanz, L A; Xu, X; Hartono, S R; Chédin, F

Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi-Goutières syndrome Journal Article

In: Elife, 4 , 2015.

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2014

27.

Loomis, E W; Sanz, L A; Chédin, F; Hagerman, P J

Transcription-associated R-loop formation across the human FMR1 CGG-repeat region Journal Article

In: PLoS Genet, 10 (4), pp. e1004294, 2014.

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28.

Yang, Y; McBride, K M; Hensley, S; Lu, Y; Chedin, F; Bedford, M T

Arginine methylation facilitates the recruitment of TOP3B to chromatin to prevent R loop accumulation Journal Article

In: Mol Cell, 53 (3), pp. 484–497, 2014.

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2013

29.

Ginno, P A; Lim, Y W; Lott, P L; Korf, I; Chédin, F

GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination Journal Article

In: Genome Res, 23 (10), pp. 1590–1600, 2013.

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30.

Powell, W T; Coulson, R L; Gonzales, M L; Crary, F K; Wong, S S; Adams, S; Ach, R A; Tsang, P; Yamada, N A; Yasui, D H; Chédin, F; LaSalle, J M

R-loop formation at Snord116 mediates topotecan inhibition of Ube3a-antisense and allele-specific chromatin decondensation Journal Article

In: Proc Natl Acad Sci U S A, 110 (34), pp. 13938–13943, 2013.

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31.

Fagan, R L; Wu, M; Chédin, F; Brenner, C

An ultrasensitive high throughput screen for DNA methyltransferase 1-targeted molecular probes Journal Article

In: PLoS One, 8 (11), pp. e78752, 2013.

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32.

Gordon, C A; Hartono, S R; Chédin, F

Inactive DNMT3B splice variants modulate de novo DNA methylation Journal Article

In: PLoS One, 8 (7), pp. e69486, 2013.

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2012

33.

Ginno, P A; Lott, P L; Christensen, H C; Korf, I; Chédin, F

R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters Journal Article

In: Mol Cell, 45 (6), pp. 814–825, 2012.

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2011

34.

Nady, N; Lemak, A; Walker, J R; Avvakumov, G V; Kareta, M S; Achour, M; Xue, S; Duan, S; Allali-Hassani, A; Zuo, X; Wang, Y X; Bronner, C; Chédin, F; Arrowsmith, C H; Dhe-Paganon, S

Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein Journal Article

In: J Biol Chem, 286 (27), pp. 24300–24311, 2011.

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35.

Moarefi, A H; Chédin, F

ICF syndrome mutations cause a broad spectrum of biochemical defects in DNMT3B-mediated de novo DNA methylation Journal Article

In: J Mol Biol, 409 (5), pp. 758–772, 2011.

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36.

Chédin, F

The DNMT3 family of mammalian de novo DNA methyltransferases Journal Article

In: Prog Mol Biol Transl Sci, 101 , pp. 255–285, 2011.

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2010

37.

Wienholz, B L; Kareta, M S; Moarefi, A H; Gordon, C A; Ginno, P A; Chédin, F

DNMT3L modulates significant and distinct flanking sequence preference for DNA methylation by DNMT3A and DNMT3B in vivo Journal Article

In: PLoS Genet, 6 (9), pp. e1001106, 2010.

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38.

Bronner, C; Fuhrmann, G; Chédin, F L; Macaluso, M; Dhe-Paganon, S

UHRF1 Links the Histone code and DNA Methylation to ensure Faithful Epigenetic Memory Inheritance Journal Article

In: Genet Epigenet, 2009 (2), pp. 29–36, 2010.

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2009

39.

El-Maarri, O; Kareta, M S; Mikeska, T; Becker, T; Diaz-Lacava, A; Junen, J; Nüsgen, N; Behne, F; Wienker, T; Waha, A; Oldenburg, J; Chédin, F

A systematic search for DNA methyltransferase polymorphisms reveals a rare DNMT3L variant associated with subtelomeric hypomethylation Journal Article

In: Hum Mol Genet, 18 (10), pp. 1755–1768, 2009.

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2008

40.

Nady, N; Min, J; Kareta, M S; Chédin, F; Arrowsmith, C H

A SPOT on the chromatin landscape? Histone peptide arrays as a tool for epigenetic research Journal Article

In: Trends Biochem Sci, 33 (7), pp. 305–313, 2008.

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2006

41.

Kareta, M S; Botello, Z M; Ennis, J J; Chou, C; Chédin, F

Reconstitution and mechanism of the stimulation of de novo methylation by human DNMT3L Journal Article

In: J Biol Chem, 281 (36), pp. 25893–25902, 2006.

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42.

Chédin, F; Handa, N; Dillingham, M S; Kowalczykowski, S C

The AddAB helicase/nuclease forms a stable complex with its cognate chi sequence during translocation Journal Article

In: J Biol Chem, 281 (27), pp. 18610–18617, 2006.

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2005

43.

Chen, Z X; Mann, J R; Hsieh, C L; Riggs, A D; Chédin, F

Physical and functional interactions between the human DNMT3L protein and members of the de novo methyltransferase family Journal Article

In: J Cell Biochem, 95 (5), pp. 902–917, 2005.

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2003

44.

Yu, K; Chedin, F; Hsieh, C L; Wilson, T E; Lieber, M R

R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells Journal Article

In: Nat Immunol, 4 (5), pp. 442–451, 2003.

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2002

45.

Chedin, F; Lieber, M R; Hsieh, C L

The DNA methyltransferase-like protein DNMT3L stimulates de novo methylation by Dnmt3a Journal Article

In: Proc Natl Acad Sci U S A, 99 (26), pp. 16916–16921, 2002.

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46.

Chédin, F; Kowalczykowski, S C

A novel family of regulated helicases/nucleases from Gram-positive bacteria: insights into the initiation of DNA recombination Journal Article

In: Mol Microbiol, 43 (4), pp. 823–834, 2002.

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2000

47.

Chédin, F; Ehrlich, S D; Kowalczykowski, S C

The Bacillus subtilis AddAB helicase/nuclease is regulated by its cognate Chi sequence in vitro Journal Article

In: J Mol Biol, 298 (1), pp. 7–20, 2000.

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1998

48.

Chédin, F; Noirot, P; Biaudet, V; Ehrlich, S D

A five-nucleotide sequence protects DNA from exonucleolytic degradation by AddAB, the RecBCD analogue of Bacillus subtilis Journal Article

In: Mol Microbiol, 29 (6), pp. 1369–1377, 1998.

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49.

Chédin, F; Seitz, E M; Kowalczykowski, S C

Novel homologs of replication protein A in archaea: implications for the evolution of ssDNA-binding proteins Journal Article

In: Trends Biochem Sci, 23 (8), pp. 273–277, 1998.

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50.

Pujol, C; Chédin, F; Ehrlich, S D; Jannière, L

Inhibition of a naturally occurring rolling-circle replicon in derivatives of the theta-replicating plasmid pIP501 Journal Article

In: Mol Microbiol, 29 (3), pp. 709–718, 1998.

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1997

51.

Tracy, R B; Chédin, F; Kowalczykowski, S C

The recombination hot spot chi is embedded within islands of preferred DNA pairing sequences in the E. coli genome Journal Article

In: Cell, 90 (2), pp. 205–206, 1997.

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52.

Chédin, F; Dervyn, R; Ehrlich, S D; Noirot, P

Apparent and real recombination frequencies in multicopy plasmids: the need for a novel approach in frequency determination Journal Article

In: J Bacteriol, 179 (3), pp. 754–761, 1997.

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1994

53.

Chédin, F; Dervyn, E; Dervyn, R; Ehrlich, S D; Noirot, P

Frequency of deletion formation decreases exponentially with distance between short direct repeats Journal Article

In: Mol Microbiol, 12 (4), pp. 561–569, 1994.

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