Elsässer SJ

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Family name Elsässer
Given name Simon J
Initials SJ
ORCID

ORCID 0000-0001-8724-4849
Affiliations Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden

71 publications

PubMed DOI Crossref
Pooled overexpression screening identifies PIPPI as a novel microprotein involved in the ER stress response.
Lafranchi L, Raja GL, Arenas AM, ..., Branca RMM, Elsӓsser SJ
Nucleic Acids Res. 53 (20) - [2025-10-28; online 2025-11-09]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
RNA transcripts regulate G-quadruplex landscapes through G-loop formation.
Sato K, Lyu J, van den Berg J, ..., Elsässer SJ, Knipscheer P
Science (New York, N.Y.) 388 (6752) 1225-1231 [2025-06-12; online 2025-06-12]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
G-quadruplex profiling in complex tissues using single-cell CUT&Tag
Lyu J, Hetey S, Castelo-Branco G, Bartosovic M, Elsässer SJ
- - (-) - [2025-04-05; online 2025-04-05]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors.
Kumar B, Navarro C, Yung PYK, ..., Martin M, Elsässer SJ
Nat Protoc 20 (3) 779-809 [2025-03-00; online 2024-10-03]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
The Role of BAZ2-dependent Chromatin Remodeling in Suppressing G4 DNA Structures and Associated Genomic Instability
Vandeuren AL, O’Dare K, Wilson RHC, ..., Reed SH, Day TA
- - (-) - [2024-12-11; online 2024-12-11]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Pooled overexpression screening identifies PIPPI as a novel microprotein involved in the ER stress response
Lafranchi L, Spinner A, Hornisch M, ..., Piazza I, Elsässer SJ
- - (-) - [2024-12-09; online 2024-12-09]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Detection and quantification of Na,K-ATPase dimers in the plasma membrane of living cells by FRET-FCS.
Nordahl L, Akkuratov EE, Heimgärtner J, ..., Wennmalm S, Brismar H
Biochim Biophys Acta Gen Subj 1868 (7) 130619 [2024-07-00; online 2024-04-20]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Dual stop codon suppression in mammalian cells with genomically integrated genetic code expansion machinery.
Meineke B, Heimgärtner J, Caridha R, ..., Landreh M, Elsässer SJ
Cell Rep Methods 3 (11) 100626 [2023-11-20; online 2023-11-06]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
A large-scale sORF screen identifies putative microproteins and provides insights into their interaction partners, localisation and function
Schlesinger D, Dirks C, Luzon CN, ..., Eirich J, Elsässer SJ
- - (-) - [2023-06-13; online 2023-06-13]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Click chemistry, FRET-FCS, and expansion microscopy reveal that Na, K-ATPase forms complexes in the plasma membrane
Brismar H, Edwards S, Bauer S, ..., Elsässer S, Wennmalm S
Physiology 38 (S1) - [2023-05-00; online 2023-05-00]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
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, ..., Elsässer S, Brismar H
Physiology 38 (S1) - [2023-05-00; online 2023-05-00]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Dynamic antagonism between key repressive pathways maintains the placental epigenome.
Weigert R, Hetzel S, Bailly N, ..., Smith ZD, Meissner A
Nat. Cell Biol. 25 (4) 579-591 [2023-04-00; online 2023-04-06]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Dual stop codon suppression in mammalian cells with genomically integrated genetic code expansion machinery
Meineke B, Heimgärtner J, Caridha R, ..., Landreh M, Elsässer SJ
- - (-) - [2023-03-27; online 2023-03-27]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
TET1 regulates gene expression and repression of endogenous retroviruses independent of DNA demethylation.
Stolz P, Mantero AS, Tvardovskiy A, ..., Elsässer SJ, Bultmann S
Nucleic Acids Res. 50 (15) 8491-8511 [2022-08-26; online 2022-07-30]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Polycomb repressive complex 2 shields naïve human pluripotent cells from trophectoderm differentiation.
Kumar B, Navarro C, Winblad N, ..., Lanner F, Elsässer SJ
Nat. Cell Biol. 24 (6) 845-857 [2022-06-00; online 2022-05-30]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Direct Observation of Na,K‐ATPase Oligomers in The Plasma Membrane of Living Cells by FRET‐FCS
Nordahl L, Wennmalm S, Jönsson J, ..., Akkuratov EE, Brismar H
The FASEB Journal 36 (S1) - [2022-05-00; online 2022-05-13]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Cancer cells use self-inflicted DNA breaks to evade growth limits imposed by genotoxic stress.
Larsen BD, Benada J, Yung PYK, ..., Bartek J, Sørensen CS
Science (New York, N.Y.) 376 (6592) 476-483 [2022-04-29; online 2022-04-28]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
minute: A MINUTE-ChIP data analysis workflow
Navarro C, Martin M, Elsässer S
- - (-) - [2022-03-17; online 2022-03-17]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Sirtuin-1 sensitive lysine-136 acetylation drives phase separation and pathological aggregation of TDP-43.
Garcia Morato J, Hans F, von Zweydorf F, ..., Neumann M, Kahle PJ
Nat Commun 13 (1) 1223 [2022-03-09; online 2022-03-09]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Genome-wide mapping of G-quadruplex structures with CUT&Tag.
Lyu J, Shao R, Kwong Yung PY, Elsässer SJ
Nucleic Acids Res. 50 (3) e13 [2022-02-22; online 2021-11-19]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Revisiting sORFs: overcoming challenges to identify and characterize functional microproteins.
Schlesinger D, Elsässer SJ
FEBS J. 289 (1) 53-74 [2022-01-00; online 2021-02-24]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Distinct transcription kinetics of pluripotent cell states.
Shao R, Kumar B, Lidschreiber K, ..., Cramer P, Elsässer SJ
Mol Syst Biol 18 (1) e10407 [2022-01-00; online 2022-01-13]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Polycomb Repressive Complex 2 shields naïve human pluripotent cells from trophectoderm differentiation
Kumar B, Navarro C, Winblad N, ..., Lanner F, Elsässer SJ
bioRxiv - (-) - [2021-08-22; online 2021-08-22]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
The exon-junction complex helicase eIF4A3 controls cell fate via coordinated regulation of ribosome biogenesis and translational output.
Kanellis DC, Espinoza JA, Zisi A, ..., Lindström MS, Bartek J
Sci Adv 7 (32) - [2021-08-00; online 2021-08-04]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Engineered human induced pluripotent cells enable genetic code expansion in brain organoids
van Husen LS, Katsori AM, Meineke B, ..., Schedin-Weiss S, Elsässer SJ
- - (-) - [2021-06-24; online 2021-06-24]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Multianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2.
Roxhed N, Bendes A, Dale M, ..., Fredolini C, Schwenk JM
Nat Commun 12 (1) 3695 [2021-06-17; online 2021-06-17]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Newly synthesized RNA Sequencing Characterizes Transcription Dynamics in Three Pluripotent States
Shao R, Kumar B, Lidschreiber K, ..., Cramer P, Elsässer SJ
- - (-) - [2021-06-13; online 2021-06-13]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Towards policies that capture the expected value of biomolecular diversity for drug discovery, human health, and well-being.
Pesic M, Egamberdieva D, Kolodziejczyk B, ..., Neergheen VS, Kagansky A
Biol Futur 72 (2) 119-125 [2021-06-00; online 2020-09-07]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Correction to: Towards policies that capture the expected value of biomolecular diversity for drug discovery, human health, and well-being.
Pesic M, Egamberdieva D, Kolodziejczyk B, ..., Neergheen VS, Kagansky A
Biol Futur 72 (2) 127 [2021-06-00; online 2021-09-24]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Faculty Opinions recommendation of Replication timing maintains the global epigenetic state in human cells.
Elsässer S, Lafranchi L
- - (-) - [2021-05-21; online 2021-05-05]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Genome-wide mapping of G-quadruplex structures with CUT&Tag
Lyu J, Shao R, Elsässer SJ
- - (-) - [2021-04-26; online 2021-04-26]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples.
Alekseenko A, Barrett D, Pareja-Sanchez Y, ..., Yin X, Pelechano V
Sci Rep 11 (1) 1820 [2021-01-19; online 2021-01-19]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Universal Single-Residue Terminal Labels for Fluorescent Live Cell Imaging of Microproteins.
Lafranchi L, Schlesinger D, Kimler KJ, Elsässer SJ
Journal of the American Chemical Society 142 (47) 20080-20087 [2020-11-25; online 2020-11-11]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Faculty Opinions recommendation of Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq.
Elsässer S
- - (-) - [2020-11-25; online 2020-11-13]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
An embryonic stem cell-specific heterochromatin state promotes core histone exchange in the absence of DNA accessibility.
Navarro C, Lyu J, Katsori AM, Caridha R, Elsässer SJ
Nat Commun 11 (1) 5095 [2020-10-09; online 2020-10-09]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Human RTEL1 associates with Poldip3 to facilitate responses to replication stress and R-loop resolution.
Björkman A, Johansen SL, Lin L, ..., Bartek J, Schou KB
Genes Dev. 34 (15-16) 1065-1074 [2020-08-01; online 2020-06-19]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
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, ..., Fredolini C, Schwenk JM
- - (-) - [2020-07-02; online 2020-07-02]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
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
Cell Reports 31 (12) 107811 [2020-06-23; online 2020-06-25]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Sirtuin-1 Sensitive Lysine-136 Acetylation Drives Phase Separation and Pathological Aggregation of TDP-43
Morato JG, Hans F, von Zweydorf F, ..., Neumann M, Kahle PJ
- - (-) - [2020-05-26; online 2020-05-26]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
An embryonic stem cell-specific heterochromatin state allows core histone exchange in the absence of DNA accessibility
Navarro C, Elsässer SJ
- - (-) - [2020-05-22; online 2020-05-22]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
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, ..., Elsässer SJ, Tjernberg LO
J. Alzheimers Dis. 72 (2) 537-548 [2019-10-15; online 2019-10-15]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
EvoChromo: towards a synthesis of chromatin biology and evolution.
Drinnenberg IA, Berger F, Elsässer SJ, ..., Warnecke T, Wolfe KH
Development 146 (19) - [2019-09-26; online 2019-09-26]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Faculty Opinions recommendation of The nucleosome core particle remembers its position through DNA replication and RNA transcription.
Elsässer S
- - (-) - [2019-09-23; online 2019-09-17]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Quantitative Multiplexed ChIP Reveals Global Alterations that Shape Promoter Bivalency in Ground State Embryonic Stem Cells.
Kumar B, Elsässer SJ
Cell Reports 28 (12) 3274-3284.e5 [2019-09-17; online 2019-09-19]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Faculty Opinions recommendation of Engineering Epigenetic Regulation Using Synthetic Read-Write Modules.
Elsässer S, Lafranchi L
- - (-) - [2019-03-19; online 2019-03-12]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Faculty Opinions recommendation of Structures of human PRC2 with its cofactors AEBP2 and JARID2.
Elsässer S
- - (-) - [2019-03-13; online 2019-03-05]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Quantitative multiplexed ChIP reveals global alterations that shape promoter bivalency in ground state embryonic stem cells
Kumar B, Elsässer SJ
- - (-) - [2019-03-06; online 2019-03-06]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
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
ACS chemical biology 13 (11) 3087-3096 [2018-11-16; online 2018-10-12]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
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
- - (-) - [2018-07-19; online 2018-07-19]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Faculty Opinions recommendation of Capturing the Onset of PRC2-Mediated Repressive Domain Formation.
Elsässer S
- - (-) - [2018-07-10; online 2018-07-04]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Faculty Opinions recommendation of Accurate H3K27 methylation can be established de novo by SUZ12-directed PRC2.
Elsässer S
- - (-) - [2018-07-10; online 2018-07-04]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Faculty Opinions recommendation of Rewritable multi-event analog recording in bacterial and mammalian cells.
Elsässer S
- - (-) - [2018-02-22; online 2018-02-18]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Generation of Stable Amber Suppression Cell Lines.
Elsässer SJ
Methods in molecular biology (Clifton, N.J.) 1728 (-) 237-245 [2018-02-07; online 2018-02-07]
SciLifeLab Fellow Simon Elsässer
DOI Crossref
Faculty Opinions recommendation of A semi-synthetic organism that stores and retrieves increased genetic information.
Elsässer S
- - (-) - [2017-12-11; online 2017-12-04]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Evolution of epigenetic chromatin states.
Yung PYK, Elsässer SJ
Curr Opin Chem Biol 41 (-) 36-42 [2017-12-00; online 2017-11-02]
Affiliated researcher SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
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, ..., Pešić M, Kagansky A
Journal of global health 7 (2) 020304 [2017-12-00; online 2018-01-06]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Elsässer et al. reply.
Elsässer SJ, Noh KM, Diaz N, Allis CD, Banaszynski LA
Nature 548 (7665) E7-E9 [2017-08-02; online 2017-08-05]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Genetic code expansion in stable cell lines enables encoded chromatin modification.
Elsässer SJ, Ernst RJ, Walker OS, Chin JW
Nat. Methods 13 (2) 158-164 [2016-02-00; online 2016-01-04]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Photoactivation of Mutant Isocitrate Dehydrogenase 2 Reveals Rapid Cancer-Associated Metabolic and Epigenetic Changes.
Walker OS, Elsässer SJ, Mahesh M, ..., Balasubramanian S, Chin JW
Journal of the American Chemical Society 138 (3) 718-721 [2016-01-27; online 2016-01-12]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Critical Role of Histone Turnover in Neuronal Transcription and Plasticity.
Maze I, Wenderski W, Noh KM, ..., Molina H, Allis CD
Neuron 87 (1) 77-94 [2015-07-01; online 2015-07-04]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells.
Elsässer SJ, Noh KM, Diaz N, Allis CD, Banaszynski LA
Nature 522 (7555) 240-244 [2015-06-11; online 2015-05-04]
PubMed DOI Crossref
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
J. Am. Chem. Soc. 136 (44) 15577-15583 [2014-11-05; online 2014-10-28]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Proteome labeling and protein identification in specific tissues and at specific developmental stages in an animal
Elliott TS, Townsley FM, Bianco A, ..., Lilley KS, Chin JW
Nat Biotechnol 32 (5) 465-472 [2014-05-00; online 2014-04-13]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
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
Nucleic Acids Res. 42 (7) 4318-4331 [2014-04-00; online 2014-01-31]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Genetic Encoding of Photocaged Cysteine Allows Photoactivation of TEV Protease in Live Mammalian Cells
Nguyen DP, Mahesh M, Elsässer SJ, ..., Uttamapinant C, Chin JW
J. Am. Chem. Soc. 136 (6) 2240-2243 [2014-02-12; online 2014-01-30]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Hira-Dependent Histone H3.3 Deposition Facilitates PRC2 Recruitment at Developmental Loci in ES Cells
Banaszynski LA, Wen D, Dewell S, ..., Zheng D, Allis CD
Cell 155 (1) 107-120 [2013-09-00; online 2013-09-00]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
A common structural theme in histone chaperones mimics interhistone contacts.
Elsässer SJ
Trends Biochem. Sci. 38 (7) 333-336 [2013-07-00; online 2013-06-26]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
DAXX envelops a histone H3.3–H4 dimer for H3.3-specific recognition
Elsässer SJ, Huang H, Lewis PW, ..., Allis CD, Patel DJ
Nature 491 (7425) 560-565 [2012-11-00; online 2012-10-17]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Phosphorylation of histone H3 Ser10 establishes a hierarchy for subsequent intramolecular modification events
Liokatis S, Stützer A, Elsässer SJ, ..., Fischle W, Selenko P
Nat Struct Mol Biol 19 (8) 819-823 [2012-08-00; online 2012-07-15]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Towards a mechanism for histone chaperones
Elsässer SJ, D'Arcy S
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1819 (3-4) 211-221 [2012-03-00; online 2012-03-00]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Cancer. New epigenetic drivers of cancers.
Elsässer SJ, Allis CD, Lewis PW
Science (New York, N.Y.) 331 (6021) 1145-1146 [2011-03-04; online 2011-03-10]
SciLifeLab Fellow Simon Elsässer
SciLifeLab Data Centre
Publications 9.5.1