Related Experiment Video
Updated: Oct 23, 2025
07:24
Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA
Published on: July 9, 2021
2.5K
Purification and Structural Characterization of the Long Noncoding RNAs.
Allison Yankey1, Sean C Clark1, Michael C Owens1
1Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA.
Methods in Molecular Biology (Clifton, N.J.)
|August 21, 2021
Summary
This study details a protocol for purifying long noncoding RNAs (lncRNAs) and determining their secondary structures. These methods enable a deeper understanding of lncRNA structure-function relationships.
Area of Science:
- Molecular Biology
- Genetics
- Biochemistry
Background:
- Long noncoding RNAs (lncRNAs) play crucial roles in cellular functions.
- Understanding lncRNA structure is essential for elucidating their functions.
- The large size of lncRNAs poses purification challenges for structural studies.
Purpose of the Study:
- To provide a detailed protocol for the homogenous purification of lncRNAs.
- To outline strategies for identifying optimal folding conditions for lncRNAs.
- To describe methods for determining and validating lncRNA secondary structures.
Main Methods:
- Homogenous purification of lncRNAs, addressing challenges of large RNA size.
- Identification of target lncRNA folding conditions.
- Application of SHAPE-MaP and DMS-MaP techniques for RNA structure probing.
- Integration of chemical probing with next-generation sequencing for high-throughput structure determination.
Main Results:
- An adaptable protocol for lncRNA purification is presented.
- SHAPE-MaP and DMS-MaP enable high-throughput RNA structure determination.
- Datasets from orthogonal probing experiments facilitate secondary structure validation.
Conclusions:
- The described protocol facilitates lncRNA purification and structural analysis.
- This work contributes to understanding lncRNA structure-function relationships.
- The methods support the investigation of diverse lncRNA functions.
Related Concept Videos
02:39lncRNA - Long Non-coding RNAs
9.1K
In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...
9.1K
01:20Types of RNA
7.1K
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in regulating gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA Performs Diverse...
RNA Performs Diverse...
7.1K
02:24Ribosome Profiling
3.7K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.7K
03:21RNA-seq
10.6K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.6K
02:53Ribosomal RNA Synthesis
13.8K
Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
13.8K
01:53RNA Stability
34.2K
Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
34.2K