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Article ; Online: Dose-Dependent Transcriptional Response to Ionizing Radiation Is Orchestrated with DNA Repair within the Nuclear Space.

Chaturvedi, Garima / Sarusi-Portuguez, Avital / Loza, Olga / Shimoni-Sebag, Ariel / Yoron, Orly / Lawrence, Yaacov Richard / Zach, Leor / Hakim, Ofir

International journal of molecular sciences

2024 Volume 25, Issue 2

Abstract: Radiation therapy is commonly used to treat glioblastoma multiforme (GBM) brain tumors. Ionizing radiation (IR) induces dose-specific variations in transcriptional programs, implicating that they are tightly regulated and critical components in the tumor ...

Abstract	Radiation therapy is commonly used to treat glioblastoma multiforme (GBM) brain tumors. Ionizing radiation (IR) induces dose-specific variations in transcriptional programs, implicating that they are tightly regulated and critical components in the tumor response and survival. Yet, our understanding of the downstream molecular events triggered by effective vs. non-effective IR doses is limited. Herein, we report that variations in the genetic programs are positively and functionally correlated with the exposure to effective or non-effective IR doses. Genome architecture analysis revealed that gene regulation is spatially and temporally coordinated with DNA repair kinetics. The radiation-activated genes were pre-positioned in active sub-nuclear compartments and were upregulated following the DNA damage response, while the DNA repair activity shifted to the inactive heterochromatic spatial compartments. The IR dose affected the levels of DNA damage repair and transcription modulation, but not the order of the events, which was linked to their spatial nuclear positioning. Thus, the distinct coordinated temporal dynamics of DNA damage repair and transcription reprogramming in the active and inactive sub-nuclear compartments highlight the importance of high-order genome organization in synchronizing the molecular events following IR.
MeSH term(s)	Humans ; Radiation, Ionizing ; DNA Repair/genetics ; Radiation, Nonionizing ; Biological Transport ; Glioblastoma/genetics ; Glioblastoma/radiotherapy
Language	English
Publishing date	2024-01-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms25020970
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The Position and Complex Genomic Architecture of Plant T-DNA Insertions Revealed by 4SEE.

Krispil, Ronen / Tannenbaum, Miriam / Sarusi-Portuguez, Avital / Loza, Olga / Raskina, Olga / Hakim, Ofir

International journal of molecular sciences

2020 Volume 21, Issue 7

Abstract: The integration of T-DNA in plant genomes is widely used for basic research and agriculture. The high heterogeneity in the number of integration events per genome, their configuration, and their impact on genome integrity highlight the critical need to ... ...

Abstract	The integration of T-DNA in plant genomes is widely used for basic research and agriculture. The high heterogeneity in the number of integration events per genome, their configuration, and their impact on genome integrity highlight the critical need to detect the genomic locations of T-DNA insertions and their associated chromosomal rearrangements, and the great challenge in doing so. Here, we present 4SEE, a circular chromosome conformation capture (4C)-based method for robust, rapid, and cost-efficient detection of the entire scope of T-DNA locations. Moreover, by measuring the chromosomal architecture of the plant genome flanking the T-DNA insertions, 4SEE outlines their associated complex chromosomal aberrations. Applying 4SEE to a collection of confirmed T-DNA lines revealed previously unmapped T-DNA insertions and chromosomal rearrangements such as inversions and translocations. Uncovering such events in a feasible, robust, and cost-effective manner by 4SEE in any plant of interest has implications for accurate annotation and phenotypic characterization of T-DNA insertion mutants and transgene expression in basic science applications as well as for plant biotechnology.
MeSH term(s)	Arabidopsis/genetics ; Chromosome Mapping ; Chromosomes, Plant ; DNA, Bacterial/genetics ; DNA, Plant/genetics ; Genome, Plant ; Genomics ; Mutation ; Plants, Genetically Modified/genetics ; Translocation, Genetic
Chemical Substances	DNA, Bacterial ; DNA, Plant ; T-DNA
Language	English
Publishing date	2020-03-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms21072373
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Article: Mapping genome-wide accessible chromatin in primary human t lymphocytes by atac-seq

Grbesa, Ivana / Tannenbaum, Miriam / Sarusi-Portuguez, Avital / Schwartz, Michal / Hakim, Ofir

Journal of visualized experiments. 2017 Nov. 13, , no. 129

2017

Abstract: Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) is a method used for the identification of open (accessible) regions of chromatin. These regions represent regulatory DNA elements (e.g., promoters, enhancers, locus ... ...

Abstract	Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) is a method used for the identification of open (accessible) regions of chromatin. These regions represent regulatory DNA elements (e.g., promoters, enhancers, locus control regions, insulators) to which transcription factors bind. Mapping the accessible chromatin landscape is a powerful approach for uncovering active regulatory elements across the genome. This information serves as an unbiased approach for discovering the network of relevant transcription factors and mechanisms of chromatin structure that govern gene expression programs. ATAC-seq is a robust and sensitive alternative to DNase I hypersensitivity analysis coupled with next-generation sequencing (DNase-seq) and formaldehyde-assisted isolation of regulatory elements (FAIRE-seq) for genome-wide analysis of chromatin accessibility and to the sequencing of micrococcal nuclease-sensitive sites (MNase-seq) to determine nucleosome positioning. We present a detailed ATAC-seq protocol optimized for human primary immune cells i.e. CD4+ lymphocytes (T helper 1 (Th1) and Th2 cells). This comprehensive protocol begins with cell harvest, then describes the molecular procedure of chromatin tagmentation, sample preparation for next-generation sequencing, and also includes methods and considerations for the computational analyses used to interpret the results. Moreover, to save time and money, we introduced quality control measures to assess the ATAC-seq library prior to sequencing. Importantly, the principles presented in this protocol allow its adaptation to other human immune and non-immune primary cells and cell lines. These guidelines will also be useful for laboratories which are not proficient with next-generation sequencing methods.
Keywords	CD4-positive T-lymphocytes ; DNA ; cell lines ; deoxyribonuclease I ; gene expression ; genome ; genome-wide association study ; guidelines ; high-throughput nucleotide sequencing ; humans ; hypersensitivity ; loci ; nucleosomes ; quality control ; regulatory sequences ; transcription factors
Language	English
Dates of publication	2017-1113
Size	p. e56313.
Publishing place	Journal of Visualized Experiments
Document type	Article
ZDB-ID	2259946-0
ISSN	1940-087X
ISSN	1940-087X
DOI	10.3791/56313
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Article ; Online: TENT4A Non-Canonical Poly(A) Polymerase Regulates DNA-Damage Tolerance via Multiple Pathways That Are Mutated in Endometrial Cancer.

Swain, Umakanta / Friedlander, Gilgi / Sehrawat, Urmila / Sarusi-Portuguez, Avital / Rotkopf, Ron / Ebert, Charlotte / Paz-Elizur, Tamar / Dikstein, Rivka / Carell, Thomas / Geacintov, Nicholas E / Livneh, Zvi

International journal of molecular sciences

2021 Volume 22, Issue 13

Abstract: TENT4A (PAPD7) is a non-canonical poly(A) polymerase, of which little is known. Here, we show that TENT4A regulates multiple biological pathways and focuses on its multilayer regulation of translesion DNA synthesis (TLS), in which error-prone DNA ... ...

Abstract	TENT4A (PAPD7) is a non-canonical poly(A) polymerase, of which little is known. Here, we show that TENT4A regulates multiple biological pathways and focuses on its multilayer regulation of translesion DNA synthesis (TLS), in which error-prone DNA polymerases bypass unrepaired DNA lesions. We show that TENT4A regulates mRNA stability and/or translation of DNA polymerase η and RAD18 E3 ligase, which guides the polymerase to replication stalling sites and monoubiquitinates PCNA, thereby enabling recruitment of error-prone DNA polymerases to damaged DNA sites. Remarkably, in addition to the effect on RAD18 mRNA stability via controlling its poly(A) tail, TENT4A indirectly regulates RAD18 via the tumor suppressor CYLD and via the long non-coding antisense RNA
MeSH term(s)	Blotting, Western ; Cell Line, Tumor ; Chromosomal Proteins, Non-Histone/genetics ; Chromosomal Proteins, Non-Histone/metabolism ; Computational Biology ; DNA Damage/genetics ; DNA Damage/physiology ; DNA Repair/genetics ; DNA Repair/physiology ; DNA Replication/genetics ; DNA Replication/physiology ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed DNA Polymerase/metabolism ; Endometrial Neoplasms/genetics ; Endometrial Neoplasms/metabolism ; Female ; HEK293 Cells ; Humans ; Immunoprecipitation ; MCF-7 Cells ; Mutation/genetics ; Polymerase Chain Reaction ; Polynucleotide Adenylyltransferase/genetics ; Polynucleotide Adenylyltransferase/metabolism ; RNA Stability/genetics ; RNA Stability/physiology ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination/genetics ; Ubiquitination/physiology
Chemical Substances	Chromosomal Proteins, Non-Histone ; DNA-Binding Proteins ; PAXIP1 protein, human ; RAD18 protein, human ; RNA, Messenger ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Polynucleotide Adenylyltransferase (EC 2.7.7.19) ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; TENT4A protein, human (EC 2.7.7.7)
Language	English
Publishing date	2021-06-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22136957
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Article ; Online: Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq.

Grbesa, Ivana / Tannenbaum, Miriam / Sarusi-Portuguez, Avital / Schwartz, Michal / Hakim, Ofir

Journal of visualized experiments : JoVE

2017 , Issue 129

Abstract	Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) is a method used for the identification of open (accessible) regions of chromatin. These regions represent regulatory DNA elements (e.g., promoters, enhancers, locus control regions, insulators) to which transcription factors bind. Mapping the accessible chromatin landscape is a powerful approach for uncovering active regulatory elements across the genome. This information serves as an unbiased approach for discovering the network of relevant transcription factors and mechanisms of chromatin structure that govern gene expression programs. ATAC-seq is a robust and sensitive alternative to DNase I hypersensitivity analysis coupled with next-generation sequencing (DNase-seq) and formaldehyde-assisted isolation of regulatory elements (FAIRE-seq) for genome-wide analysis of chromatin accessibility and to the sequencing of micrococcal nuclease-sensitive sites (MNase-seq) to determine nucleosome positioning. We present a detailed ATAC-seq protocol optimized for human primary immune cells i.e. CD4+ lymphocytes (T helper 1 (Th1) and Th2 cells). This comprehensive protocol begins with cell harvest, then describes the molecular procedure of chromatin tagmentation, sample preparation for next-generation sequencing, and also includes methods and considerations for the computational analyses used to interpret the results. Moreover, to save time and money, we introduced quality control measures to assess the ATAC-seq library prior to sequencing. Importantly, the principles presented in this protocol allow its adaptation to other human immune and non-immune primary cells and cell lines. These guidelines will also be useful for laboratories which are not proficient with next-generation sequencing methods.
MeSH term(s)	Chromatin/metabolism ; Chromosome Mapping/methods ; DNA/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Sequence Analysis, DNA/methods ; T-Lymphocytes/physiology
Chemical Substances	Chromatin ; DNA (9007-49-2)
Language	English
Publishing date	2017-11-13
Publishing country	United States
Document type	Journal Article ; Video-Audio Media
ZDB-ID	2259946-0
ISSN	1940-087X ; 1940-087X
ISSN (online)	1940-087X
ISSN	1940-087X
DOI	10.3791/56313
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: p53 deficient breast cancer cells reprogram preadipocytes toward tumor-protective immunomodulatory cells.

Hassin, Ori / Sernik, Miriam / Seligman, Adi / Vogel, Felix C E / Wellenstein, Max D / Smollich, Joachim / Halperin, Coral / Pirona, Anna Chiara / Toledano, Liron Nomi / Caballero, Carolina Dehesa / Schlicker, Lisa / Salame, Tomer-Meir / Sarusi Portuguez, Avital / Aylon, Yael / Scherz-Shouval, Ruth / Geiger, Tamar / de Visser, Karin E / Schulze, Almut / Oren, Moshe

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 52, Page(s) e2311460120

Abstract: ... ...

Abstract	The
MeSH term(s)	Humans ; Female ; Tumor Suppressor Protein p53/genetics ; Tumor Suppressor Protein p53/metabolism ; Breast Neoplasms/pathology ; Genes, p53 ; Adipose Tissue/metabolism ; Adipocytes/metabolism ; Tumor Microenvironment/genetics
Chemical Substances	Tumor Suppressor Protein p53
Language	English
Publishing date	2023-12-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2311460120
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Article: Regulatory chromatin landscape in

Tannenbaum, Miriam / Sarusi-Portuguez, Avital / Krispil, Ronen / Schwartz, Michal / Loza, Olga / Benichou, Jennifer I C / Mosquna, Assaf / Hakim, Ofir

Plant methods

2018 Volume 14, Page(s) 113

Abstract: Background: There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever-growing availability of genome-wide gene expression data, understanding how transcription programs are established and ... ...

Abstract	Background: There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever-growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is the binding of transcription factors (TFs) to specific DNA sequence motifs across the genome. However, these sequences are hindered by the packaging of DNA to chromatin. Thus, the accessibility of these loci for TF binding is highly regulated and determines where and when TFs bind. We present a workflow for measuring chromatin accessibility in Results: We coupled the recently described isolation of nuclei tagged in specific cell types (INTACT) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) as a genome-wide strategy to uncover accessible regulatory sites in Conclusions: By coupling INTACT with ATAC-seq methods, we present a feasible pipeline to profile accessible chromatin in plants. We also introduce a rapid measure of the experiment quality. We find that chromatin accessibility at promoter regions is strongly associated with transcription and active histone marks. However, root-specific chromatin accessibility is primarily found at intergenic regions, suggesting their predominance in defining organ identity possibly via long-range chromatin interactions. This workflow can be rapidly applied to study the regulatory landscape in other cell types, plant species and conditions.
Language	English
Publishing date	2018-12-20
Publishing country	England
Document type	Journal Article
ZDB-ID	2203723-8
ISSN	1746-4811
ISSN	1746-4811
DOI	10.1186/s13007-018-0381-9
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Article: Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq

Tannenbaum, Miriam / Sarusi-Portuguez, Avital / Krispil, Ronen / Schwartz, Michal / Loza, Olga / Benichou, Jennifer I. C / Mosquna, Assaf / Hakim, Ofir

Plant methods. 2018 Dec., v. 14, no. 1

2018

Abstract: BACKGROUND: There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever-growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated ...

Abstract	BACKGROUND: There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever-growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is the binding of transcription factors (TFs) to specific DNA sequence motifs across the genome. However, these sequences are hindered by the packaging of DNA to chromatin. Thus, the accessibility of these loci for TF binding is highly regulated and determines where and when TFs bind. We present a workflow for measuring chromatin accessibility in Arabidopsis thaliana and define organ-specific regulatory sites and binding motifs of TFs at these sites. RESULTS: We coupled the recently described isolation of nuclei tagged in specific cell types (INTACT) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) as a genome-wide strategy to uncover accessible regulatory sites in Arabidopsis based on their accessibility to nuclease digestion. By applying this pipeline in Arabidopsis roots, we revealed 41,419 accessible sites, of which approximately half are found in gene promoters and contain the H3K4me3 active histone mark. The root-unique accessible sites from this group are enriched for root processes. Interestingly, most of the root-unique accessible sites are found in nongenic regions but are correlated with root-specific expression of distant genes. Importantly, these gene-distant sites are enriched for binding motifs of TFs important for root development as well as motifs for TFs that may play a role as novel transcriptional regulators in roots, suggesting that these accessible loci are functional novel gene-distant regulatory elements. CONCLUSIONS: By coupling INTACT with ATAC-seq methods, we present a feasible pipeline to profile accessible chromatin in plants. We also introduce a rapid measure of the experiment quality. We find that chromatin accessibility at promoter regions is strongly associated with transcription and active histone marks. However, root-specific chromatin accessibility is primarily found at intergenic regions, suggesting their predominance in defining organ identity possibly via long-range chromatin interactions. This workflow can be rapidly applied to study the regulatory landscape in other cell types, plant species and conditions.
Keywords	Arabidopsis thaliana ; chromatin ; gene expression ; genes ; high-throughput nucleotide sequencing ; histones ; intergenic DNA ; loci ; promoter regions ; roots ; transcription (genetics) ; transcription factors
Language	English
Dates of publication	2018-12
Size	p. 113.
Publishing place	BioMed Central
Document type	Article
ISSN	1746-4811
DOI	10.1186/s13007-018-0381-9
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Article ; Online: LY6S,

ImmunoHorizons

2022 Volume 6, Issue 4, Page(s) 253–272

Abstract: Syntenic genomic loci on human chromosome 8 and mouse chromosome 15 (mChr15) code for LY6/Ly6 (lymphocyte Ag 6) family proteins. The 23 ... ...

Abstract	Syntenic genomic loci on human chromosome 8 and mouse chromosome 15 (mChr15) code for LY6/Ly6 (lymphocyte Ag 6) family proteins. The 23 murine
MeSH term(s)	Animals ; Antigens, Ly/genetics ; Humans ; Inflammation/genetics ; Lymphocytes ; Membrane Proteins/genetics ; Mice ; Multigene Family ; Spleen ; Virus Diseases/genetics
Chemical Substances	Antigens, Ly ; Ly6a protein, mouse ; Membrane Proteins
Language	English
Publishing date	2022-04-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2573-7732
ISSN (online)	2573-7732
DOI	10.4049/immunohorizons.2200018
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Article ; Online: Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis.

Sarusi Portuguez, Avital / Schwartz, Michal / Siersbaek, Rasmus / Nielsen, Ronni / Sung, Myong-Hee / Mandrup, Susanne / Kaplan, Tommy / Hakim, Ofir

The FEBS journal

2017 Volume 284, Issue 19, Page(s) 3230–3244

Abstract: The three dimensional folding of mammalian genomes is cell type specific and difficult to alter suggesting that it is an important component of gene regulation. However, given the multitude of chromatin-associating factors, the mechanisms driving the ... ...

Abstract	The three dimensional folding of mammalian genomes is cell type specific and difficult to alter suggesting that it is an important component of gene regulation. However, given the multitude of chromatin-associating factors, the mechanisms driving the colocalization of active chromosomal domains and the role of this organization in regulating the transcription program in adipocytes are not clear. Analysis of genome-wide chromosomal associations revealed cell type-specific spatial clustering of adipogenic genes in 3T3-L1 cells. Time course analysis demonstrated that the adipogenic 'hub', sampled by PPARγ and Lpin1, undergoes orchestrated reorganization during adipogenesis. Coupling the dynamics of genome architecture with multiple chromatin datasets indicated that among all the transcription factors (TFs) tested, RXR is central to genome reorganization at the beginning of adipogenesis. Interestingly, at the end of differentiation, the adipogenic hub was shifted to an H3K27me3-repressive environment in conjunction with attenuation of gene transcription. We propose a stage-specific hierarchy for the activity of TFs contributing to the establishment of an adipogenic genome architecture that brings together the adipogenic genetic program. In addition, the repositioning of this network in a H3K27me3-rich environment at the end of differentiation may contribute to the stabilization of gene transcription levels and reduce the developmental plasticity of these specialized cells. Database: All sequence data reported in this paper have been deposited at GEO (http://www.ncbi.nlm.nih.gov/geo/) (GSE92475).
MeSH term(s)	3T3-L1 Cells ; Adipocytes/cytology ; Adipocytes/metabolism ; Adipogenesis/genetics ; Animals ; B-Lymphocytes/cytology ; B-Lymphocytes/metabolism ; CCAAT-Enhancer-Binding Protein-beta/genetics ; CCAAT-Enhancer-Binding Protein-beta/metabolism ; CCAAT-Enhancer-Binding Proteins/genetics ; CCAAT-Enhancer-Binding Proteins/metabolism ; Cell Differentiation ; Chromatin/chemistry ; Chromatin/metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; Histones/genetics ; Histones/metabolism ; Interferon-gamma/genetics ; Interferon-gamma/metabolism ; Mice ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Organ Specificity ; PPAR gamma/genetics ; PPAR gamma/metabolism ; Phosphatidate Phosphatase/genetics ; Phosphatidate Phosphatase/metabolism ; Primary Cell Culture ; Retinoid X Receptors/genetics ; Retinoid X Receptors/metabolism ; Signal Transduction ; Transcription, Genetic
Chemical Substances	CCAAT-Enhancer-Binding Protein-beta ; CCAAT-Enhancer-Binding Proteins ; CEBPA protein, mouse ; Cebpb protein, mouse ; Chromatin ; Histones ; IFNG protein, mouse ; Nuclear Proteins ; PPAR gamma ; Retinoid X Receptors ; Interferon-gamma (82115-62-6) ; Lpin1 protein, mouse (EC 3.1.3.4) ; Phosphatidate Phosphatase (EC 3.1.3.4)
Language	English
Publishing date	2017-08-16
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.14183
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