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Article ; Online: Context-Dependent Regulation of Gene Expression by Non-Canonical Small RNAs.

Plawgo, Kinga / Raczynska, Katarzyna Dorota

2022 Volume 8, Issue 3

Abstract: In recent functional genomics studies, a large number of non-coding RNAs have been identified. It has become increasingly apparent that noncoding RNAs are crucial players in a wide range of cellular and physiological functions. They have been shown to ... ...

Abstract	In recent functional genomics studies, a large number of non-coding RNAs have been identified. It has become increasingly apparent that noncoding RNAs are crucial players in a wide range of cellular and physiological functions. They have been shown to modulate gene expression on different levels, including transcription, post-transcriptional processing, and translation. This review aims to highlight the diverse mechanisms of the regulation of gene expression by small noncoding RNAs in different conditions and different types of human cells. For this purpose, various cellular functions of microRNAs (miRNAs), circular RNAs (circRNAs), snoRNA-derived small RNAs (sdRNAs) and tRNA-derived fragments (tRFs) will be exemplified, with particular emphasis on the diversity of their occurrence and on the effects on gene expression in different stress conditions and diseased cell types. The synthesis and effect on gene expression of these noncoding RNAs varies in different cell types and may depend on environmental conditions such as different stresses. Moreover, noncoding RNAs play important roles in many diseases, including cancer, neurodegenerative disorders, and viral infections.
Language	English
Publishing date	2022-04-29
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2813993-8
ISSN	2311-553X ; 2311-553X
ISSN (online)	2311-553X
ISSN	2311-553X
DOI	10.3390/ncrna8030029
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Article ; Online: Long Intergenic Noncoding RNAs Affect Biological Pathways Underlying Autoimmune and Neurodegenerative Disorders.

Plewka, Patrycja / Raczynska, Katarzyna Dorota

Molecular neurobiology

2022 Volume 59, Issue 9, Page(s) 5785–5808

Abstract: Long intergenic noncoding RNAs (lincRNAs) are a class of independently transcribed molecules longer than 200 nucleotides that do not overlap known protein-coding genes. LincRNAs have diverse roles in gene expression and participate in a spectrum of ... ...

Abstract	Long intergenic noncoding RNAs (lincRNAs) are a class of independently transcribed molecules longer than 200 nucleotides that do not overlap known protein-coding genes. LincRNAs have diverse roles in gene expression and participate in a spectrum of biological processes. Dysregulation of lincRNA expression can abrogate cellular homeostasis, cell differentiation, and development and can also deregulate the immune and nervous systems. A growing body of literature indicates their important and multifaceted roles in the pathogenesis of several different diseases. Furthermore, certain lincRNAs can be considered potential therapeutic targets and valuable diagnostic or prognostic biomarkers capable of predicting the onset of a disease, its degree of activity, or the progression phase. In this review, we discuss possible mechanisms and molecular functions of lincRNAs in the pathogenesis of selected autoimmune and neurodegenerative disorders: multiple sclerosis, rheumatoid arthritis, systemic lupus erythematosus, Sjögren's syndrome, Huntington's disease, Parkinson's disease, Alzheimer's disease, and amyotrophic lateral sclerosis. This summary can provide new ideas for future research, diagnosis, and treatment of these highly prevalent and devastating diseases.
MeSH term(s)	Humans ; Neurodegenerative Diseases/genetics ; Neurodegenerative Diseases/pathology ; RNA, Long Noncoding/genetics
Chemical Substances	RNA, Long Noncoding
Language	English
Publishing date	2022-07-07
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	645020-9
ISSN	1559-1182 ; 0893-7648
ISSN (online)	1559-1182
ISSN	0893-7648
DOI	10.1007/s12035-022-02941-0
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Zs.A 2411: Show issues

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Article ; Online: U7 snRNA: A tool for gene therapy.

Gadgil, Ankur / Raczyńska, Katarzyna Dorota

The journal of gene medicine

2021 Volume 23, Issue 4, Page(s) e3321

Abstract: Most U-rich small nuclear ribonucleoproteins (snRNPs) are complexes that mediate the splicing of pre-mRNAs. U7 snRNP is an exception in that it is not involved in splicing but is a key factor in the unique 3' end processing of replication-dependent ... ...

Abstract	Most U-rich small nuclear ribonucleoproteins (snRNPs) are complexes that mediate the splicing of pre-mRNAs. U7 snRNP is an exception in that it is not involved in splicing but is a key factor in the unique 3' end processing of replication-dependent histone mRNAs. However, by introducing controlled changes in the U7 snRNA histone binding sequence and in the Sm motif, it can be used as an effective tool for gene therapy. The modified U7 snRNP (U7 Sm OPT) is thus not involved in the processing of replication-dependent histone pre-mRNA but targets splicing by inducing efficient skipping or inclusion of selected exons. U7 Sm OPT is of therapeutic importance in diseases that are an outcome of splicing defects, such as myotonic dystrophy, Duchenne muscular dystrophy, amyotrophic lateral sclerosis, β-thalassemia, HIV-1 infection and spinal muscular atrophy. The benefits of using U7 Sm OPT for gene therapy are its compact size, ability to accumulate in the nucleus without causing any toxic effects in the cells, and no immunoreactivity. The risk of transgene misregulation by using U7 Sm OPT is also low because it is involved in correcting the expression of an endogenous gene controlled by its own regulatory elements. Altogether, using U7 Sm OPT as a tool in gene therapy can ensure lifelong treatment, whereas an oligonucleotide or other drug/compound would require repeated administration. It would thus be strategic to harness these unique properties of U7 snRNP and deploy it as a tool in gene therapy.
MeSH term(s)	Binding Sites/genetics ; Cell Nucleus/genetics ; Genetic Therapy ; Histones/genetics ; Humans ; Protein Binding/genetics ; RNA, Small Nuclear/genetics ; Ribonucleoproteins, Small Nuclear/genetics ; Ribonucleoproteins, Small Nuclear/therapeutic use
Chemical Substances	Histones ; RNA, Small Nuclear ; Ribonucleoproteins, Small Nuclear ; U7 small nuclear RNA
Language	English
Publishing date	2021-02-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1458024-x
ISSN	1521-2254 ; 1099-498X
ISSN (online)	1521-2254
ISSN	1099-498X
DOI	10.1002/jgm.3321
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Article ; Online: Role of Long Intergenic Noncoding RNAs in Cancers with an Overview of MicroRNA Binding.

Pasieka, Robert / Zasoński, Gilbert / Raczyńska, Katarzyna Dorota

Molecular diagnosis & therapy

2022 Volume 27, Issue 1, Page(s) 29–47

Abstract: Long intergenic noncoding RNAs are transcripts originating from the regions without annotated coding genes. They are located mainly in the nucleus and regulate gene expression. Long intergenic noncoding RNAs can be also found in the cytoplasm acting as ... ...

Abstract	Long intergenic noncoding RNAs are transcripts originating from the regions without annotated coding genes. They are located mainly in the nucleus and regulate gene expression. Long intergenic noncoding RNAs can be also found in the cytoplasm acting as molecular sponges of certain microRNAs. This is crucial in various biological and signaling pathways. Expression levels of many long intergenic noncoding RNAs are disease related. In this article, we focus on the long intergenic noncoding RNAs and their relation to different types of cancer. Studies showed that abnormal expression of long intergenic noncoding RNA deregulates signaling pathways due to the disrupted free microRNA pool. Hampered signaling pathways leads to abnormal cell proliferation and restricts cell death, thus resulting in oncogenesis. This review highlights promising therapeutic targets and enables the identification of potential biomarkers specific for a certain type of cancer. Moreover, we provide an outline of long intergenic noncoding RNAs/microRNA axes, which might be applied in further detailed experiments broadening our knowledge about the cellular role of those RNA species.
MeSH term(s)	Humans ; MicroRNAs/genetics ; MicroRNAs/metabolism ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; Neoplasms/genetics
Chemical Substances	MicroRNAs ; RNA, Long Noncoding
Language	English
Publishing date	2022-10-26
Publishing country	New Zealand
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2232796-4
ISSN	1179-2000 ; 1177-1062
ISSN (online)	1179-2000
ISSN	1177-1062
DOI	10.1007/s40291-022-00619-w
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Article ; Online: The Novel Role of hnRNP UL1 in Human Cell Nucleoli.

Cichocka, Marlena / Karlik, Anna / Plewka, Patrycja / Gawade, Kishor / Stępień, Agata / Świergiel, Patrycja / Gadgil, Ankur / Raczyńska, Katarzyna Dorota

International journal of biological sciences

2022 Volume 18, Issue 13, Page(s) 4809–4823

Abstract: hnRNP UL1 plays an important role in cell nuclei, where it is recruited to DNA damage sites and is involved in the repair of DNA double-strand breaks. Furthermore, this protein is known as a transcriptional repressor of RNA polymerase II genes. In the ... ...

Abstract	hnRNP UL1 plays an important role in cell nuclei, where it is recruited to DNA damage sites and is involved in the repair of DNA double-strand breaks. Furthermore, this protein is known as a transcriptional repressor of RNA polymerase II genes. In the present study, we have shown that hnRNP UL1 is also localized in the nucleoli of human cells. Upon investigating its function, we found that hnRNP UL1 stimulates ribosomal DNA (rDNA) gene transcription. Moreover, we observed that cells with hnRNP UL1 silencing exhibited increased sensitivity to DNA damage. We also showed that hnRNP UL1 interacts with γH2A.X, RPA32, XRCC1, and Chk1 in cell nucleoli, suggesting its involvement in the repair of rDNA damage.
MeSH term(s)	Cell Nucleolus/genetics ; DNA Breaks, Double-Stranded ; DNA Repair ; DNA, Ribosomal/genetics ; Heterogeneous-Nuclear Ribonucleoproteins/genetics ; Humans ; Nuclear Proteins/genetics ; Transcription Factors/genetics ; Transcription, Genetic ; X-ray Repair Cross Complementing Protein 1/genetics
Chemical Substances	DNA, Ribosomal ; HNRNPUL1 protein, human ; Heterogeneous-Nuclear Ribonucleoproteins ; Nuclear Proteins ; Transcription Factors ; X-ray Repair Cross Complementing Protein 1 ; XRCC1 protein, human
Language	English
Publishing date	2022-07-18
Publishing country	Australia
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2179208-2
ISSN	1449-2288 ; 1449-2288
ISSN (online)	1449-2288
ISSN	1449-2288
DOI	10.7150/ijbs.75084
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Article ; Online: ALS-linked FUS mutants affect the localization of U7 snRNP and replication-dependent histone gene expression in human cells.

Gadgil, Ankur / Walczak, Agnieszka / Stępień, Agata / Mechtersheimer, Jonas / Nishimura, Agnes Lumi / Shaw, Christopher E / Ruepp, Marc-David / Raczyńska, Katarzyna Dorota

Scientific reports

2021 Volume 11, Issue 1, Page(s) 11868

Abstract: Genes encoding replication-dependent histones lack introns, and the mRNAs produced are a unique class of RNA polymerase II transcripts in eukaryotic cells that do not end in a polyadenylated tail. Mature mRNAs are thus formed by a single endonucleolytic ... ...

Abstract	Genes encoding replication-dependent histones lack introns, and the mRNAs produced are a unique class of RNA polymerase II transcripts in eukaryotic cells that do not end in a polyadenylated tail. Mature mRNAs are thus formed by a single endonucleolytic cleavage that releases the pre-mRNA from the DNA and is the only processing event necessary. U7 snRNP is one of the key factors that determines the cleavage site within the 3'UTR of replication-dependent histone pre-mRNAs. We have previously showed that the FUS protein interacts with U7 snRNA/snRNP and regulates the expression of histone genes by stimulating transcription and 3' end maturation. Mutations in the FUS gene first identified in patients with amyotrophic lateral sclerosis (ALS) lead to the accumulation of the FUS protein in cytoplasmic inclusions. Here, we report that mutations in FUS lead to disruption of the transcriptional activity of FUS and mislocalization of U7 snRNA/snRNP in cytoplasmic aggregates in cellular models and primary neurons. As a consequence, decreased transcriptional efficiency and aberrant 3' end processing of histone pre-mRNAs were observed. This study highlights for the first time the deregulation of replication-dependent histone gene expression and its involvement in ALS.
MeSH term(s)	3' Untranslated Regions ; Amyotrophic Lateral Sclerosis/genetics ; Cell Line, Tumor ; Cell Nucleus/metabolism ; Cytoplasm/metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; HeLa Cells ; Histones/metabolism ; Humans ; In Situ Hybridization, Fluorescence ; Mutation ; Neurosciences ; Plasmids/metabolism ; RNA, Small Nuclear/genetics ; RNA-Binding Protein FUS/genetics ; Ribonucleoprotein, U7 Small Nuclear/genetics ; Ribonucleoproteins, Small Nuclear/genetics
Chemical Substances	3' Untranslated Regions ; FUS protein, human ; Histones ; RNA, Small Nuclear ; RNA-Binding Protein FUS ; Ribonucleoprotein, U7 Small Nuclear ; Ribonucleoproteins, Small Nuclear
Language	English
Publishing date	2021-06-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-91453-3
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Article ; Online: Positive cofactor 4 (PC4) contributes to the regulation of replication-dependent canonical histone gene expression.

Brzek, Aleksandra / Cichocka, Marlena / Dolata, Jakub / Juzwa, Wojciech / Schümperli, Daniel / Raczynska, Katarzyna Dorota

BMC molecular biology

2018 Volume 19, Issue 1, Page(s) 9

Abstract: Background: Core canonical histones are required in the S phase of the cell cycle to pack newly synthetized DNA, therefore the expression of their genes is highly activated during DNA replication. In mammalian cells, this increment is achieved by both ... ...

Abstract	Background: Core canonical histones are required in the S phase of the cell cycle to pack newly synthetized DNA, therefore the expression of their genes is highly activated during DNA replication. In mammalian cells, this increment is achieved by both enhanced transcription and 3' end processing. In this paper, we described positive cofactor 4 (PC4) as a protein that contributes to the regulation of replication-dependent histone gene expression. Results: We showed that PC4 influences RNA polymerase II recruitment to histone gene loci in a cell cycle-dependent manner. The most important effect was observed in S phase where PC4 knockdown leads to the elevated level of RNA polymerase II on histone genes, which corresponds to the increased total level of those gene transcripts. The opposite effect was caused by PC4 overexpression. Moreover, we found that PC4 has a negative effect on the unique 3' end processing of histone pre-mRNAs that can be based on the interaction of PC4 with U7 snRNP and CstF64. Interestingly, this effect does not depend on the cell cycle. Conclusions: We conclude that PC4 might repress RNA polymerase II recruitment and transcription of replication-dependent histone genes in order to maintain the very delicate balance between histone gene expression and DNA synthesis. It guards the cell from excess of histones in S phase. Moreover, PC4 might promote the interaction of cleavage and polyadenylation complex with histone pre-mRNAs, that might impede with the recruitment of histone cleavage complex. This in turn decreases the 3' end processing efficiency of histone gene transcripts.
MeSH term(s)	Cell Cycle ; Cleavage Stimulation Factor/metabolism ; DNA Replication ; DNA-Binding Proteins/metabolism ; Gene Expression Regulation ; HEK293 Cells ; HeLa Cells ; Histones/genetics ; Humans ; RNA 3' End Processing ; RNA Polymerase II/metabolism ; Ribonucleoprotein, U7 Small Nuclear/metabolism ; Transcription Factors/metabolism
Chemical Substances	Cleavage Stimulation Factor ; DNA-Binding Proteins ; Histones ; Ribonucleoprotein, U7 Small Nuclear ; SUB1 protein, human ; Transcription Factors ; RNA Polymerase II (EC 2.7.7.-)
Language	English
Publishing date	2018-07-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1471-2199
ISSN (online)	1471-2199
DOI	10.1186/s12867-018-0110-y
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Article ; Online: The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana.

Raczynska, Katarzyna Dorota / Stepien, Agata / Kierzkowski, Daniel / Kalak, Malgorzata / Bajczyk, Mateusz / McNicol, Jim / Simpson, Craig G / Szweykowska-Kulinska, Zofia / Brown, John W S / Jarmolowski, Artur

Nucleic acids research

2020 Volume 48, Issue 3, Page(s) 1604–1605

Language	English
Publishing date	2020-01-16
Publishing country	England
Document type	Journal Article ; Published Erratum
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkaa045
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Article: Białka PPR wiazace kwasy nukleinowe.

Raczyńska, Katarzyna Dorota / Augustyniak, Halina

Postepy biochemii

2005 Volume 51, Issue 4, Page(s) 440–446

Abstract: PPR proteins belong to large family of nucleic acid binding proteins, mainly RNA-binding proteins. Their name is defined by the presence of so-called pentatricopeptide repeat (PPR), a degenerate 35-aminoacid repeats containing from 2 up to 26 such motifs ...

Title translation	Family of pentatricopeptide repeat proteins.
Abstract	PPR proteins belong to large family of nucleic acid binding proteins, mainly RNA-binding proteins. Their name is defined by the presence of so-called pentatricopeptide repeat (PPR), a degenerate 35-aminoacid repeats containing from 2 up to 26 such motifs arrayed in tandem of at least in one pair. PPR motif consists of two a helices A and B forming a superhelix enclosing a groove or tunnel which is likely to be the ligand-binding site. PPR proteins are targeted mainly to mitochondria and chloroplasts where they are mainly involved in posttranscriptional processes and translation. Among PPR proteins they were also found restorer gene products which restorer pollen fertility. Some PPR proteins play roles as adaptors and partner in protein-protein interaction. PPR protein genes were discovered in all analyzed eukariotic genomes. They are especially abundant in plants.
MeSH term(s)	Binding Sites ; Chloroplasts/metabolism ; Gene Expression ; Ligands ; Mitochondria/metabolism ; Plant Proteins/metabolism ; Pollen/metabolism ; Protein Biosynthesis ; RNA Processing, Post-Transcriptional ; RNA-Binding Proteins/metabolism ; Repetitive Sequences, Amino Acid
Chemical Substances	Ligands ; Plant Proteins ; RNA-Binding Proteins
Language	Polish
Publishing date	2005
Publishing country	Poland
Document type	English Abstract ; Journal Article ; Review
ZDB-ID	414019-9
ISSN	0032-5422
ISSN	0032-5422
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Article ; Online: FUS/TLS contributes to replication-dependent histone gene expression by interaction with U7 snRNPs and histone-specific transcription factors.

Raczynska, Katarzyna Dorota / Ruepp, Marc-David / Brzek, Aleksandra / Reber, Stefan / Romeo, Valentina / Rindlisbacher, Barbara / Heller, Manfred / Szweykowska-Kulinska, Zofia / Jarmolowski, Artur / Schümperli, Daniel

Nucleic acids research

2015 Volume 43, Issue 20, Page(s) 9711–9728

Abstract: Replication-dependent histone genes are up-regulated during the G1/S phase transition to meet the requirement for histones to package the newly synthesized DNA. In mammalian cells, this increment is achieved by enhanced transcription and 3' end ... ...

Abstract	Replication-dependent histone genes are up-regulated during the G1/S phase transition to meet the requirement for histones to package the newly synthesized DNA. In mammalian cells, this increment is achieved by enhanced transcription and 3' end processing. The non-polyadenylated histone mRNA 3' ends are generated by a unique mechanism involving the U7 small ribonucleoprotein (U7 snRNP). By using affinity purification methods to enrich U7 snRNA, we identified FUS/TLS as a novel U7 snRNP interacting protein. Both U7 snRNA and histone transcripts can be precipitated by FUS antibodies predominantly in the S phase of the cell cycle. Moreover, FUS depletion leads to decreased levels of correctly processed histone mRNAs and increased levels of extended transcripts. Interestingly, FUS antibodies also co-immunoprecipitate histone transcriptional activator NPAT and transcriptional repressor hnRNP UL1 in different phases of the cell cycle. We further show that FUS binds to histone genes in S phase, promotes the recruitment of RNA polymerase II and is important for the activity of histone gene promoters. Thus, FUS may serve as a linking factor that positively regulates histone gene transcription and 3' end processing by interacting with the U7 snRNP and other factors involved in replication-dependent histone gene expression.
MeSH term(s)	Cell Cycle ; Cell Cycle Proteins/metabolism ; DNA Replication ; Gene Expression Regulation ; HEK293 Cells ; HeLa Cells ; Heterogeneous-Nuclear Ribonucleoproteins/metabolism ; Histones/biosynthesis ; Histones/genetics ; Humans ; Nuclear Proteins/metabolism ; Promoter Regions, Genetic ; RNA, Small Nuclear/metabolism ; RNA-Binding Protein FUS/metabolism ; Ribonucleoprotein, U7 Small Nuclear/metabolism ; Transcription Factors/metabolism ; Transcription, Genetic
Chemical Substances	Cell Cycle Proteins ; HNRNPUL1 protein, human ; Heterogeneous-Nuclear Ribonucleoproteins ; Histones ; NPAT protein, human ; Nuclear Proteins ; RNA, Small Nuclear ; RNA-Binding Protein FUS ; Ribonucleoprotein, U7 Small Nuclear ; Transcription Factors ; U7 small nuclear RNA
Language	English
Publishing date	2015-11-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkv794
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