Simon Elsässer

Publications
Grants
Public outreach and news

Selected publications

Article: SCIENCE. 2022;376(6592):476-483
Cancer cells use self-inflicted DNA breaks to evade growth limits imposed by genotoxic stress
Larsen BD; Benada J; Yung PYK; Bell RAV; Pappas G; Urban V; Ahlskog JK; Kuo TT; Janscak P; Megeney LA; Elsaesser SJ; Bartek J; Sorensen CS
Article: NUCLEIC ACIDS RESEARCH (NAR). 2022;50(3):e13
Genome-wide mapping of G-quadruplex structures with CUT&Tag
Lyu J; Shao R; Yung PYK; Elsasser SJ
Article: CHEMBIOCHEM. 2021;22(22):3208-3213
Engineered Human Induced Pluripotent Cells Enable Genetic Code Expansion in Brain Organoids
van Husen LS; Katsori A-M; Meineke B; Tjernberg LO; Schedin-Weiss S; Elsasser SJ
Preprint: BIORXIV. 2021
Polycomb Repressive Complex 2 shields naïve human pluripotent cells from trophectoderm differentiation
Kumar B; Navarro C; Winblad N; Schell J; Zhao C; Lanner F; Elsässer S
Article: NATURE METHODS. 2016;13(2):158-164
Genetic code expansion in stable cell lines enables encoded chromatin modification
Elsaesser SJ; Ernst RJ; Walker OS; Chin JW
Article: NATURE. 2015;522(7555):240-244
Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells
Elsasser SJ; Noh K-M; Diaz N; Allis CD; Banaszynski LA
Article: NATURE. 2012;491(7425):560-565
DAXX envelops a histone H3.3-H4 dimer for H3.3-specific recognition
Elsaesser SJ; Huang H; Lewis PW; Chin JW; Allis CD; Patel DJ

Articles

Journal article: NATURE PROTOCOLS. 2024;:1-31
Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors
Kumar B; Navarro C; Yung PYK; Lyu J; Mantero AS; Katsori A-M; Schwaemmle H; Martin M; Elsaesser SJ
Article: BIOCHIMICA ET BIOPHYSICA ACTA - GENERAL SUBJECTS. 2024;1868(7):130619
Detection and quantification of Na,K-ATPase dimers in the plasma membrane of living cells by FRET-FCS
Nordahl L; Akkuratov EE; Heimgartner J; Schach K; Meineke B; Elsasser S; Wennmalm S; Brismar H
Article: CELL REPORTS: METHODS. 2023;3(11):100626
Dual stop codon suppression in mammalian cells with genomically integrated genetic code expansion machinery
Meineke B; Heimgartner J; Caridha R; Block MF; Kimler KJ; Pires MF; Landreh M; Elsasser SJ
Journal article: PHYSIOLOGY. 2023;38:5732603
Click chemistry, FRET-FCS, and expansion microscopy reveal that Na, K-ATPase forms complexes in the plasma membrane
Brismar H; Edwards S; Bauer S; Meineke B; Elsasser S; Wennmalm S
Journal article: PHYSIOLOGY. 2023;38:5732753
Expansion microscopy and biorthogonal labeling with non-canonical amino acids enables cluster analysis of Na, K-ATPase in the plasma membrane
Edwards S; Bauer S; Graef P; Meineke B; Elsasser S; Brismar H
Article: NATURE CELL BIOLOGY. 2023;25(4):579-591
Dynamic antagonism between key repressive pathways maintains the placental epigenome
Weigert R; Hetzel S; Bailly N; Haggerty C; Ilik IA; Yung PYK; Navarro C; Bolondi A; Kumar AS; Anania C; Braendl B; Meierhofer D; Lupianez DG; Mueller F-J; Aktas T; Elsaesser SJ; Kretzmer H; Smith ZD; Meissner A
Article: METHODS IN MOLECULAR BIOLOGY. 2023;2676:169-180
Generation of Amber Suppression Cell Lines Using CRISPR-Cas9.
Meineke B; Elsässer SJ
Article: NUCLEIC ACIDS RESEARCH (NAR). 2022;50(15):8491-8511
TET1 regulates gene expression and repression of endogenous retroviruses independent of DNA demethylation
Stolz P; Mantero AS; Tvardovskiy A; Ugur E; Wange LE; Mulholland CB; Cheng Y; Wierer M; Enard W; Schneider R; Bartke T; Leonhardt H; Elsasser SJ; Bultmann S
Article: NATURE CELL BIOLOGY. 2022;24(6):845-857
Polycomb repressive complex 2 shields naive human pluripotent cells from trophectoderm differentiation
Kumar B; Navarro C; Winblad N; Schell JP; Zhao C; Weltner J; Baque-Vidal L; Salazar Mantero A; Petropoulos S; Lanner F; Elsasser SJ
Journal article: THE FASEB JOURNAL. 2022;36
Direct Observation of Na,K-ATPase Oligomers in The Plasma Membrane of Living Cells by FRET-FCS
Nordahl L; Wennmalm S; Jonsson J; Elsasser S; Akkuratov EE; Brismar H
Article: NATURE COMMUNICATIONS. 2022;13(1):1223
Sirtuin-1 sensitive lysine-136 acetylation drives phase separation and pathological aggregation of TDP-43
Morato JG; Hans F; von Zweydorf F; Feederle R; Elsasser SJ; Skodras AA; Gloeckner CJ; Buratti E; Neumann M; Kahle PJ
Article: MOLECULAR SYSTEMS BIOLOGY. 2022;18(1):e10407
Distinct transcription kinetics of pluripotent cell states
Shao R; Kumar B; Lidschreiber K; Lidschreiber M; Cramer P; Elsaesser SJ
Journal article: CHEMBIOCHEM. 2021;22(22):3108
Cover Feature: Engineered Human Induced Pluripotent Cells Enable Genetic Code Expansion in Brain Organoids (ChemBioChem 22/2021)
van Husen LS; Katsori A; Meineke B; Tjernberg LO; Schedin‐Weiss S; Elsässer SJ
Article: SCIENCE ADVANCES. 2021;7(32):eabf7561
The exon-junction complex helicase eIF4A3 controls cell fate via coordinated regulation of ribosome biogenesis and translational output
Kanellis DC; Espinoza JA; Zisi A; Sakkas E; Bartkova J; Katsori A-M; Bostrom J; Dyrskjot L; Broholm H; Altun M; Elsasser SJ; Lindstrom MS; Bartek J
Article: NATURE COMMUNICATIONS. 2021;12(1):3695
Multianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2
Roxhed N; Bendes A; Dale M; Mattsson C; Hanke L; Dodig-Crnkovic T; Christian M; Meineke B; Elsasser S; Andrell J; Havervall S; Thalin C; Eklund C; Dillner J; Beck O; Thomas CE; McInerney G; Hong M-G; Murrell B; Fredolini C; Schwenk JM
Article: BIOLOGIA FUTURA. 2021;72(2):119-125
Towards policies that capture the expected value of biomolecular diversity for drug discovery, human health, and well-being
Pesic M; Egamberdieva D; Kolodziejczyk B; Elsasser SJ; Neergheen VS; Kagansky A
Article: SCIENTIFIC REPORTS. 2021;11(1):1820
Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples
Alekseenko A; Barrett D; Pareja-Sanchez Y; Howard RJ; Strandback E; Ampah-Korsah H; Rovsnik U; Zuniga-Veliz S; Klenov A; Malloo J; Ye S; Liu X; Reinius B; Elsasser SJ; Nyman T; Sandh G; Yin X; Pelechano V
Article: FRONTIERS IN CHEMISTRY. 2021;9:768535
A Genetically Encoded Picolyl Azide for Improved Live Cell Copper Click Labeling
Meineke B; Heimgartner J; Craig AJ; Landreh M; Moodie LWK; Elsasser SJ
Article: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2020;142(47):20080-20087
Universal Single-Residue Terminal Labels for Fluorescent Live Cell Imaging of Microproteins
Lafranchi L; Schlesinger D; Kimler KJ; Elsasser SJ
Article: NATURE COMMUNICATIONS. 2020;11(1):5095
An embryonic stem cell-specific heterochromatin state promotes core histone exchange in the absence of DNA accessibility
Navarro C; Lyu J; Katsori A-M; Caridha R; Elsasser SJ
Article: GENES & DEVELOPMENT. 2020;34(15-16):1065-1074
Human RTEL1 associates with Poldip3 to facilitate responses to replication stress and R-loop resolution
Bjorkman A; Johansen SL; Lin L; Schertzer M; Kanellis DC; Katsori A-M; Christensen ST; Luo Y; Andersen JS; Elsasser SJ; Londono-Vallejo A; Bartek J; Schou KB
Article: CELL REPORTS. 2020;31(12):107811
Site-Specific Incorporation of Two ncAAs for Two-Color Bioorthogonal Labeling and Crosslinking of Proteins on Live Mammalian Cells
Meineke B; Heimgertner J; Eirich J; Landreh M; Elsasser SJ
Article: JOURNAL OF ALZHEIMER'S DISEASE. 2019;72(2):537-548
Dual Bioorthogonal Labeling of the Amyloid-β Protein Precursor Facilitates Simultaneous Visualization of the Protein and Its Cleavage Products
van Husen LS; Schedin-Weiss S; Minh NT; Kazmi MA; Winblad B; Sakmar TP; Elsaesser SJ; Tjernberg LO
Article: CELL REPORTS. 2019;28(12):3274-3284.e5
Quantitative Multiplexed ChIP Reveals Global Alterations that Shape Promoter Bivalency in Ground State Embryonic Stem Cells
Kumar B; Elsasser SJ
Article: ACS CHEMICAL BIOLOGY. 2018;13(11):3087-3096
Methanomethylophilus alvus Mx1201 Provides Basis for Mutual Orthogonal Pyrrolysyl tRNA/Aminoacyl-tRNA Synthetase Pairs in Mammalian Cells
Meineke B; Heimgartner J; Lafranchi L; Elsasser SJ
Article: METHODS IN MOLECULAR BIOLOGY. 2018;1728:237-245
Generation of Stable Amber Suppression Cell Lines.
Elsässer SJ
Article: MOLECULAR SYSTEMS BIOLOGY. 2017;13(8):938
Network analyses identify liver-specific targets for treating liver diseases
Lee S; Zhang C; Liu Z; Klevstig M; Mukhopadhyay B; Bergentall M; Cinar R; Stahlman M; Sikanic N; Park JK; Deshmukh S; Harzandi AM; Kuijpers T; Grotli M; Elsasser SJ; Piening BD; Snyder M; Smith U; Nielsen J; Backhed F; Kunos G; Uhlen M; Boren J; Mardinoglu A
Article: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2016;138(3):718-721
Photoactivation of Mutant Isocitrate Dehydrogenase 2 Reveals Rapid Cancer-Associated Metabolic and Epigenetic Changes
Walker OS; Elsaesser SJ; Mahesh M; Bachman M; Balasubramanian S; Chin JW
Article: NEURON. 2015;87(1):77-94
Critical Role of Histone Turnover in Neuronal Transcription and Plasticity
Maze I; Wenderski W; Noh K-M; Bagot RC; Tzavaras N; Purushothaman I; Elsaesser SJ; Guo Y; Ionete C; Hurd YL; Tamminga CA; Halene T; Farrelly L; Soshnev AA; Wen D; Rafii S; Birtwistle MR; Akbarian S; Buchholz BA; Blitzer RD; Nestler EJ; Yuan Z-F; Garcia BA; Shen L; Molina H; Allis CD
Article: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2014;136(44):15577-15583
Efficient Multisite Unnatural Amino Acid Incorporation in Mammalian Cells via Optimized Pyrrolysyl tRNA Synthetase/tRNA Expression and Engineered eRF1
Schmied WH; Elsaesser SJ; Uttamapinant C; Chin JW
Article: NATURE BIOTECHNOLOGY. 2014;32(5):465-472
Proteome labeling and protein identification in specific tissues and at specific developmental stages in an animal
Elliott TS; Townsley FM; Bianco A; Ernst RJ; Sachdeva A; Elsaesser SJ; Davis L; Lang K; Pisa R; Greiss S; Lilley KS; Chin JW
Article: NUCLEIC ACIDS RESEARCH (NAR). 2014;42(7):4318-4331
DAXX co-folds with H3.3/H4 using high local stability conferred by the H3.3 variant recognition residues
DeNizio JE; Elsaesser SJ; Black BE
Article: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2014;136(6):2240-2243
Genetic Encoding of Photocaged Cysteine Allows Photoactivation of TEV Protease in Live Mammalian Cells
Nguyen DP; Mahesh M; Elsaesser SJ; Hancock SM; Uttamapinant C; Chin JW
Article: CELL. 2013;155(1):107-120
Hira-Dependent Histone H3.3 Deposition Facilitates PRC2 Recruitment at Developmental Loci in ES Cells
Banaszynski LA; Wen D; Dewell S; Whitcomb SJ; Lin M; Diaz N; Elsaesser SJ; Chapgier A; Goldberg AD; Canaani E; Rafii S; Zheng D; Allis CD
Article: BIOCHIMICA ET BIOPHYSICA ACTA: INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND BIOPHYSICS. 2013;1819(3-4):211-221
Towards a mechanism for histone chaperones
Elsaesser SJ; D'Arcy S
Article: NATURE STRUCTURAL & MOLECULAR BIOLOGY. 2012;19(8):819-823
Phosphorylation of histone H3 Ser10 establishes a hierarchy for subsequent intramolecular modification events
Liokatis S; Stuetzer A; Elsaesser SJ; Theillet F-X; Klingberg R; van Rossum B; Schwarzer D; Allis CD; Fischle W; Selenko P
Article: BIOCHEMICAL PHARMACOLOGY. 2011;81(1):32-42
Anti-apoptotic Bc1-2 fails to form efficient complexes with pro-apoptotic Bak to protect from Celecoxib-induced apoptosis
Rudner J; Elsaesser SJ; Jendrossek V; Huber SM
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2010;107(32):14075-14080
Daxx is an H3.3-specific histone chaperone and cooperates with ATRX in replication-independent chromatin assembly at telomeres
Lewis PW; Elsaesser SJ; Noh K-M; Stadler SC; Allis CD
Article: CELL. 2010;140(5):678-691
Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions
Goldberg AD; Banaszynski LA; Noh K-M; Lewis PW; Elsaesser SJ; Stadler S; Dewell S; Law M; Guo X; Li X; Wen D; Chapgier A; DeKelver RC; Miller JC; Lee Y-L; Boydston EA; Holmes MC; Gregory PD; Greally JM; Rafii S; Yang C; Scambler PJ; Garrick D; Gibbons RJ; Higgs DR; Cristea IM; Urnov FD; Zheng D; Allis CD
Article: COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY. 2010;75:27-34
HIRA and Daxx constitute two independent histone H3.3-containing predeposition complexes.
Elsaesser SJ; Allis CD
Article: BIOCHEMICAL PHARMACOLOGY. 2010;79(1):10-20
Differential effects of anti-apoptotic Bcl-2 family members Mcl-1, Bcl-2, and Bcl-xL on Celecoxib-induced apoptosis
Rudner J; Elsaesser SJ; Mueller A-C; Belka C; Jendrossek V
Article: BIOCHEMICAL PHARMACOLOGY. 2008;76(9):1082-1096
Importance of Bak for celecoxib-induced apoptosis
Mueller A-C; Handrick R; Elsaesser SJ; Rudner J; Henke G; Ganswindt U; Belka C; Jendrossek V
Article: NATURE STRUCTURAL & MOLECULAR BIOLOGY. 2008;15(3):321-329
In situ observation of protein phosphorylation by high-resolution NMR spectroscopy
Selenko P; Frueh DP; Elsaesser SJ; Haas W; Gygi SP; Wagner G
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All other publications

Preprint: BIORXIV. 2024
Pooled overexpression screening identifies PIPPI as a novel microprotein involved in the ER stress response
Lafranchi L; Spinner A; Hornisch M; Schlesinger D; Luzon CN; Brinkenstråhle L; Shao R; Piazza I; Elsässer SJ
Preprint: BIORXIV. 2023
A large-scale sORF screen identifies putative microproteins and provides insights into their interaction partners, localisation and function
Schlesinger D; Dirks C; Luzon CN; Lafranchi L; Eirich J; Elsässer S
Preprint: BIORXIV. 2023
Dual stop codon suppression in mammalian cells with genomically integrated genetic code expansion machinery
Meineke B; Heimgärtner J; Caridha R; Block M; Kimler K; Pires M; Landreh M; Elsässer S
Preprint: BIORXIV. 2022
minute: A MINUTE-ChIP data analysis workflow
Navarro C; Martin M; Elsässer S
Review: THE FEBS JOURNAL. 2022;289(1):53-74
Revisiting sORFs: overcoming challenges to identify and characterize functional microproteins
Schlesinger D; Elsasser SJ
Preprint: BIORXIV. 2021
Engineered human induced pluripotent cells enable genetic code expansion in brain organoids
van Husen L; Katsori A-M; Meineke B; Tjernberg L; Schedin-Weiss S; Elsässer S
Preprint: BIORXIV. 2021
Newly synthesized RNA Sequencing Characterizes Transcription Dynamics in Three Pluripotent States
Shao R; Kumar B; Lidschreiber K; Lidschreiber M; Cramer P; Elsässer S
Preprint: BIORXIV. 2021
Genome-wide mapping of G-quadruplex structures with CUT&Tag
Lyu J; Shao R; Elsässer S
Preprint: MEDRXIV. 2020
Detection of SARS-CoV-2 using non-commercial RT-LAMP reagents and raw samples
Alekseenko A; Barrett D; Pareja-Sanchez Y; J Howard R; Strandback E; Ampah-Korsah H; Rovšnik U; Zuniga-Veliz S; Klenov A; Malloo J; Ye S; Liu X; Reinius B; Elsässer S; Nyman T; Sandh G; Yin X; Pelechano V
Preprint: MEDRXIV. 2020
A translational multiplex serology approach to profile the prevalence of anti-SARS-CoV-2 antibodies in home-sampled blood
Roxhed N; Bendes A; Dale M; Mattsson C; Hanke L; Dodig-Crnkovic T; Christian M; Meineke B; Elsässer S; Andréll J; Havervall S; Thålin C; Eklund C; Dillner J; Beck O; Thomas C; McInerney G; Hong M-G; Murrell B; Fredolini C; Schwenk J
Preprint: BIORXIV. 2020
Sirtuin-1 Sensitive Lysine-136 Acetylation Drives Phase Separation and Pathological Aggregation of TDP-43
Morato JG; Hans F; von Zweydorf F; Feederle R; Elsässer S; Skodras A; Gloeckner CJ; Buratti E; Neumann M; Kahle P
Preprint: BIORXIV. 2020
An embryonic stem cell-specific heterochromatin state allows core histone exchange in the absence of DNA accessibility
Navarro C; Elsässer S
Review: DEVELOPMENT. 2019;146(19):dev178962
EvoChromo: towards a synthesis of chromatin biology and evolution
Drinnenberg IA; Berger F; Elsasser SJ; Andersen PR; Ausio J; Bickmore WA; Blackwell AR; Erwin DH; Gahan JM; Gaut BS; Harvey ZH; Henikoff S; Kao JY; Kurdistani SK; Lemos B; Levine MT; Luger K; Malik HS; Martin-Duran JM; Peichel CL; Renfree MB; Rutowicz K; Sarkies P; Schmitz RJ; Technau U; Thornton JW; Warnecke T; Wolfe KH
Preprint: BIORXIV. 2019
Quantitative multiplexed ChIP reveals global alterations that shape promoter bivalency in ground state embryonic stem cells
Kumar B; Elsässer S
Preprint: BIORXIV. 2018
Methanomethylophilus alvus Mx1201 provides basis for mutual orthogonal pyrrolysyl tRNA/aminoacyl-tRNA synthetase pairs in mammalian cells
Meineke B; Heimgärtner J; Lafranchi L; Elsässer S
Review: CURRENT OPINION IN CHEMICAL BIOLOGY. 2017;41:36-42
Evolution of epigenetic chromatin states
Yung PYK; Elsasser SJ
Editorial comment: JOURNAL OF GLOBAL HEALTH. 2017;7(2):020304
Biodiversity, drug discovery, and the future of global health: Introducing the biodiversity to biomedicine consortium, a call to action
Neergheen-Bhujun V; Awan AT; Baran Y; Bunnefeld N; Chan K; Edison Dela Cruz T; Egamberdieva D; Elsasser S; Johnson M-VV; Komai S; Konevega AL; Malone JH; Mason P; Nguon R; Piper R; Shrestha UB; Pesic M; Kagansky A
Letter: NATURE. 2017;548(7665):E7-E9
On the role of H3.3 in retroviral silencing reply
Elsasser SJ; Noh K-M; Diaz N; Allis CD; Banaszynski LA
Editorial comment: TRENDS IN BIOCHEMICAL SCIENCES. 2013;38(7):333-336
A common structural theme in histone chaperones mimics interhistone contacts
Elsaesser SJ
Meeting abstract: BIOPHYSICAL JOURNAL. 2013;104(2):29a-30a
Co-Folding of the Histone Chaperone DAXX and H3.3/H4
DeNizio JE; Elsaesser SJ; Allis CD; Black BE
Editorial comment: SCIENCE. 2011;331(6021):1145-1146
New Epigenetic Drivers of Cancers
Elsaesser SJ; Allis CD; Lewis PW
Review: CURRENT OPINION IN GENETICS AND DEVELOPMENT. 2010;20(2):110-117
New functions for an old variant: no substitute for histone H3.3
Elsaesser SJ; Goldberg AD; Allis CD
Conference publication: STRAHLENTHERAPIE UND ONKOLOGIE. 2008;184:15-16
The down regulation of Mcl-1 is a early and necessary step during the Celecoxib-induced apoptosis
Rudner J; Elsaesser S; Mueller A-C; Belka C; Jendrossek V
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Grants

Molecular mechanism underlying cell identity and lineage choices in mammalian early embryonic development
Swedish Research Council
1 January 2024 - 31 December 2028
Building the early human embryo
Swedish Research Council
1 December 2023 - 30 November 2028
Highly multiplexed, quantitative epigenetic profiling
European Research Council
1 January 2021 - 30 June 2022
Dynamic interplay of Polycomb complexes in establishing and maintaining cellular memory
Swedish Research Council
1 January 2021 - 31 December 2024
Genetic code expansion in neurons to elucidate pathogenic mechanisms in Alzheimer disease
Swedish Research Council
1 January 2018 - 31 December 2021
Studies of epigenetic mechanisms in the pancreas and brain tumors
Swedish Cancer Society
1 January 2018
Chromatin dynamics resolved by rapid protein labeling and bioorthogonal capture
European Research Council
1 January 2017 - 30 June 2022
Deciphering Spatial Signaling of Protein Clusters at the Membrane
Knut and Alice Wallenberg Foundation
1 January 2017 - 1 January 2022
Studies of epigenetic mechanisms in the pancreas and brain tumors
Swedish Cancer Society
1 January 2017
Chromatin plasticity and epigenetic silencing in pluripotent cells - understanding the dynamics and inheritance of stem cell chromatin
Swedish Research Council
1 January 2016 - 31 December 2019
Studies of epigenetic mechanisms in the pancreas and brain tumors
Swedish Cancer Society
1 January 2016

Selected publications

Articles

All other publications

Grants

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