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Three-dimensional regulation of transcription.

Cao J, Luo Z, Cheng Q, Xu Q, Zhang Y, Wang F, Wu Y, Song X - Protein Cell (2015)

Bottom Line: Cells can adapt to environment and development by reconstructing their transcriptional networks to regulate diverse cellular processes without altering the underlying DNA sequences.Numerous evidences demonstrate that epigenetic changes are governed by various types of determinants, including DNA methylation patterns, histone posttranslational modification signatures, histone variants, chromatin remodeling, and recently discovered chromosome conformation characteristics and non-coding RNAs (ncRNAs).Here, we highlight recent efforts on how the two latter epigenetic factors participate in the sophisticated transcriptional process and describe emerging techniques which permit us to uncover and gain insights into the fascinating genomic regulation.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Brain Function and Disease and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.

ABSTRACT
Cells can adapt to environment and development by reconstructing their transcriptional networks to regulate diverse cellular processes without altering the underlying DNA sequences. These alterations, namely epigenetic changes, occur during cell division, differentiation and cell death. Numerous evidences demonstrate that epigenetic changes are governed by various types of determinants, including DNA methylation patterns, histone posttranslational modification signatures, histone variants, chromatin remodeling, and recently discovered chromosome conformation characteristics and non-coding RNAs (ncRNAs). Here, we highlight recent efforts on how the two latter epigenetic factors participate in the sophisticated transcriptional process and describe emerging techniques which permit us to uncover and gain insights into the fascinating genomic regulation.

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The classification of lncRNAs. Based on the genomic localization and context, lncRNAs can be classified as eRNAs, pRNAs, NATs, lincRNAs and intronic lncRNAs. eRNAs broadly defined as bidirectional and nonpolyadenylated transcripts which are transcribed from enhancers. pRNAs originate from intragenic promoters. NATs are transcribed from the opposite strand of either protein or non-protein coding genes. LincRNAs are transcriptional units,which are transcribed from regions intervening protein-coding loci. Intronic lncRNAs derived from specific introns of protein-coding genes
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Fig3: The classification of lncRNAs. Based on the genomic localization and context, lncRNAs can be classified as eRNAs, pRNAs, NATs, lincRNAs and intronic lncRNAs. eRNAs broadly defined as bidirectional and nonpolyadenylated transcripts which are transcribed from enhancers. pRNAs originate from intragenic promoters. NATs are transcribed from the opposite strand of either protein or non-protein coding genes. LincRNAs are transcriptional units,which are transcribed from regions intervening protein-coding loci. Intronic lncRNAs derived from specific introns of protein-coding genes

Mentions: As early as 1990, Brannan and colleagues found a regulatory ncRNA when they aimed to find the mouse H19 gene which was involved in a particular biological function by screening the cDNA library of a fetal liver. This ncRNA is different from classic structural ncRNAs such as rRNAs and tRNAs (Brannan et al., 1990). With the innovations in next-generation sequencing technologies and computational biology, a seemingly endless stream of ncRNAs are being identified and characterized at a rapid pace. Researches on ncRNAs have now gained the No.1 ranking in the top ten scientific breakthroughs in the early decades of the twenty-first century (News, 2010; Pennisi, 2010). Over the past fifteen years, small regulatory ncRNA (<200 nucleotides in length), such as small interfering RNA (siRNAs) and microRNAs (miRNAs), have been extensively investigated and the underlying molecular mechanisms have been well documented, suggesting that these ncRNAs play major roles in many cellular processes (Chitwood and Timmermans, 2010; Stuwe et al., 2014; Toscano-Garibay and Aquino-Jarquin, 2014). The surprises didn’t stop at small ncRNAs, and an expanding body of evidence reveals that long non-coding RNAs (lncRNAs, >200 nucleotides in length), once were described as ‘dark matter’, act as essential regulators in diverse cellular progresses. These include regulation of gene transcription (Orom et al., 2010; Sun et al., 2013), dosage compensation (Ilik et al., 2013; Maenner et al., 2013), genomic imprinting (Lee and Bartolomei, 2013; Simon et al., 2013), DNA damage and nuclear organization (Wang et al., 2011b; Wang et al., 2011c; Wan et al., 2013), via a number of complex yet not fully understood mechanisms. Along with the dramatic development in deep sequencing, major hurdles rise to the surface. For example, how these transcripts execute the specific function in different conditions and how to classify them (Derrien et al., 2012; Guttman and Rinn, 2012; Schonrock et al., 2012). Considering only limited information about lncRNAs’ functions and structures are known, the loci in genome where lncRNAs were transcribed become the top choice to define these transcripts. Based on the genomic localization and context, lncRNAs can be classified as enhancer RNAs (eRNAs) (Lam et al., 2014), promoter-associtated RNAs (pRNAs or PROMPTs) (Marques et al., 2013), natural antisense transcripts (NATs) (Katayama et al., 2005; Magistri et al., 2012), intergenic lncRNAs (lincRNAs) (Guttman et al., 2009; Cabili et al., 2011; Ulitsky and Bartel, 2013) and intronic lncRNAs (Guil et al., 2012). The detail classification and definition are described in Fig. 3.Figure 3


Three-dimensional regulation of transcription.

Cao J, Luo Z, Cheng Q, Xu Q, Zhang Y, Wang F, Wu Y, Song X - Protein Cell (2015)

The classification of lncRNAs. Based on the genomic localization and context, lncRNAs can be classified as eRNAs, pRNAs, NATs, lincRNAs and intronic lncRNAs. eRNAs broadly defined as bidirectional and nonpolyadenylated transcripts which are transcribed from enhancers. pRNAs originate from intragenic promoters. NATs are transcribed from the opposite strand of either protein or non-protein coding genes. LincRNAs are transcriptional units,which are transcribed from regions intervening protein-coding loci. Intronic lncRNAs derived from specific introns of protein-coding genes
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4383755&req=5

Fig3: The classification of lncRNAs. Based on the genomic localization and context, lncRNAs can be classified as eRNAs, pRNAs, NATs, lincRNAs and intronic lncRNAs. eRNAs broadly defined as bidirectional and nonpolyadenylated transcripts which are transcribed from enhancers. pRNAs originate from intragenic promoters. NATs are transcribed from the opposite strand of either protein or non-protein coding genes. LincRNAs are transcriptional units,which are transcribed from regions intervening protein-coding loci. Intronic lncRNAs derived from specific introns of protein-coding genes
Mentions: As early as 1990, Brannan and colleagues found a regulatory ncRNA when they aimed to find the mouse H19 gene which was involved in a particular biological function by screening the cDNA library of a fetal liver. This ncRNA is different from classic structural ncRNAs such as rRNAs and tRNAs (Brannan et al., 1990). With the innovations in next-generation sequencing technologies and computational biology, a seemingly endless stream of ncRNAs are being identified and characterized at a rapid pace. Researches on ncRNAs have now gained the No.1 ranking in the top ten scientific breakthroughs in the early decades of the twenty-first century (News, 2010; Pennisi, 2010). Over the past fifteen years, small regulatory ncRNA (<200 nucleotides in length), such as small interfering RNA (siRNAs) and microRNAs (miRNAs), have been extensively investigated and the underlying molecular mechanisms have been well documented, suggesting that these ncRNAs play major roles in many cellular processes (Chitwood and Timmermans, 2010; Stuwe et al., 2014; Toscano-Garibay and Aquino-Jarquin, 2014). The surprises didn’t stop at small ncRNAs, and an expanding body of evidence reveals that long non-coding RNAs (lncRNAs, >200 nucleotides in length), once were described as ‘dark matter’, act as essential regulators in diverse cellular progresses. These include regulation of gene transcription (Orom et al., 2010; Sun et al., 2013), dosage compensation (Ilik et al., 2013; Maenner et al., 2013), genomic imprinting (Lee and Bartolomei, 2013; Simon et al., 2013), DNA damage and nuclear organization (Wang et al., 2011b; Wang et al., 2011c; Wan et al., 2013), via a number of complex yet not fully understood mechanisms. Along with the dramatic development in deep sequencing, major hurdles rise to the surface. For example, how these transcripts execute the specific function in different conditions and how to classify them (Derrien et al., 2012; Guttman and Rinn, 2012; Schonrock et al., 2012). Considering only limited information about lncRNAs’ functions and structures are known, the loci in genome where lncRNAs were transcribed become the top choice to define these transcripts. Based on the genomic localization and context, lncRNAs can be classified as enhancer RNAs (eRNAs) (Lam et al., 2014), promoter-associtated RNAs (pRNAs or PROMPTs) (Marques et al., 2013), natural antisense transcripts (NATs) (Katayama et al., 2005; Magistri et al., 2012), intergenic lncRNAs (lincRNAs) (Guttman et al., 2009; Cabili et al., 2011; Ulitsky and Bartel, 2013) and intronic lncRNAs (Guil et al., 2012). The detail classification and definition are described in Fig. 3.Figure 3

Bottom Line: Cells can adapt to environment and development by reconstructing their transcriptional networks to regulate diverse cellular processes without altering the underlying DNA sequences.Numerous evidences demonstrate that epigenetic changes are governed by various types of determinants, including DNA methylation patterns, histone posttranslational modification signatures, histone variants, chromatin remodeling, and recently discovered chromosome conformation characteristics and non-coding RNAs (ncRNAs).Here, we highlight recent efforts on how the two latter epigenetic factors participate in the sophisticated transcriptional process and describe emerging techniques which permit us to uncover and gain insights into the fascinating genomic regulation.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Brain Function and Disease and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.

ABSTRACT
Cells can adapt to environment and development by reconstructing their transcriptional networks to regulate diverse cellular processes without altering the underlying DNA sequences. These alterations, namely epigenetic changes, occur during cell division, differentiation and cell death. Numerous evidences demonstrate that epigenetic changes are governed by various types of determinants, including DNA methylation patterns, histone posttranslational modification signatures, histone variants, chromatin remodeling, and recently discovered chromosome conformation characteristics and non-coding RNAs (ncRNAs). Here, we highlight recent efforts on how the two latter epigenetic factors participate in the sophisticated transcriptional process and describe emerging techniques which permit us to uncover and gain insights into the fascinating genomic regulation.

Show MeSH
Related in: MedlinePlus