Abstract
Genome-scale studies have provided strong support to the prevalent transcription of nonprotein-coding RNAs (ncRNAs) in various organisms. The immense functional potential embedded in long intergenic ncRNAs (>200 nucleotides) have especially aroused excitement in the scientific community. ncRNA–protein complexes are now known to participate in an astonishing array of processes in transcriptional and posttranscriptional gene regulations; the mechanisms reviewed here may just be a minor fraction of the vast unknowns. These ncRNA-mediated cellular activities contribute to an expansive spectrum of developmental processes such as embryogenesis and organogenesis, and the misregulation of these leads to tumor growth and diseases. The characterization of ncRNAs is progressing at a very fast pace, so much aided by innovations in genome-wide high-throughput technologies (e.g., mass spectrometry, deep sequencing, large scale RNAi screen), and the development of computational tools for data processing. We here present an up-to-date view of the expanding field of ncRNAs in epigenetic regulation, and the development of genome-wide high-throughput methodologies that facilitates our understanding of ncRNAs in a systematic manner.
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Abbreviations
- CD:
-
Chromodomain
- CHART:
-
Capture hybridization analysis of RNA targets
- ChIP-seq:
-
Chromatin immunoprecipitation followed by sequencing
- ChIRP:
-
Chromatin isolation by RNA Purification
- CLIP:
-
Cross-linking and immunoprecipitation
- CRP:
-
Chromatin-remodeling proteins
- CUTS:
-
Cryptic unstable transcripts
- eRNAs:
-
Enhancer derived RNAs
- ESCs:
-
Embryonic stem cell
- HOTAIR:
-
Hox antisense intergenic RNA
- lncRNAs:
-
Long intergenic noncoding RNAs
- LSD/co-rest:
-
Lysine-specific demethylase corepressor for element1 silencing transcription factor
- mRNA:
-
Messenger RNA
- Nats:
-
Natural antisense transcripts
- ncRNAs:
-
Noncoding RNAs
- NoDS:
-
ncRNA with nuclear detention sequence
- PAR-CLIP:
-
Photo-activable ribonucleoside-enhanced CLIP
- PASRs:
-
Promoter-associated short RNAs
- PRC2:
-
Polycome repressive complex 2
- PROMPTS:
-
Promoter upstream transcripts
- RBP:
-
RNA-binding proteins
- RIP:
-
Ribonucleoprotein immunoprecipitation for RNA
- RIP-seq:
-
RIP sequencing
RNAcompete
- RNAPII:
-
RNA polymerase II
- SELEX:
-
Systematic evolution of ligands by exponential enrichment
- TASRs:
-
Terminator-associated short RNAs
- TF:
-
Transcription factor
- tiRNAs:
-
Transcription initiation-associated RNAs
- TSSa-RNAs:
-
Transcription start site-associated RNAs
- uaRNAs:
-
Upstream antisense RNAs
- UNTS:
-
Upstream noncoding transcripts
- Xuts:
-
Xrn1 sensitive unstable transcripts
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Acknowledgment
This work was supported by Ontario Research Fund—Global Leader (Round 2) to JG and ZZ. YL is co-funded by NSERC Canada Graduate Scholarship and Ontario Graduate Scholarship.
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Zhao, D.Y., Li, Y., Greenblatt, J., Zhang, Z. (2014). ncRNA–Protein Interactions in Development and Disease from the Perspective of High-Throughput Studies. In: Emili, A., Greenblatt, J., Wodak, S. (eds) Systems Analysis of Chromatin-Related Protein Complexes in Cancer. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7931-4_5
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