Function of lncRNAs and approaches to lncRNA-protein interactions

Zhu, Juanjuan; Fu, Hanjiang; Wu, Yongge; Zheng, Xiaofei

doi:10.1007/s11427-013-4553-6

Cited by 302 publications

(194 citation statements)

References 152 publications

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“…Most lncRNAs, unlike protein-coding genes, lack sequence conservation between species in both plants and animals (Dong and Chen, 2013;Necsulea et al, 2014;Zhang et al, 2014). LincRNAs in higher eukaryotes might be transcribed by RNA polymerase II and processed by both 5′-capping and 3′-poly(A) additions (Guttman et al, 2009), and like most of the protein-coding genes, many contain one or more introns (Liu et al, 2012;Ulitsky et al, 2011;Zhu et al, 2013). LncRNAs are usually expressed at low levels and often exhibit tissue-specific patterns (Cabili et al, 2011;Rinn and Chang, 2012;Zhang et al, 2014), raising the possibility that lncRNAs participate in tissue development.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis reveals long noncoding RNAs involved in fiber development in cotton (Gossypium arboreum)

Zou

Wang

et al. 2016

Sci. China Life Sci.

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Long noncoding RNAs (lncRNAs) play important roles in various biological regulatory processes in yeast, mammals, and plants. However, no systematic identification of lncRNAs has been reported in Gossypium arboreum. In this study, the strand-specific RNA sequencing (ssRNA-seq) of samples from cotton fibers and leaves was performed, and lncRNAs involved in fiber initiation and elongation processes were systematically identified and analyzed. We identified 5,996 lncRNAs, of which 3,510 and 2,486 can be classified as long intergenic noncoding RNAs (lincRNAs) and natural antisense transcripts (lncNAT), respectively. LincRNAs and lncNATs are similar in many aspects, but have some differences in exon number, exon length, and transcript length. Expression analysis revealed that 51.9% of lincRNAs and 54.5% of lncNATs transcripts were preferentially expressed at one stage of fiber development, and were significantly highly expressed than protein-coding transcripts (21.7%). During the fiber and rapid elongation stages, rapid and dynamic changes in lncRNAs may contribute to fiber development in cotton. This work describes a set of lncRNAs that are involved in fiber development. The characterization and expression analysis of lncRNAs will facilitate future studies on their roles in fiber development in cotton. long noncoding RNAs, strand specific RNA sequencing, fiber, transcriptome, expression Citation:

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Section: Introductionmentioning

confidence: 99%

Transcriptome analysis reveals long noncoding RNAs involved in fiber development in cotton (Gossypium arboreum)

Zou

Wang

et al. 2016

Sci. China Life Sci.

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“…The present results may provide clues for additional basic studies (Table II). The theory of target gene predictions may reveal that lncRNA functions via lncRNA-mRNA-protein interactions (26). The majority of these proteins code genes that function in the splicing, binding, transport, localization, transcription, translation and processing of RNA, according to GO function prediction.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome analysis reveals dysregulated long non‑coding RNAs and mRNAs associated with extrahepatic cholangiocarcinoma progression

Zhang

et al. 2017

Oncol Lett

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Abstract. The incidence of extrahepatic cholangiocarcinoma (ECC) is the highest of all the cholangiocarcinoma cases. However, the molecular mechanism of ECC genesis and progression remains unclear. Long non-coding RNAs (lncRNAs) have been revealed to perform critical regulatory roles in cancer biology. In order to understand lncRNA expression patterns and their potential function in ECC, a transcriptome analysis of lncRNA and mRNA expression was performed in ECC and paired adjacent non-cancerous tissues using Agilent human lncRNA + mRNA arrayV4.0 (4x180 K format). It was identified that 268 lncRNAs and 459 mRNAs were differentially expressed in ECC. Among these, 78 lncRNAs and 66 mRNAs were upregulated >2-fold compared with adjacent non-cancerous tissues, and 190 lncRNAs and 393 mRNAs were downregulated in the ECC samples. Differences in lncRNA expression between ECC and paired adjacent non-cancerous tissues were confirmed using reverse transcription-quantitative polymerase chain reactionas proof of principle. Functional analysis of co-expressed mRNAs with lncRNAs indicated that these dysregulated lncRNAsmay be involved in known ECC-associated biological processes and pathways. The present findings indicated that mRNAs and lncRNAs perform important roles in the development and progression of ECC.The present findings may lay the foundation for future efforts to understand the role of lncRNAs and develop novel biomarkers in ECC IntroductionExtrahepatic cholangiocarcinoma (ECC) is a highly malignant cancer, representing ~80% of all cholangiocarcinoma clinical cases. In previous years, the incidence and mortality of ECC has continued to increase worldwide (1). Although continued advances in surgical techniques and treatment strategies have been achieved, the 5-year survival rate for patients who undergo surgical resection has been reported to be only 20-40% (2,3). The main reasons for the poor prognosis of ECC are a low rate of early diagnosis, fast progression and a high rate of recurrence. There is currently no effective method to improve the diagnosis and treatment of ECC, and the major cause of the molecular pathogenesis of oncogenesis and the progression of ECC remains largely unclear.Long non-coding RNAs (lncRNAs) are a large class of ncRNAs. It has been revealed that lncRNAs are involved in the development and progression of tumors, and that their abnormal expression is associated with tumor proliferation, apoptosis, the cell cycle, angiogenesis, recurrence and metastasis in numerous different types of cancer (4,5). Previous studies have demonstrated the potential roles of lncRNAs to serve as diagnostic markers and therapeutic targets for cancers (6)(7)(8)(9)(10)(11)(12)(13)(14). However, the role and mechanism of lncRNAs in ECC remains largely unknown. Via transcriptome analysis, the present study aimed to investigate lncRNA and mRNA expression that is up-or downregulated in ECC tissues compared with paired peritumoral tissues. Additional bioinformatics analysis and validation studies were performed to revea...

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“…More reliable and user-friendly techniques need to be developed to detect RNA interactions with DNA/RNA/proteins, the spatial localization of low-abundance RNAs, the structures of lncRNA complexes, etc (Zhang et al, 2015;Zhu et al, 2013). For example, to detect chromatin interactions, conformation capture-based assays (HiC, ChIA-PET, etc.)…”

Section: Discussionmentioning

confidence: 99%

Long noncoding RNAs as Organizers of Nuclear Architecture

Cheng

Ming

Zhu

et al. 2016

Sci. China Life Sci.

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In the eukaryotic cell nucleus, chromatin and its associated macromolecules must be organized into a higher-ordered conformation to function normally. However, mechanisms underlying the organization and dynamics of the nucleus remain unclear. Long noncoding RNAs (lncRNAs), i.e., transcripts longer than 200 nucleotides with little or no protein-coding capacity, are increasingly recognized as important regulators in diverse biological processes. Recent studies have shown that some lncRNAs are involved in various aspects of genome organization, including the facilitation of chromosomal interactions and establishment of nuclear bodies, suggesting that lncRNAs act as general organizers of the nuclear architecture. Here, we discuss recent advances in this emerging and intriguing field. long noncoding RNAs, chromatin, nuclear architecture

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Function of lncRNAs and approaches to lncRNA-protein interactions

Cited by 302 publications

References 152 publications

Transcriptome analysis reveals long noncoding RNAs involved in fiber development in cotton (Gossypium arboreum)

Transcriptome analysis reveals long noncoding RNAs involved in fiber development in cotton (Gossypium arboreum)

Transcriptome analysis reveals dysregulated long non‑coding RNAs and mRNAs associated with extrahepatic cholangiocarcinoma progression

Long noncoding RNAs as Organizers of Nuclear Architecture

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