Publications

2024

txtools: an R package facilitating analysis of RNA modifications, structures, and interactions

Garcia-Campos M. A. & Schwartz S. (2024) Nucleic Acids Research. 52, 8, e42.

No evidence for ac4C within human mRNA upon data reassessment

Georgeson J. & Schwartz S. (2024) Molecular Cell. 84, 8, p. 1601-1610.e2

Dissecting the sequence and structural determinants guiding m6A deposition and evolution via inter- and intra-species hybrids

Shachar R., Dierks D., Garcia-Campos M. A., Uzonyi A., Toth U., Rossmanith W. & Schwartz S. (2024) Genome Biology. 25, 48.

Directing RNA-modifying machineries towards endogenous RNAs: opportunities and challenges

Witzenberger M. & Schwartz S. (2024) Trends in Genetics. 40, 4, p. 313-325

2023

Dissecting the basis for differential substrate specificity of ADAR1 and ADAR2

Zambrano-Mila M. S., Witzenberger M., Rosenwasser Z., Uzonyi A., Nir R., Ben-Aroya S., Levanon E. Y. & Schwartz S. (2023) Nature Communications. 14, 1, 8212.

A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei

Rajan K. S., Madmoni H., Bashan A., Taoka M., Aryal S., Nobe Y., Doniger T., Galili Kostin B., Blumberg A., Cohen-Chalamish S., Schwartz S., Rivalta A., Zimmerman E., Unger R., Isobe T., Yonath A. & Michaeli S. (2023) Nature Communications. 14, 1, 7462.

Comprehensive mapping of exon junction complex binding sites reveals universal EJC deposition in Drosophila

Morillo L., Paternina T., Alasseur Q., Genovesio A., Schwartz S. & Le Hir H. (2023) BMC Biology. 21, 1, 246.

The yeast RNA methylation complex consists of conserved yet reconfigured components with m6A-dependent and independent roles

Ensinck I., Maman A., Albihlal W. S., Lassandro M., Salzano G., Sideri T., Howell S. A., Calvani E., Patel H., Bushkin G., Ralser M., Snijders A. P., Skehel M., Casañal A., Schwartz S. & van Werven F. J. (2023) eLife. 12, RP87860.

Exclusion of m6A from splice-site proximal regions by the exon junction complex dictates m6A topologies and mRNA stability

Uzonyi A., Dierks D., Nir R., Kwon O. S., Toth U., Barbosa I., Burel C., Brandis A., Rossmanith W., Le Hir H., Slobodin B. & Schwartz S. (2023) Molecular Cell. 83, 2, p. 237-251.e7

2022

A late-stage assembly checkpoint of the human mitochondrial ribosome large subunit

Rebelo-Guiomar P., Pellegrino S., Dent K. C., Sas-Chen A., Miller-Fleming L., Garone C., Van Haute L., Rogan J. F., Dinan A., Firth A. E., Andrews B., Whitworth A. J., Schwartz S., Warren A. J. & Minczuk M. (2022) Nature Communications. 13, 1, 929.

Antisense pairing and SNORD13 structure guide RNA cytidine acetylation

Thalalla Gamage S., Bortolin-Cavaillé M., Link C., Bryson K., Sas-Chen A., Schwartz S., Cavaillé J. & Meier J. L. (2022) RNA. 28, 12, p. 1582-1596

m6A is required for resolving progenitor identity during planarian stem cell differentiation

Dagan Y., Yesharim Y., Bonneau A. R., Frankovits T., Schwartz S., Reddien P. W. & Wurtzel O. (2022) EMBO Journal. 41, 21, e109895.

IRF3 inhibits IFN-γ-mediated restriction of intracellular pathogens in macrophages independently of IFNAR

Maciag K., Raychowdhury R., Smith K., Schneider A. M., Coers J., Mumbach M. R., Schwartz S. & Hacohen N. (2022) Journal of Leukocyte Biology. 112, 2, p. 257-271

Probing small ribosomal subunit RNA helix 45 acetylation across eukaryotic evolution

Bortolin-Cavaillé M. L., Quillien A., Gamage S. T., Thomas J. M., Sas-Chen A., Sharma S., Plisson-Chastang C., Vandel L., Blader P., Lafontaine D. L., Schwartz S., Meier J. L. & Cavaillé J. (2022) Nucleic Acids Research. 50, 11, p. 6284-6299

A systematic dissection of determinants and consequences of snoRNA-guided pseudouridylation of human mRNA

Nir R., Hoernes T. P., Muramatsu H., Faserl K., Karikó K., Erlacher M. D., Sas-Chen A. & Schwartz S. (2022) Nucleic Acids Research. 50, 9, p. 4900-4916

Cloning of DNA oligo pools for in vitro expression

Uzonyi A., Nir R. & Schwartz S. (2022) STAR Protocols. 3, 1, 101103.

2021

Decoupling of degradation from deadenylation reshapes poly(A) tail length in yeast meiosis

Wiener D., Antebi Y. & Schwartz S. (2021) Nature Structural & Molecular Biology. 28, 12, p. 1038-1049

The ribosome epitranscriptome: inert-or a platform for functional plasticity?

Georgeson J. & Schwartz S. (2021) RNA (Cambridge). 27, 11, p. 1293-1301

Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing

Begik O., Lucas M. C., Pryszcz L. P., Ramirez J. M., Medina R., Milenkovic I., Cruciani S., Liu H., Vieira H. G. S., Sas-Chen A., Mattick J. S., Schwartz S. & Novoa E. M. (2021) Nature biotechnology. 39, 10, p. 1278-1291

Multiplexed profiling facilitates robust m6A quantification at site, gene and sample resolution

Dierks D., Garcia-Campos M. A., Uzonyi A., Safra M., Edelheit S., Rossi A., Sideri T., Varier R. A., Brandis A., Stelzer Y., van Werven F., Scherz-Shouval R. & Schwartz S. (2021) Nature Methods. 18, 9, p. 1060-1067

The germinal center reaction depends on RNA methylation and divergent functions of specific methyl readers

Grenov A. C., Moss L., Edelheit S., Cordiner R., Schmiedel D., Biram A., Hanna J. H., Jensen T. H., Schwartz S. & Shulman Z. (2021) Journal of Experimental Medicine. 218, 10, e20210360.

Deciphering the principles of the RNA editing code via large-scale systematic probing

Uzonyi A., Nir R., Shliefer O., Stern-Ginossar N., Antebi Y., Stelzer Y., Levanon E. Y. & Schwartz S. (2021) Molecular Cell. 81, 11, p. 2374-2387.e3

How many tRNAs are out there?

Wiener D. & Schwartz S. (2021) Molecular Cell. 81, 8, p. 1595-1597

Quantitative nucleotide resolution profiling of RNA cytidine acetylation by ac4C-seq

Thalalla Gamage S., Sas-Chen A., Schwartz S. & Meier J. L. (2021) Nature protocols. 16, p. 2286-2307

mito-Ψ-Seq: A High-Throughput Method for Systematic Mapping of Pseudouridine Within Mitochondrial RNA

Sas-Chen A., Nir R. & Schwartz S. (2021) Mitochondrial Gene Expression : Methods and Protocols . Rorbach J. & Minczuk M.(eds.). p. 103-115

2020

NOP10 predicts lung cancer prognosis and its associated small nucleolar RNAs drive proliferation and migration

Cui C., Liu Y., Gerloff D., Rohde C., Pauli C., Koehn M., Misiak D., Oellerich T., Schwartz S., Schmidt L., Wiewrodt R., Marra A., Hillejan L., Bartel F., Wickenhauser C., Huettelmaier S., Goellner S., Zhou F., Edemir B. & Mueller-Tidow C. (2020) Oncogene. 40, 5, p. 909-921

The epitranscriptome beyond m6A

Wiener D. & Schwartz S. (2020) Nature Reviews Genetics. 2, p. 119-131

Context-dependent functional compensation between Ythdf m6A reader proteins

Lasman L., Krupalnik V., Viukov S., Mor N., Aguilera-Castrejon A., Schneir D., Bayerl J., Mizrahi O., Peles S., Tawil S., Sathe S., Nachshon A., Shani T., Zerbib M., Kilimnik I., Aigner S., Shankar A., Mueller J. R., Schwartz S., Stern-Ginossar N., Yeo G. W., Geula S., Novershtern N. & Hanna J. H. (2020) Genes and Development. 34, 19-20, p. 1373-1391

Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping

Sas-Chen A., Thomas J. M., Matzov D., Taoka M., Nance K. D., Nir R., Bryson K. M., Shachar R., Liman G. L. S., Burkhart B. W., Gamage S. T., Nobe Y., Briney C. A., Levy M. J., Fuchs R. T., Robb G. B., Hartmann J., Sharma S., Lin Q., Florens L., Washburn M. P., Isobe T., Santangelo T. J., Shalev-Benami M., Meier J. L. & Schwartz S. (2020) Nature. 583, 7817, p. 638-643

2019

Accurate detection of m6A RNA modifications in native RNA sequences

Liu H., Begik O., Lucas M. C., Ramirez J. M., Mason C. E., Wiener D., Schwartz S., Mattick J. S., Smith M. A. & Novoa E. M. (2019) Nature Communications. 10, 1, 4079.

Germline NPM1 mutations lead to altered rRNA 2 '-O-methylation and cause dyskeratosis congenita

Nachmani D., Bothmer A. H., Grisendi S., Mele A., Bothmer D., Lee J. D., Monteleone E., Cheng K., Zhang Y., Bester A. C., Guzzetti A., Mitchell C. A., Mendez L. M., Pozdnyakova O., Sportoletti P., Martelli M., Vulliamy T. J., Safra M., Schwartz S., Luzzatto L., Bluteau O., Soulier J., Darnell R. B., Falini B., Dokal I., Ito K., Clohessy J. G. & Pandolfi P. P. (2019) Nature Genetics. 51, 10, p. 1518-1529

Deciphering the "m6A Code" via Antibody-Independent Quantitative Profiling

Garcia-Campos M. A., Edelheit S., Toth U., Safra M., Shachar R., Viukov S., Winkler R., Nir R., Lasman L., Brandis A., Hanna J. H., Rossmanith W. & Schwartz S. (2019) Cell. 178, 3, p. 731-747

Misincorporation signatures for detecting modifications in mRNA: Not as simple as it sounds

Sas-Chen A. & Schwartz S. (2019) Methods. 156, p. 53-59

m6A modification controls the innate immune response to infection by targeting type I interferons

Winkler R., Gillis E., Lasman L., Safra M., Geula S., Soyris C., Nachshon A., Tai-Schmiedel J., Friedman N., Le-Trilling V. T. K., Trilling M., Mandelboim M., Hanna J. H., Schwartz S. & Stern-Ginossar N. (2019) Nature Immunology. 20, 2, p. 173-182

2018

Variants in PUS7 Cause Intellectual Disability with Speech Delay, Microcephaly, Short Stature, and Aggressive Behavior

De Brouwer A. P. M., Abou Jamra R., Koertel N., Soyris C., Polla D. L., Safra M., Zisso A., Powell C. A., Rebelo-Guiomar P., Dinges N., Morin V., Stock M., Hussain M., Shahzad M., Riazuddin S., Ahmed Z. M., Pfundt R., Schwarz F., de Boer L., Reis A., Grozeva D., Raymond F. L., Riazuddin S., Koolen D. A., Minczuk M., Roignant J., van Bokhoven H. & Schwartz S. (2018) American Journal of Human Genetics. 103, 6, p. 1045-1052

m(1)A within cytoplasmic mRNAs at single nucleotide resolution: a reconciled transcriptome-wide map

Schwartz S. (2018) Rna-A Publication Of The Rna Society. 24, 11, p. 1427-1436

Positioning Europe for the EPITRANSCRIPTOMICS challenge

Jantsch M., Quattrone A., O'Connell M., Helm M., Frye M., Macias-Gonzales M., Ohman M., Ameres S., Willems L., Fuks F., Oulas A., Vanacova S., Nielsen H., Bousquet-Antonelli C., Motorin Y., Roignant J., Balatsos N., Dinnyes A., Baranov P., Kelly V., Lamm A., Rechavi G., Pelizzola M., Liepins J., Holodnuka Kholodnyuk I., Zammit V., Ayers D., Drablos F., Dahl J. A., Bujnicki J., Jeronimo C., Almeida R., Neagu M., Costache M., Bankovic J., Banovic B., Kyselovic J., Valor L. M., Selbert S., Pir P., Demircan T., Cowling V., Schäfer M., Rossmanith W., Lafontaine D., David A., Carre C., Lyko F., Schaffrath R. & Schwartz S. (2018) RNA Biology. 15, 6, p. 829-831

2017

The m(1)A landscape on cytosolic and mitochondrial mRNA at single-base resolution

Safra M., Sas-Chen A., Nir R., Winkler R., Nachshon A., Bar-Yaacov D., Erlacher M., Rossmanith W., Stern-Ginossar N. & Schwartz S. (2017) Nature. 551, 7679, p. 251-255

RNA editing in bacteria recodes multiple proteins and regulates an evolutionarily conserved toxin-antitoxin system

Bar-Yaacov D., Mordret E., Towers R., Biniashvili T., Soyris C., Schwartz S., Dahan O. & Pilpel Y. (2017) Genome Research. 27, 10, p. 1696-1703

Corrigendum: TRUB1 is the predominant pseudouridine synthase acting on mammalian mRNA via a predictable and conserved code

Safra M., Nir R., Farouq D., Vainberg Slutskin I. & Schwartz S. (2017) Genome Research. 27, 8, p. 1460

AML1-ETO requires enhanced C/D box snoRNA/RNP formation to induce self-renewal and leukaemia

Zhou F., Liu Y., Rohde C., Pauli C., Gerloff D., Koehn M., Misiak D., Baeumer N., Cui C., Goellner S., Oellerich T., Serve H., Garcia-Cuellar M., Slany R., Maciejewski J. P., Przychodzen B., Seliger B., Klein H., Bartenhagen C., Berdel W. E., Dugas M., Taketo M. M., Farouq D., Schwartz S., Regev A., Hebert J., Sauvageau G., Pabst C., Huettelmaier S. & Mueller-Tidow C. (2017) Nature Cell Biology. 19, 7, p. 844-855

TRUB1 is the predominant pseudouridine synthase acting on mammalian mRNA via a predictable and conserved code

Safra M., Nir R., Farouq D., Slutzkin I. V. & Schwartz S. (2017) Genome Research. 27, 3, p. 393-406

Next-generation sequencing technologies for detection of modified nucleotides in RNAs

Schwartz S. & Motorin Y. (2017) RNA Biology. 14, 9, p. 1124-1137

2016

A network-based analysis of colon cancer Splicing changes reveals a tumorigenesis-favoring regulatory pathway emanating from ELK1

Hollander D., Donyo M., Atias N., Mekahel K., Melamed Z., Yannai S., Lev-Maor G., Shilo A., Schwartz S., Barshack I., Sharan R. & Ast G. (2016) Genome Research. 26, 4, p. 541-553

Cracking the epitranscriptome

Schwartz S. (2016) RNA. 22, 2, p. 169-174

2015

Quantitative visualization of alternative exon expression from RNA-seq data

Katz Y., Wang E. T., Silterra J., Schwartz S., Wong B., Thorvaldsdottir H., Robinson J. T., Mesirov J. P., Airoldi E. M. & Burge C. B. (2015) Bioinformatics. 31, 14, p. 2400-2402

Dynamic profiling of the protein life cycle in response to pathogens

Jovanovic M., Rooney M. S., Mertins P., Przybylski D., Chevrier N., Satija R., Rodriguez E. H., Fields A. P., Schwartz S., Raychowdhury R., Mumbach M. R., Eisenhaure T., Rabani M., Gennert D., Lu D., Delorey T., Weissman J. S., Carr S. A., Hacohen N. & Regev A. (2015) Science. 347, 6226, 1259038.

2014

Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA

Schwartz S., Bernstein D. A., Mumbach M. R., Jovanovic M., Herbst R. H., Leon-Ricardo B. X., Engreitz J. M., Guttman M., Satija R., Lander E. S., Fink G. & Regev A. (2014) Cell. 159, 1, p. 148-162

Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites

Schwartz S., Mumbach M. R., Jovanovic M., Wang T., Maciag K., Bushkin G. G., Mertins P., Ter-Ovanesyan D., Habib N., Cacchiarelli D., Sanjana N. E., Freinkman E., Pacold M. E., Satija R., Mikkelsen T. S., Hacohen N., Zhang F., Carr S. A., Lander E. S. & Regev A. (2014) Cell Reports. 8, 1, p. 284-296

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

Shalek A. K., Satija R., Shuga J., Trombetta J. J., Gennert D., Lu D., Chen P., Gertner R. S., Gaublomme J. T., Yosef N., Schwartz S., Fowler B., Weaver S., Wang J., Wang X., Ding R., Raychowdhury R., Friedman N., Hacohen N., Park H., May A. P. & Regev A. (2014) Nature. 510, 7505, p. 363-369

2013

High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis

Schwartz S., Agarwala S. D., Mumbach M. R., Jovanovic M., Mertins P., Shishkin A., Tabach Y., Mikkelsen T. S., Satija R., Ruvkun G., Carr S. A., Lander E. S., Fink G. R. & Regev A. (2013) Cell. 155, 6, p. X1409-1421

Transcriptome-Wide Mapping of 5-methylcytidine RNA Modifications in Bacteria, Archaea, and Yeast Reveals m5C within Archaeal mRNAs

Edelheit S., Schwartz S., Mumbach M. R., Wurtzel O. & Sorek R. (2013) PLoS Genetics. 9, 6, e1003602.

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

Shalek A. K., Satija R., Adiconis X., Gertner R. S., Gaublomme J. T., Raychowdhury R., Schwartz S., Yosef N., Malboeuf C., Lu D., Trombetta J. J., Gennert D., Gnirke A., Goren A., Hacohen N., Levin J. Z., Park H. & Regev A. (2013) Nature. 498, 7453, p. 236-240

2012

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

Dominissini D., Moshitch-Moshkovitz S., Schwartz S., Salmon-Divon M., Ungar L., Osenberg S., Cesarkas K., Jacob-Hirsch J., Amariglio N., Kupiec M., Sorek R. & Rechavi G. (2012) Nature. 485, 7397, p. 201-206

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

Amit M., Donyo M., Hollander D., Goren A., Kim E., Gelfman S., Lev-Maor G., Burstein D., Schwartz S., Postolsky B., Pupko T. & Ast G. (2012) Cell Reports. 1, 5, p. 543-556

Transcriptome-wide discovery of circular RNAs in Archaea

Danan M., Schwartz S., Edelheit S. & Sorek R. (2012) Nucleic Acids Research. 40, 7, p. 3131-3142

Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons

Gelfman S., Burstein D., Penn O., Savchenko A., Amit M., Schwartz S., Pupko T. & Ast G. (2012) Genome Research. 22, 1, p. 35-50

2011

Detection and removal of biases in the analysis of next-generation sequencing reads

Schwartz S., Ram O. & Ast G. (2011) PLoS ONE. 6, 1, e16685.

2010

Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB

Llorian M., Schwartz S., Clark T. A., Hollander D., Tan L., Spellman R., Gordon A., Schweitzer A. C., de la Grange P., Ast G. & Smith C. W. J. (2010) Nature Structural & Molecular Biology. 17, 9, p. 1114-1123

Chromatin density and splicing destiny: On the cross-talk between chromatin structure and splicing

Schwartz S. & Ast G. (2010) EMBO Journal. 29, 10, p. 1629-1636

Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements

Levy A., Schwartz S. & Ast G. (2010) Nucleic Acids Research. 38, 5, p. 1515-1530 gkp1134.

2009

The Pivotal Roles of TIA Proteins in 5 ' Splice-Site Selection of Alu Exons and Across Evolution

Gal-Mark N., Schwartz S., Ram O., Eyras E. & Ast G. (2009) PLoS Genetics. 5, 11, 1000717.

Chromatin organization marks exon-intron structure

Schwartz S., Meshorer E. & Ast G. (2009) Nature Structural & Molecular Biology. 16, 9, p. 990-U117

Alu exonization events reveal features required for precise recognition of exons by the splicing machinery

Schwartz S., Gal-Mark N., Kfir N., Ram O., Kim E. & Ast G. (2009) PLoS Computational Biology. 5, 3,

SROOGLE: Webserver for integrative, user-friendly visualization of splicing signals

Schwartz S., Hall E. & Ast G. (2009) Nucleic Acids Research. 37, SUPPL. 2, p. W189-W192

2008

Multifactorial interplay controls the splicing profile of Alu-derived exons

Ram O., Schwartz S. & Ast G. (2008) Molecular and Cellular Biology. 28, 10, p. 3513-25

Alternative splicing of Alu exons: two arms are better than one

Gal-Mark N., Schwartz S. & Ast G. (2008) Nucleic Acids Research. 36, 6, p. 2012-2023

Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes

Schwartz S. H., Silva J., Burstein D., Pupko T., Eyras E. & Ast G. (2008) Genome Research. 18, 1, p. 88-103