LIVIVO - Search results -

Search results

Result 1 - 10 of total 23

Search options

Article ; Online: TRIBE-STAMP reveals new insights into the functions of RNA binding proteins.

Owens, Michael C / Liu, Kathy Fange

2022 Volume 36, Issue 17-18, Page(s) 954–955

Abstract: RNA binding proteins (RBPs) are important players in RNA metabolism and gene regulation. In this issue ... ...

Abstract	RNA binding proteins (RBPs) are important players in RNA metabolism and gene regulation. In this issue of
MeSH term(s)	RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; RNA, Messenger/metabolism ; Gene Expression Regulation ; RNA
Chemical Substances	RNA-Binding Proteins ; RNA, Messenger ; RNA (63231-63-0)
Language	English
Publishing date	2022-11-15
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	806684-x
ISSN	1549-5477 ; 0890-9369
ISSN (online)	1549-5477
ISSN	0890-9369
DOI	10.1101/gad.350207.122
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2292: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 54: Show issues

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Coordination of RNA modifications in the brain and beyond.

Chen, Anthony Yulin / Owens, Michael C / Liu, Kathy Fange

Molecular psychiatry

2023 Volume 28, Issue 7, Page(s) 2737–2749

Abstract: Gene expression regulation is a critical process throughout the body, especially in the nervous system. One mechanism by which biological systems regulate gene expression is via enzyme-mediated RNA modifications, also known as epitranscriptomic ... ...

Abstract	Gene expression regulation is a critical process throughout the body, especially in the nervous system. One mechanism by which biological systems regulate gene expression is via enzyme-mediated RNA modifications, also known as epitranscriptomic regulation. RNA modifications, which have been found on nearly all RNA species across all domains of life, are chemically diverse covalent modifications of RNA nucleotides and represent a robust and rapid mechanism for the regulation of gene expression. Although numerous studies have been conducted regarding the impact that single modifications in single RNA molecules have on gene expression, emerging evidence highlights potential crosstalk between and coordination of modifications across RNA species. These potential coordination axes of RNA modifications have emerged as a new direction in the field of epitranscriptomic research. In this review, we will highlight several examples of gene regulation via RNA modification in the nervous system, followed by a summary of the current state of the field of RNA modification coordination axes. In doing so, we aim to inspire the field to gain a deeper understanding of the roles of RNA modifications and coordination of these modifications in the nervous system.
MeSH term(s)	RNA/genetics ; Gene Expression Regulation ; Brain/metabolism ; Epigenesis, Genetic
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2023-05-03
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1330655-8
ISSN	1476-5578 ; 1359-4184
ISSN (online)	1476-5578
ISSN	1359-4184
DOI	10.1038/s41380-023-02083-2
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 4812: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: CLIP-Seq to identify targets and interactions of RNA binding proteins and RNA modifying enzymes.

Stoute, Julian / Liu, Kathy Fange

Methods in enzymology

2021 Volume 658, Page(s) 419–434

Abstract: The study of RNA chemical modifications is currently one of the most rapid-growing fields. Many types of RNA modifications in diverse RNA species have been shown to play versatile roles in a wide array of cellular processes. These modifications are ... ...

Abstract	The study of RNA chemical modifications is currently one of the most rapid-growing fields. Many types of RNA modifications in diverse RNA species have been shown to play versatile roles in a wide array of cellular processes. These modifications are installed and erased by writer and eraser enzymes, respectively. Additionally, RNA chemical modifications have downstream biological effects through either influencing changes in the chemistry or structure of RNA molecules or through recognition of the modification; these functions are primarily executed by the modification reader proteins. Reader proteins may bind to the modification site and cause a downstream signal cascade. One of the essential tools for studying erasers, writers, and readers is cross-linking immunoprecipitation followed by high-throughput sequencing (CLIP-seq). This method can detect the sites on endogenous RNAs bound by RNA-binding proteins or RNA modifying enzymes. Essentially, this strategy allows for snapshots of the epitranscriptome and molecular events occurring within the cell. In this article, we go through in detail the various steps involved in CLIP-seq.
MeSH term(s)	Chromatin Immunoprecipitation Sequencing ; Immunoprecipitation ; RNA/genetics ; RNA-Binding Proteins/genetics ; Sequence Analysis, RNA
Chemical Substances	RNA-Binding Proteins ; RNA (63231-63-0)
Language	English
Publishing date	2021-08-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1557-7988
ISSN (online)	1557-7988
DOI	10.1016/bs.mie.2021.08.001
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Recent technical advances in the study of nucleic acid modifications

Owens, Michael C. / Zhang, Celia / Liu, Kathy Fange

Molecular cell. 2021 Oct. 21, v. 81, no. 20

2021

Abstract: Enzyme-mediated chemical modifications of nucleic acids are indispensable regulators of gene expression. Our understanding of the biochemistry and biological significance of these modifications has largely been driven by an ever-evolving landscape of ... ...

Abstract	Enzyme-mediated chemical modifications of nucleic acids are indispensable regulators of gene expression. Our understanding of the biochemistry and biological significance of these modifications has largely been driven by an ever-evolving landscape of technologies that enable accurate detection, mapping, and manipulation of these marks. Here we provide a summary of recent technical advances in the study of nucleic acid modifications with a focus on techniques that allow accurate detection and mapping of these modifications. For each modification discussed (N⁶-methyladenosine, 5-methylcytidine, inosine, pseudouridine, and N⁴-acetylcytidine), we begin by introducing the “gold standard” technique for its mapping and detection, followed by a discussion of techniques developed to address any shortcomings of the gold standard. By highlighting the commonalities and differences of these techniques, we hope to provide a perspective on the current state of the field and to lay out a guideline for development of future technologies.
Keywords	gene expression ; guidelines ; inosine ; landscapes ; nucleic acids
Language	English
Dates of publication	2021-1021
Size	p. 4116-4136.
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.2021.07.036
Database	NAL-Catalogue (AGRICOLA)

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Bonn / Germany

Z 2005/501: Show issues

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article ; Online: RNA modifications and the link to human disease.

Yanas, Amber / Liu, Kathy Fange

Methods in enzymology

2019 Volume 626, Page(s) 133–146

Abstract: Ribonucleic acid (RNA) is involved in translation and transcription, which are the mechanisms in which cells express genes (Alberts et al., 2002). The three classes of RNA discussed are transfer RNA (tRNA), messenger RNA (mRNA), and ribosomal RNA (rRNA). ...

Abstract	Ribonucleic acid (RNA) is involved in translation and transcription, which are the mechanisms in which cells express genes (Alberts et al., 2002). The three classes of RNA discussed are transfer RNA (tRNA), messenger RNA (mRNA), and ribosomal RNA (rRNA). mRNA is the transcript encoded from DNA, rRNA is associated with ribosomes, and tRNA is associated with amino acids and is used to read mRNA transcripts to make proteins (Lodish, Berk, Zipursky, et al., 2000). Interestingly, the function of tRNA, rRNA, and mRNA can be significantly altered by chemical modifications at the co-transcriptional and post-transcriptional levels, and there are over 171 of these modifications identified thus far (Boccaletto et al., 2018; Modomics-Modified bases, 2017). Several of these modifications are linked to diseases such as cancer, diabetes, and neurological disorders. In this review, we will introduce a few RNA modifications with biological functions and how dysregulation of these RNA modifications is linked to human disease.
MeSH term(s)	5-Methylcytosine/analysis ; 5-Methylcytosine/metabolism ; Adenosine/analogs & derivatives ; Adenosine/analysis ; Adenosine/metabolism ; Animals ; Guanosine/analogs & derivatives ; Guanosine/analysis ; Guanosine/metabolism ; Humans ; Methylation ; Nucleic Acid Conformation ; Pseudouridine/analysis ; Pseudouridine/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Messenger/chemistry ; RNA, Messenger/metabolism ; RNA, Ribosomal/chemistry ; RNA, Ribosomal/metabolism ; RNA, Transfer/chemistry ; RNA, Transfer/metabolism ; Uridine/analogs & derivatives ; Uridine/analysis ; Uridine/metabolism
Chemical Substances	8-methylguanosine ; RNA, Messenger ; RNA, Ribosomal ; Guanosine (12133JR80S) ; Pseudouridine (1445-07-4) ; 1-methyladenosine (15763-06-1) ; 5,6-dihydrouridine (5627-05-4) ; 5-Methylcytosine (6R795CQT4H) ; RNA, Transfer (9014-25-9) ; Adenosine (K72T3FS567) ; Uridine (WHI7HQ7H85)
Language	English
Publishing date	2019-09-03
Publishing country	United States
Document type	Journal Article ; Review
ISSN	1557-7988
ISSN (online)	1557-7988
DOI	10.1016/bs.mie.2019.08.003
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: DDX3X and DDX3Y constitutively form nano-sized RNA-protein clusters that foster enzymatic activity.

Yanas, Amber / Shweta, Him / Owens, Michael C / Liu, Kathy Fange / Goldman, Yale E

bioRxiv : the preprint server for biology

2023

Abstract: DEAD-box helicases, which are crucial for many aspects of RNA metabolism, often contain intrinsically disordered regions (IDRs), whose functions remain unclear. Using multiparameter confocal microscopy, we reveal that sex chromosome-encoded homologous ... ...

Abstract	DEAD-box helicases, which are crucial for many aspects of RNA metabolism, often contain intrinsically disordered regions (IDRs), whose functions remain unclear. Using multiparameter confocal microscopy, we reveal that sex chromosome-encoded homologous RNA helicases, DDX3X and DDX3Y, form nano-sized RNA-protein clusters (RPCs) that foster their catalytic activities
Language	English
Publishing date	2023-11-29
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.11.29.569239
Database	MEDical Literature Analysis and Retrieval System OnLINE

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article ; Online: Recent technical advances in the study of nucleic acid modifications.

Owens, Michael C / Zhang, Celia / Liu, Kathy Fange

Molecular cell

2021 Volume 81, Issue 20, Page(s) 4116–4136

Abstract	Enzyme-mediated chemical modifications of nucleic acids are indispensable regulators of gene expression. Our understanding of the biochemistry and biological significance of these modifications has largely been driven by an ever-evolving landscape of technologies that enable accurate detection, mapping, and manipulation of these marks. Here we provide a summary of recent technical advances in the study of nucleic acid modifications with a focus on techniques that allow accurate detection and mapping of these modifications. For each modification discussed (N
MeSH term(s)	Adenosine/analogs & derivatives ; Adenosine/metabolism ; Animals ; Cytidine/analogs & derivatives ; Cytidine/metabolism ; DNA/genetics ; DNA/metabolism ; DNA Methylation ; Epigenesis, Genetic ; Genetic Techniques ; Humans ; Inosine/metabolism ; Pseudouridine/metabolism ; RNA/genetics ; RNA/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Messenger/genetics ; RNA, Messenger/metabolism
Chemical Substances	RNA, Messenger ; Pseudouridine (1445-07-4) ; N-acetylcytidine (3768-18-1) ; Inosine (5A614L51CT) ; Cytidine (5CSZ8459RP) ; RNA (63231-63-0) ; DNA (9007-49-2) ; N-methyladenosine (CLE6G00625) ; Adenosine (K72T3FS567) ; 5-methylcytidine (TL9PB228DC)
Language	English
Publishing date	2021-09-03
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2021.07.036
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 5055: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: Transitions in the framework of condensate biology

Seydoux, Geraldine / Zhang, Mingjie / Forman-Kay, Julie D. / McStay, Brian / Liu, Kathy Fange / Li, Pilong

Molecular Cell. 2023 Apr., v. 83, no. 7 p.1016-1021

2023

Abstract: As phase separation is found in an increasing variety of biological contexts, additional challenges have arisen in understanding the underlying principles of condensate formation and function. We spoke with researchers across disciplines about their ... ...

Abstract	As phase separation is found in an increasing variety of biological contexts, additional challenges have arisen in understanding the underlying principles of condensate formation and function. We spoke with researchers across disciplines about their views on the ever-changing landscape of biomolecular condensates.
Keywords	condensates ; landscapes ; separation
Language	English
Dates of publication	2023-04
Size	p. 1016-1021.
Publishing place	Elsevier Inc.
Document type	Article ; Online
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2023.03.014
Database	NAL-Catalogue (AGRICOLA)

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Bonn / Germany

Z 2005/501: Show issues

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article ; Online: Structural and catalytic roles of the human 18

Shen, Hui / Stoute, Julian / Liu, Kathy Fange

The Journal of biological chemistry

2020 Volume 295, Issue 34, Page(s) 12058–12070

Abstract: rRNA-modifying enzymes participate in ribosome assembly. However, whether the catalytic activities of these enzymes are important for the ribosome assembly and other cellular processes is not fully understood. Here, we report the crystal structure of WT ... ...

Abstract	rRNA-modifying enzymes participate in ribosome assembly. However, whether the catalytic activities of these enzymes are important for the ribosome assembly and other cellular processes is not fully understood. Here, we report the crystal structure of WT human dimethyladenosine transferase 1 (DIMT1), an 18
MeSH term(s)	Amino Acid Substitution ; Catalysis ; Crystallography, X-Ray ; HEK293 Cells ; Humans ; Methyltransferases/chemistry ; Methyltransferases/genetics ; Methyltransferases/metabolism ; Mutation, Missense ; Protein Biosynthesis ; RNA, Ribosomal, 18S/chemistry ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 18S/metabolism ; Ribosome Subunits, Small, Eukaryotic/chemistry ; Ribosome Subunits, Small, Eukaryotic/genetics ; Ribosome Subunits, Small, Eukaryotic/metabolism
Chemical Substances	RNA, Ribosomal, 18S ; DIMT1 protein, human (EC 2.1.1.-) ; Methyltransferases (EC 2.1.1.-)
Language	English
Publishing date	2020-07-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.RA120.014236
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Uc I Zs.108: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Human DIMT1 generates N

Shen, Hui / Gonskikh, Yulia / Stoute, Julian / Liu, Kathy Fange

The Journal of biological chemistry

2021 Volume 297, Issue 4, Page(s) 101146

Abstract: Dimethyladenosine transferase 1 (DIMT1) is an evolutionarily conserved RNA ... ...

Abstract	Dimethyladenosine transferase 1 (DIMT1) is an evolutionarily conserved RNA N
MeSH term(s)	Amino Acid Substitution ; HEK293 Cells ; Humans ; Leukemia, Myeloid, Acute/enzymology ; Leukemia, Myeloid, Acute/genetics ; Methylation ; Methyltransferases/genetics ; Methyltransferases/metabolism ; Mutation, Missense ; Neoplasm Proteins/genetics ; Neoplasm Proteins/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Neoplasm/genetics ; RNA, Neoplasm/metabolism
Chemical Substances	Neoplasm Proteins ; RNA, Neoplasm ; DIMT1 protein, human (EC 2.1.1.-) ; Methyltransferases (EC 2.1.1.-)
Language	English
Publishing date	2021-08-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2021.101146
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Uc I Zs.108: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

To top

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito