Uv-RNA immunoprecipitation (Uv-rip) protocol in neurons

Katie Schaukowitch, Jae Yeol Joo, Tae Kyung Kim

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Citations (Scopus)

Abstract

With the many advances in genome-wide sequencing, it has been discovered that much more of the genome is transcribed into RNA than previously appreciated. These nonprotein-coding RNAs (ncRNAs) come in many different forms, and they have been shown to have a variety of functions within the cell, infl uencing processes such as gene expression, mRNA splicing, and transport, just as a few examples. As we delve deeper into studying their mechanisms of action, it becomes important to understand how they play these roles, in particular by understanding what proteins these ncRNAs interact with. This protocol describes one technique that can be used to study this, ultra-violet light cross-linking RNA immunoprecipitation (UV-RIP), which uses an antibody to pull down a specifi c protein of interest and then detects RNA that is bound to it. This technique utilizes UV light to cross-link the cells, which takes advantage of the fact that UV light will only cross-link proteins and nucleic acids that are directly interacting. This approach can provide key mechanistic insight into the function of these newly identifi ed ncRNAs.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages33-38
Number of pages6
Volume1468
DOIs
StatePublished - 2017

Publication series

NameMethods in Molecular Biology
Volume1468
ISSN (Print)10643745

Fingerprint

Immunoprecipitation
RNA
Neurons
Ultraviolet Rays
Genome
Nucleic Acids
Proteins
Gene Expression
Light
Messenger RNA
Antibodies

Keywords

  • LncRNA
  • RNA immunoprecipitation
  • RNA-binding proteins
  • UV cross-linking

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Schaukowitch, K., Joo, J. Y., & Kim, T. K. (2017). Uv-RNA immunoprecipitation (Uv-rip) protocol in neurons. In Methods in Molecular Biology (Vol. 1468, pp. 33-38). (Methods in Molecular Biology; Vol. 1468). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-4035-6_4

Uv-RNA immunoprecipitation (Uv-rip) protocol in neurons. / Schaukowitch, Katie; Joo, Jae Yeol; Kim, Tae Kyung.

Methods in Molecular Biology. Vol. 1468 Humana Press Inc., 2017. p. 33-38 (Methods in Molecular Biology; Vol. 1468).

Research output: Chapter in Book/Report/Conference proceedingChapter

Schaukowitch, K, Joo, JY & Kim, TK 2017, Uv-RNA immunoprecipitation (Uv-rip) protocol in neurons. in Methods in Molecular Biology. vol. 1468, Methods in Molecular Biology, vol. 1468, Humana Press Inc., pp. 33-38. https://doi.org/10.1007/978-1-4939-4035-6_4
Schaukowitch K, Joo JY, Kim TK. Uv-RNA immunoprecipitation (Uv-rip) protocol in neurons. In Methods in Molecular Biology. Vol. 1468. Humana Press Inc. 2017. p. 33-38. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-4035-6_4
Schaukowitch, Katie ; Joo, Jae Yeol ; Kim, Tae Kyung. / Uv-RNA immunoprecipitation (Uv-rip) protocol in neurons. Methods in Molecular Biology. Vol. 1468 Humana Press Inc., 2017. pp. 33-38 (Methods in Molecular Biology).
@inbook{6095e21b958440f6819529e7d38c152c,
title = "Uv-RNA immunoprecipitation (Uv-rip) protocol in neurons",
abstract = "With the many advances in genome-wide sequencing, it has been discovered that much more of the genome is transcribed into RNA than previously appreciated. These nonprotein-coding RNAs (ncRNAs) come in many different forms, and they have been shown to have a variety of functions within the cell, infl uencing processes such as gene expression, mRNA splicing, and transport, just as a few examples. As we delve deeper into studying their mechanisms of action, it becomes important to understand how they play these roles, in particular by understanding what proteins these ncRNAs interact with. This protocol describes one technique that can be used to study this, ultra-violet light cross-linking RNA immunoprecipitation (UV-RIP), which uses an antibody to pull down a specifi c protein of interest and then detects RNA that is bound to it. This technique utilizes UV light to cross-link the cells, which takes advantage of the fact that UV light will only cross-link proteins and nucleic acids that are directly interacting. This approach can provide key mechanistic insight into the function of these newly identifi ed ncRNAs.",
keywords = "LncRNA, RNA immunoprecipitation, RNA-binding proteins, UV cross-linking",
author = "Katie Schaukowitch and Joo, {Jae Yeol} and Kim, {Tae Kyung}",
year = "2017",
doi = "10.1007/978-1-4939-4035-6_4",
language = "English (US)",
volume = "1468",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "33--38",
booktitle = "Methods in Molecular Biology",

}

TY - CHAP

T1 - Uv-RNA immunoprecipitation (Uv-rip) protocol in neurons

AU - Schaukowitch, Katie

AU - Joo, Jae Yeol

AU - Kim, Tae Kyung

PY - 2017

Y1 - 2017

N2 - With the many advances in genome-wide sequencing, it has been discovered that much more of the genome is transcribed into RNA than previously appreciated. These nonprotein-coding RNAs (ncRNAs) come in many different forms, and they have been shown to have a variety of functions within the cell, infl uencing processes such as gene expression, mRNA splicing, and transport, just as a few examples. As we delve deeper into studying their mechanisms of action, it becomes important to understand how they play these roles, in particular by understanding what proteins these ncRNAs interact with. This protocol describes one technique that can be used to study this, ultra-violet light cross-linking RNA immunoprecipitation (UV-RIP), which uses an antibody to pull down a specifi c protein of interest and then detects RNA that is bound to it. This technique utilizes UV light to cross-link the cells, which takes advantage of the fact that UV light will only cross-link proteins and nucleic acids that are directly interacting. This approach can provide key mechanistic insight into the function of these newly identifi ed ncRNAs.

AB - With the many advances in genome-wide sequencing, it has been discovered that much more of the genome is transcribed into RNA than previously appreciated. These nonprotein-coding RNAs (ncRNAs) come in many different forms, and they have been shown to have a variety of functions within the cell, infl uencing processes such as gene expression, mRNA splicing, and transport, just as a few examples. As we delve deeper into studying their mechanisms of action, it becomes important to understand how they play these roles, in particular by understanding what proteins these ncRNAs interact with. This protocol describes one technique that can be used to study this, ultra-violet light cross-linking RNA immunoprecipitation (UV-RIP), which uses an antibody to pull down a specifi c protein of interest and then detects RNA that is bound to it. This technique utilizes UV light to cross-link the cells, which takes advantage of the fact that UV light will only cross-link proteins and nucleic acids that are directly interacting. This approach can provide key mechanistic insight into the function of these newly identifi ed ncRNAs.

KW - LncRNA

KW - RNA immunoprecipitation

KW - RNA-binding proteins

KW - UV cross-linking

UR - http://www.scopus.com/inward/record.url?scp=84988892040&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84988892040&partnerID=8YFLogxK

U2 - 10.1007/978-1-4939-4035-6_4

DO - 10.1007/978-1-4939-4035-6_4

M3 - Chapter

C2 - 27662868

AN - SCOPUS:84988892040

VL - 1468

T3 - Methods in Molecular Biology

SP - 33

EP - 38

BT - Methods in Molecular Biology

PB - Humana Press Inc.

ER -