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; Elsässer SJ; Bartek J; Sørensen CS
Article: NUCLEIC ACIDS RESEARCH. 2022;50(3):e13

Genome-wide mapping of G-quadruplex structures with CUT&Tag.

Lyu J; Shao R; Kwong Yung PY; Elsässer 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; Elsässer 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.

Elsässer 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.

Elsässer 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.

Elsässer SJ; Huang H; Lewis PW; Chin JW; Allis CD; Patel DJ

Articles

Article: CELL REPORTS METHODS. 2023;3(11):100626

Dual stop codon suppression in mammalian cells with genomically integrated genetic code expansion machinery.

Meineke B; Heimgärtner J; Caridha R; Block MF; Kimler KJ; Pires MF; Landreh M; Elsässer 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; Brändl B; Meierhofer D; Lupiáñez DG; Müller F-J; Aktas T; Elsässer SJ; Kretzmer H; Smith ZD; Meissner A
Journal 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. 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; Elsässer SJ; Bultmann S
Article: NATURE CELL BIOLOGY. 2022;24(6):845-857

Polycomb repressive complex 2 shields naïve human pluripotent cells from trophectoderm differentiation.

Kumar B; Navarro C; Winblad N; Schell JP; Zhao C; Weltner J; Baqué-Vidal L; Salazar Mantero A; Petropoulos S; Lanner F; Elsässer SJ
Journal article: 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.

Garcia Morato J; Hans F; von Zweydorf F; Feederle R; Elsässer 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; Elsässer 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; Boström J; Dyrskjøt L; Broholm H; Altun M; Elsässer SJ; Lindström 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-Crnković T; Christian M; Meineke B; Elsässer S; Andréll J; Havervall S; Thålin 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; Elsässer 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; Rovšnik U; Zuniga-Veliz S; Klenov A; Malloo J; Ye S; Liu X; Reinius B; Elsässer 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; Heimgärtner J; Craig AJ; Landreh M; Moodie LWK; Elsässer 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; Elsässer 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; Elsässer 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.

Björkman A; Johansen SL; Lin L; Schertzer M; Kanellis DC; Katsori A-M; Christensen ST; Luo Y; Andersen JS; Elsässer 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; Heimgärtner J; Eirich J; Landreh M; Elsässer SJ
Article: JOURNAL OF ALZHEIMERS 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; Trung MN; Kazmi MA; Winblad B; Sakmar TP; Elsässer 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; Elsässer 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; Heimgärtner J; Lafranchi L; Elsässer 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; Ståhlman M; Sikanic N; Park JK; Deshmukh S; Harzandi AM; Kuijpers T; Grøtli M; Elsässer SJ; Piening BD; Snyder M; Smith U; Nielsen J; Bäckhed 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; Elsässer 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; Elsässer 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; Elsässer 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; Elsässer SJ; Davis L; Lang K; Pisa R; Greiss S; Lilley KS; Chin JW
Article: NUCLEIC ACIDS RESEARCH. 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; Elsässer 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; Elsässer 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; Elsässer 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.

Elsässer 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; Stützer A; Elsässer 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 Bcl-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: 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; Müller A-C; Belka C; Jendrossek V
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. 2008;76(9):1082-1096

Importance of Bak for celecoxib-induced apoptosis.

Müller 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. 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: FEBS JOURNAL. 2022;289(1):53-74

Revisiting sORFs: overcoming challenges to identify and characterize functional microproteins.

Schlesinger D; Elsässer 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; Elsässer SJ; Andersen PR; Ausió 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; Martín-Durán 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; Elsässer 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; Dela Cruz TE; Egamberdieva D; Elsässer S; Johnson M-VV; Komai S; Konevega AL; Malone JH; Mason P; Nguon R; Piper R; Shrestha UB; Pešić M; Kagansky A
Letter: NATURE. 2017;548(7665):E7-E9

Elsässer et al. reply.

Elsässer 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.

Elsässer 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

Cancer. New epigenetic drivers of cancers.

Elsässer SJ; Allis CD; Lewis PW
Review: CURRENT OPINION IN GENETICS & 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
Studies of epigenetic mechanisms in the pancreas and brain tumors

Swedish Cancer Society

1 January 2018
Genetic code expansion in neurons to elucidate pathogenic mechanisms in Alzheimer disease

Swedish Research Council

1 January 2018 - 31 December 2021
Chromatin dynamics resolved by rapid protein labeling and bioorthogonal capture

European Research Council

1 January 2017 - 30 June 2022
Studies of epigenetic mechanisms in the pancreas and brain tumors

Swedish Cancer Society

1 January 2017
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 2016
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

Selected publications

Articles

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Grants

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