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Article ; Online: Author Correction: Deciphering eukaryotic gene-regulatory logic with 100 million random promoters.

de Boer, Carl G / Vaishnav, Eeshit Dhaval / Sadeh, Ronen / Abeyta, Esteban Luis / Friedman, Nir / Regev, Aviv

2020 Volume 38, Issue 10, Page(s) 1211

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

Abstract	An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Language	English
Publishing date	2020-07-16
Publishing country	United States
Document type	Published Erratum
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-020-0665-2
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Article ; Online: Genome-wide "re"-modeling of nucleosome positions.

Sadeh, Ronen / Allis, C David

Cell

2011 Volume 147, Issue 2, Page(s) 263–266

Abstract: Two recent studies mapped nucleosomes across the yeast and human genomes, teasing apart the relative contributions of DNA sequence and chromatin remodelers to nucleosome organization. These data suggest two emerging models: chromatin remodelers position ... ...

Abstract	Two recent studies mapped nucleosomes across the yeast and human genomes, teasing apart the relative contributions of DNA sequence and chromatin remodelers to nucleosome organization. These data suggest two emerging models: chromatin remodelers position nucleosomes around transcriptional start sites in yeast, and a few "locked" nucleosomes may serve as barriers from which nucleosome arrays emanate in human genomes.
MeSH term(s)	Adenosine Triphosphate/metabolism ; Chromatin Assembly and Disassembly ; Genome, Fungal ; Genome, Human ; Humans ; Models, Genetic ; Nucleosomes/metabolism ; Promoter Regions, Genetic
Chemical Substances	Nucleosomes ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2011-10-13
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2011.09.042
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Article: Elucidating Combinatorial Chromatin States at Single-Nucleosome Resolution

Sadeh, Ronen / Ayelet Rahat / Hava Wandel / Nir Friedman / Roee Launer-Wachs

Molecular cell. 2016 Sept. 15, v. 63, no. 6

2016

Abstract: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has been instrumental to our current view of chromatin structure and function. It allows genome-wide mapping of histone marks, which demarcate biologically relevant domains. However, ChIP- ... ...

Abstract	Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has been instrumental to our current view of chromatin structure and function. It allows genome-wide mapping of histone marks, which demarcate biologically relevant domains. However, ChIP-seq is an ensemble measurement reporting the average occupancy of individual marks in a cell population. Consequently, our understanding of the combinatorial nature of chromatin states relies almost exclusively on correlation between the genomic distributions of individual marks. Here, we report the development of combinatorial-iChIP to determine the genome-wide co-occurrence of histone marks at single-nucleosome resolution. By comparing to a null model, we show that certain combinations of overlapping marks (H3K36me3 and H3K79me3) co-occur more frequently than would be expected by chance, while others (H3K4me3 and H3K36me3) do not, reflecting differences in the underlying chromatin pathways. We further use combinatorial-iChIP to illuminate aspects of the Set2-RPD3S pathway. This approach promises to improve our understanding of the combinatorial complexity of chromatin.
Keywords	chromatin ; histones ; models ; precipitin tests
Language	English
Dates of publication	2016-0915
Size	p. 1080-1088.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2016.07.023
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Article ; Online: Elevated cfDNA after exercise is derived primarily from mature polymorphonuclear neutrophils, with a minor contribution of cardiomyocytes.

Fridlich, Ori / Peretz, Ayelet / Fox-Fisher, Ilana / Pyanzin, Sheina / Dadon, Ziv / Shcolnik, Eilon / Sadeh, Ronen / Fialkoff, Gavriel / Sharkia, Israa / Moss, Joshua / Arpinati, Ludovica / Nice, Shachar / Nogiec, Christopher D / Ahuno, Samuel Terkper / Li, Rui / Taborda, Eddie / Dunkelbarger, Sonia / Fridlender, Zvi G / Polak, Paz /

Kaplan, Tommy / Friedman, Nir / Glaser, Benjamin / Shemer, Ruth / Constantini, Naama / Dor, Yuval

Cell reports. Medicine

2023 Volume 4, Issue 6, Page(s) 101074

Abstract: Strenuous physical exercise causes a massive elevation in the concentration of circulating cell-free DNA (cfDNA), which correlates with effort intensity and duration. The cellular sources and physiological drivers of this phenomenon are unknown. Using ... ...

Abstract	Strenuous physical exercise causes a massive elevation in the concentration of circulating cell-free DNA (cfDNA), which correlates with effort intensity and duration. The cellular sources and physiological drivers of this phenomenon are unknown. Using methylation patterns of cfDNA and associated histones, we show that cfDNA in exercise originates mostly in extramedullary polymorphonuclear neutrophils. Strikingly, cardiomyocyte cfDNA concentration increases after a marathon, consistent with elevated troponin levels and indicating low-level, delayed cardiac cell death. Physical impact, low oxygen levels, and elevated core body temperature contribute to neutrophil cfDNA release, while muscle contraction, increased heart rate, β-adrenergic signaling, or steroid treatment fail to cause elevation of cfDNA. Physical training reduces neutrophil cfDNA release after a standard exercise, revealing an inverse relationship between exercise-induced cfDNA release and training level. We speculate that the release of cfDNA from neutrophils in exercise relates to the activation of neutrophils in the context of exercise-induced muscle damage.
MeSH term(s)	Neutrophils ; Myocytes, Cardiac ; Cell-Free Nucleic Acids ; Exercise/physiology ; Histones
Chemical Substances	Cell-Free Nucleic Acids ; Histones
Language	English
Publishing date	2023-06-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2666-3791
ISSN (online)	2666-3791
DOI	10.1016/j.xcrm.2023.101074
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Article ; Online: Deciphering eukaryotic gene-regulatory logic with 100 million random promoters.

de Boer, Carl G / Vaishnav, Eeshit Dhaval / Sadeh, Ronen / Abeyta, Esteban Luis / Friedman, Nir / Regev, Aviv

Nature biotechnology

2019 Volume 38, Issue 1, Page(s) 56–65

Abstract: How transcription factors (TFs) interpret cis-regulatory DNA sequence to control gene expression remains unclear, largely because past studies using native and engineered sequences had insufficient scale. Here, we measure the expression output of >100 ... ...

Abstract	How transcription factors (TFs) interpret cis-regulatory DNA sequence to control gene expression remains unclear, largely because past studies using native and engineered sequences had insufficient scale. Here, we measure the expression output of >100 million synthetic yeast promoter sequences that are fully random. These sequences yield diverse, reproducible expression levels that can be explained by their chance inclusion of functional TF binding sites. We use machine learning to build interpretable models of transcriptional regulation that predict ~94% of the expression driven from independent test promoters and ~89% of the expression driven from native yeast promoter fragments. These models allow us to characterize each TF's specificity, activity and interactions with chromatin. TF activity depends on binding-site strand, position, DNA helical face and chromatin context. Notably, expression level is influenced by weak regulatory interactions, which confound designed-sequence studies. Our analyses show that massive-throughput assays of fully random DNA can provide the big data necessary to develop complex, predictive models of gene regulation.
MeSH term(s)	Binding Sites ; DNA/metabolism ; Eukaryota/genetics ; Gene Expression Regulation ; Genes, Reporter ; Logic ; Models, Genetic ; Promoter Regions, Genetic ; Saccharomyces cerevisiae/genetics ; Transcription Factors/metabolism
Chemical Substances	Transcription Factors ; DNA (9007-49-2)
Language	English
Publishing date	2019-12-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-019-0315-8
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Article ; Online: Mapping the Landscape of a Eukaryotic Degronome.

Geffen, Yifat / Appleboim, Alon / Gardner, Richard G / Friedman, Nir / Sadeh, Ronen / Ravid, Tommer

Molecular cell

2016 Volume 63, Issue 6, Page(s) 1055–1065

Abstract: The ubiquitin-proteasome system (UPS) for protein degradation has been under intensive study, and yet, we have only partial understanding of mechanisms by which proteins are selected to be targeted for proteolysis. One of the obstacles in studying these ... ...

Abstract	The ubiquitin-proteasome system (UPS) for protein degradation has been under intensive study, and yet, we have only partial understanding of mechanisms by which proteins are selected to be targeted for proteolysis. One of the obstacles in studying these recognition pathways is the limited repertoire of known degradation signals (degrons). To better understand what determines the susceptibility of intracellular proteins to degradation by the UPS, we developed an unbiased method for large-scale identification of eukaryotic degrons. Using a reporter-based high-throughput competition assay, followed by deep sequencing, we measured a degradation potency index for thousands of native polypeptides in a single experiment. We further used this method to identify protein quality control (PQC)-specific and compartment-specific degrons. Our method provides an unprecedented insight into the yeast degronome, and it can readily be modified to study protein degradation signals and pathways in other organisms and in various settings.
MeSH term(s)	Binding Sites ; Chromosome Mapping ; Gene Expression Regulation, Fungal ; Gene Library ; Genome, Fungal ; High-Throughput Screening Assays ; Phosphorylation ; Proteasome Endopeptidase Complex/metabolism ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Folding ; Protein Interaction Domains and Motifs ; Proteolysis ; Proteome/genetics ; Proteome/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Ubiquitin/genetics ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligases/chemistry ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism
Chemical Substances	Proteome ; Saccharomyces cerevisiae Proteins ; URA3 protein, S cerevisiae ; Ubiquitin ; SSM4 protein, S cerevisiae (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2016-09-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2016.08.005
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Article ; Online: Elucidating Combinatorial Chromatin States at Single-Nucleosome Resolution.

Sadeh, Ronen / Launer-Wachs, Roee / Wandel, Hava / Rahat, Ayelet / Friedman, Nir

Molecular cell

2016 Volume 63, Issue 6, Page(s) 1080–1088

Abstract	Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has been instrumental to our current view of chromatin structure and function. It allows genome-wide mapping of histone marks, which demarcate biologically relevant domains. However, ChIP-seq is an ensemble measurement reporting the average occupancy of individual marks in a cell population. Consequently, our understanding of the combinatorial nature of chromatin states relies almost exclusively on correlation between the genomic distributions of individual marks. Here, we report the development of combinatorial-iChIP to determine the genome-wide co-occurrence of histone marks at single-nucleosome resolution. By comparing to a null model, we show that certain combinations of overlapping marks (H3K36me3 and H3K79me3) co-occur more frequently than would be expected by chance, while others (H3K4me3 and H3K36me3) do not, reflecting differences in the underlying chromatin pathways. We further use combinatorial-iChIP to illuminate aspects of the Set2-RPD3S pathway. This approach promises to improve our understanding of the combinatorial complexity of chromatin.
MeSH term(s)	Chromatin Immunoprecipitation/methods ; Chromosome Mapping ; Gene Expression Regulation, Fungal ; Genome, Fungal ; High-Throughput Nucleotide Sequencing ; Histone Deacetylases/genetics ; Histone Deacetylases/metabolism ; Histones/genetics ; Histones/metabolism ; Methylation ; Methyltransferases/genetics ; Methyltransferases/metabolism ; Nucleosomes/chemistry ; Nucleosomes/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Signal Transduction
Chemical Substances	Histones ; Nucleosomes ; Saccharomyces cerevisiae Proteins ; Methyltransferases (EC 2.1.1.-) ; Set2 protein, S cerevisiae (EC 2.1.1.-) ; RPD3 protein, S cerevisiae (EC 3.5.1.-) ; Histone Deacetylases (EC 3.5.1.98)
Language	English
Publishing date	2016-08-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2016.07.023
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Article ; Online: Fine-Resolution Mapping of TF Binding and Chromatin Interactions.

Gutin, Jenia / Sadeh, Ronen / Bodenheimer, Nitzan / Joseph-Strauss, Daphna / Klein-Brill, Avital / Alajem, Adi / Ram, Oren / Friedman, Nir

Cell reports

2018 Volume 22, Issue 10, Page(s) 2797–2807

Abstract: Transcription factor (TF) binding to DNA is crucial for transcriptional regulation. There are multiple methods for mapping such binding. These methods balance between input requirements, spatial resolution, and compatibility with high-throughput ... ...

Abstract	Transcription factor (TF) binding to DNA is crucial for transcriptional regulation. There are multiple methods for mapping such binding. These methods balance between input requirements, spatial resolution, and compatibility with high-throughput automation. Here, we describe SLIM-ChIP (short-fragment-enriched, low-input, indexed MNase ChIP), which combines enzymatic fragmentation of chromatin and on-bead indexing to address these desiderata. SLIM-ChIP reproduces a high-resolution binding map of yeast Reb1 comparable with existing methods, yet with less input material and full compatibility with high-throughput procedures. We demonstrate the robustness and flexibility of SLIM-ChIP by probing additional factors in yeast and mouse. Finally, we show that SLIM-ChIP provides information on the chromatin landscape surrounding the bound transcription factor. We identify a class of Reb1 sites where the proximal -1 nucleosome tightly interacts with Reb1 and maintains unidirectional transcription. SLIM-ChIP is an attractive solution for mapping DNA binding proteins and charting the surrounding chromatin occupancy landscape at a single-cell level.
MeSH term(s)	Animals ; Base Sequence ; Cell Line ; Chromatin/metabolism ; Chromatin Immunoprecipitation ; Genome ; Mice ; Nucleosomes/metabolism ; Promoter Regions, Genetic/genetics ; Protein Binding ; Saccharomyces cerevisiae/metabolism ; Transcription Factors/metabolism ; Transcription Initiation, Genetic
Chemical Substances	Chromatin ; Nucleosomes ; Transcription Factors
Language	English
Publishing date	2018-04-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2018.02.052
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Article ; Online: Early sample tagging and pooling enables simultaneous SARS-CoV-2 detection and variant sequencing.

Chappleboim, Alon / Joseph-Strauss, Daphna / Rahat, Ayelet / Sharkia, Israa / Adam, Miriam / Kitsberg, Daniel / Fialkoff, Gavriel / Lotem, Matan / Gershon, Omer / Schmidtner, Anna-Kristina / Oiknine-Djian, Esther / Klochendler, Agnes / Sadeh, Ronen / Dor, Yuval / Wolf, Dana / Habib, Naomi / Friedman, Nir

Science translational medicine

2021 Volume 13, Issue 618, Page(s) eabj2266

Abstract: Most severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic tests have relied on RNA extraction followed by reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays. Whereas automation improved logistics and ... ...

Abstract	Most severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic tests have relied on RNA extraction followed by reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays. Whereas automation improved logistics and different pooling strategies increased testing capacity, highly multiplexed next-generation sequencing (NGS) diagnostics remain a largely untapped resource. NGS tests have the potential to markedly increase throughput while providing crucial SARS-CoV-2 variant information. Current NGS-based detection and genotyping assays for SARS-CoV-2 are costly, mostly due to parallel sample processing through multiple steps. Here, we have established ApharSeq, in which samples are barcoded in the lysis buffer and pooled before reverse transcription. We validated this assay by applying ApharSeq to more than 500 clinical samples from the Clinical Virology Laboratory at Hadassah hospital in a robotic workflow. The assay was linear across five orders of magnitude, and the limit of detection was Ct 33 (~1000 copies/ml, 95% sensitivity) with >99.5% specificity. ApharSeq provided targeted high-confidence genotype information due to unique molecular identifiers incorporated into this method. Because of early pooling, we were able to estimate a 10- to 100-fold reduction in labor, automated liquid handling, and reagent requirements in high-throughput settings compared to current testing methods. The protocol can be tailored to assay other host or pathogen RNA targets simultaneously. These results suggest that ApharSeq can be a promising tool for current and future mass diagnostic challenges.
MeSH term(s)	COVID-19 ; COVID-19 Nucleic Acid Testing ; COVID-19 Testing ; Humans ; SARS-CoV-2 ; Specimen Handling
Language	English
Publishing date	2021-11-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2518854-9
ISSN	1946-6242 ; 1946-6234
ISSN (online)	1946-6242
ISSN	1946-6234
DOI	10.1126/scitranslmed.abj2266
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Article: PRAJA1 is a ubiquitin ligase for the polycomb repressive complex 2 proteins

Zoabi, Muhammad / Sadeh, Ronen / de Bie, Prim / Ciechanover, Aaron

Biochemical and biophysical research communications. 2011 May 13, v. 408, no. 3

2011

Abstract: Methylation of lysine 27 on histone H3 by the polycomb repressive complex 2 (PRC2) leads to transcriptional repression of genes which are critical to development. PRC2 core complex is composed of the histone methyltransferase EZH2, EED, and SUZ12. ... ...

Abstract	Methylation of lysine 27 on histone H3 by the polycomb repressive complex 2 (PRC2) leads to transcriptional repression of genes which are critical to development. PRC2 core complex is composed of the histone methyltransferase EZH2, EED, and SUZ12. Knockdown of any of the PRC2 core subunits results in a concomitant loss of the other subunits which is mediated by the ubiquitin (Ub)–proteasome system (UPS). Inhibition of cellular methyltransferases by 3-deazaneplanocin A (DZNep) also leads to dissociation of the PRC2 complex and rapid degradation of its subunits. Interestingly, the expression of several Ub ligases was induced following DZNep treatment, suggesting that PRC2 might repress the Ub ligase(s) that target its subunits for degradation. Here we confirm that individual PRC2 subunits are ubiquitinated and rapidly degraded by the proteasome. One of the DZNep-induced Ub ligases, PRAJA1, can target PRC2 subunits for proteasomal degradation. PRAJA1 directly ubiquitinates individual PRC2 subunits in a cell free system, which leads to their proteasomal degradation. Expression of PRAJA1 but not of an inactive RING finger mutant of the protein, enhanced the degradation of individual PRC2 subunits in cells. Taken together, our results suggest a role for PRAJA1 in regulating the level of PRC2 by targeting its free subunits for Ub-mediated proteasomal degradation.
Keywords	cell free system ; dissociation ; genes ; histones ; lysine ; methylation ; methyltransferases ; mutants ; proteasome endopeptidase complex ; transcription (genetics) ; ubiquitin ; ubiquitin-protein ligase
Language	English
Dates of publication	2011-0513
Size	p. 393-398.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	205723-2
ISSN	0006-291X ; 0006-291X
ISSN (online)	0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2011.04.025
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