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Literature DB >> 25565030

Technologies to probe functions and mechanisms of long noncoding RNAs.

Ci Chu¹, Robert C Spitale², Howard Y Chang³.

Abstract

Thousands of long noncoding RNAs (lncRNAs) have been discovered, but their functional characterization has been slowed by a limited set of research tools. Here we review emerging RNA-centric methods to interrogate the intrinsic structure of lncRNAs as well as their genomic localization and biochemical partners. Understanding these technologies, including their advantages and caveats, and developing them in the future will be essential to progress from description to comprehension of the myriad roles of lncRNAs.

Mesh：

Substances：
RNA, Long Noncoding

Year: 2015 PMID： 25565030 DOI： 10.1038/nsmb.2921

Source DB: PubMed Journal: Nat Struct Mol Biol ISSN： 1545-9985 Impact factor: 15.369

73 in total

Technologies to probe functions and mechanisms of long noncoding RNAs.

1. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity.

Review 2. Long noncoding RNAs: cellular address codes in development and disease.

3. Promoter-bound trinucleotide repeat mRNA drives epigenetic silencing in fragile X syndrome.

4. Purification of proteins associated with specific genomic Loci.

5. RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins.

6. SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data.

7. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo.

8. RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP).

9. The yeast Rab GTPase Ypt1 modulates unfolded protein response dynamics by regulating the stability of HAC1 RNA.

10. Landscape and variation of RNA secondary structure across the human transcriptome.

Review 1. Long Noncoding RNAs: At the Intersection of Cancer and Chromatin Biology.

2. Systematic discovery of Xist RNA binding proteins.

Review 3. The short and long of noncoding sequences in the control of vascular cell phenotypes.

Review 4. Programmable RNA manipulation in living cells.

Review 5. Modulating the expression of long non-coding RNAs for functional studies.

6. Global and cell-type specific properties of lincRNAs with ribosome occupancy.

Review 7. Long non-coding RNA regulation of reproduction and development.

Review 8. Long non-coding RNA regulation of gene expression during differentiation.

Review 9. Insight into lncRNA biology using hybridization capture analyses.

Review 10. Noncoding RNAs in neurodegeneration.