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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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Related in: MedlinePlus

An overview of chromosome conformation capture (3C) and related techniques. The common steps in all 3C-related techniques are that chromosome should be crosslinked with formaldehyde and fragmented by restriction digestion. In 4C procedure, the fragment is further cleaved by a second restriction enzyme and subsequently religated to form DNA circles. The main different in 5C is the library preparation which need anneal and ligate 5C oligonucleotide after reverse crosslink. The Hi-C method adds a unique step after restriction digestion, in which the staggered DNA ends are filled in with biotinylated nucleotides (as shown by the pink dot). 3D-DSL is similar to 5C to identify chromosome interactions at pre-selected genomic locus. However, probes pools were annealed to the biotinylated 3C samples and biotinylated DNA was bound on to streptavidin magnetic beads in 3D-DSL assay. The ligated products were then eluted from streptavidin magnetic beads. This further purification step can greatly reduce background and increase signal/noise ratio
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Fig1: An overview of chromosome conformation capture (3C) and related techniques. The common steps in all 3C-related techniques are that chromosome should be crosslinked with formaldehyde and fragmented by restriction digestion. In 4C procedure, the fragment is further cleaved by a second restriction enzyme and subsequently religated to form DNA circles. The main different in 5C is the library preparation which need anneal and ligate 5C oligonucleotide after reverse crosslink. The Hi-C method adds a unique step after restriction digestion, in which the staggered DNA ends are filled in with biotinylated nucleotides (as shown by the pink dot). 3D-DSL is similar to 5C to identify chromosome interactions at pre-selected genomic locus. However, probes pools were annealed to the biotinylated 3C samples and biotinylated DNA was bound on to streptavidin magnetic beads in 3D-DSL assay. The ligated products were then eluted from streptavidin magnetic beads. This further purification step can greatly reduce background and increase signal/noise ratio

Mentions: Many researches revealed that chromosomal interactions can contribute to the silencing and/or activation of genes within the three-dimensional organization of the nuclear architecture (Galande et al., 2007; Gondor and Ohlsson, 2009; Cavalli and Misteli, 2013). The genome forms extensive and dynamic physical interactions in the form of chromatin loops and bridges, which bring distal elements of the chromosome into close physical proximity, with potential consequences for gene expression and/or propagation of the genome. With advances in detection technology, it is now possible to examine these interactions at molecular level. The physical interactions of chromatin fibers can be measured by using chromosome conformation capture (3C) (Dekker et al., 2002) and related techniques including circular chromosome conformation capture (4C) (Simonis et al., 2006; Zhao et al., 2006), chromosome conformation capture carbon copy (5C) (Dostie et al., 2006), and Hi-C (Lieberman-Aiden et al., 2009) (Fig. 1). The common steps in all 3C-related techniques are that chromosomes should be crosslinked with formaldehyde and fragmented by restriction digestion (de Laat and Dekker, 2012). Classical 3C can detect chromosome interaction between two interested loci by checking the ligation products with PCR using locus-specific primers (one to one). 4C can capture genome-wide interaction profiles for a single locus with an inverse PCR. It is genome-wild but only focus on a single locus (one to many). 5C approach combines 3C and hybrid capture, so it can identify many chromosome interactions between two large loci (many to many). Hi-C is the first method that can get unbiased genome-wide chromosome interaction conformation (all to all). In Hi-C experiment, the restriction ends are filled in with biotin-labeled nucleotides before intramolecular ligation, and the ligated fragments are selected for further analysis with biotin pull-down. These genome-wide advances greatly contribute to our understanding on the mechanism of the genome organization, as well as its adaptive plasticity in response to environmental changes during development and disease. For example, analyses of β-globin gene loci and the regulatory regions of the H19 using 4C and 5C have revealed large domains of interacting chromatin fibers (Dostie et al., 2006; Zhao et al., 2006). Collaborated with Dr. MG Rosenfeld and Dr. XD Fu (UCSD), we also developed three-dimensional DNA selection and ligation (3D-DSL) method (Fig. 1) and successfully detected the long-range enhancer interactional network in human chromosome 9p21 region (Harismendy et al., 2011). 3D-DSL is similar to 5C to identify chromosome interactions at pre-selected genomic locus (many to many). However, it includes further purification steps which can greatly reduce background and increase signal/noise ratio. A recent study by Fanucchi et al. indicated that co-regulated genes can form long range chromosomal contacts and that these long-range interactions may regulate these co-regulated genes’ transcription. After knocking down the factors which participate in the formation of the chromosomal contacts, the contacts will lose and these co-regulated genes transcription will not happen (Fanucchi et al., 2013).Figure 1


Three-dimensional regulation of transcription.

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

An overview of chromosome conformation capture (3C) and related techniques. The common steps in all 3C-related techniques are that chromosome should be crosslinked with formaldehyde and fragmented by restriction digestion. In 4C procedure, the fragment is further cleaved by a second restriction enzyme and subsequently religated to form DNA circles. The main different in 5C is the library preparation which need anneal and ligate 5C oligonucleotide after reverse crosslink. The Hi-C method adds a unique step after restriction digestion, in which the staggered DNA ends are filled in with biotinylated nucleotides (as shown by the pink dot). 3D-DSL is similar to 5C to identify chromosome interactions at pre-selected genomic locus. However, probes pools were annealed to the biotinylated 3C samples and biotinylated DNA was bound on to streptavidin magnetic beads in 3D-DSL assay. The ligated products were then eluted from streptavidin magnetic beads. This further purification step can greatly reduce background and increase signal/noise ratio
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4383755&req=5

Fig1: An overview of chromosome conformation capture (3C) and related techniques. The common steps in all 3C-related techniques are that chromosome should be crosslinked with formaldehyde and fragmented by restriction digestion. In 4C procedure, the fragment is further cleaved by a second restriction enzyme and subsequently religated to form DNA circles. The main different in 5C is the library preparation which need anneal and ligate 5C oligonucleotide after reverse crosslink. The Hi-C method adds a unique step after restriction digestion, in which the staggered DNA ends are filled in with biotinylated nucleotides (as shown by the pink dot). 3D-DSL is similar to 5C to identify chromosome interactions at pre-selected genomic locus. However, probes pools were annealed to the biotinylated 3C samples and biotinylated DNA was bound on to streptavidin magnetic beads in 3D-DSL assay. The ligated products were then eluted from streptavidin magnetic beads. This further purification step can greatly reduce background and increase signal/noise ratio
Mentions: Many researches revealed that chromosomal interactions can contribute to the silencing and/or activation of genes within the three-dimensional organization of the nuclear architecture (Galande et al., 2007; Gondor and Ohlsson, 2009; Cavalli and Misteli, 2013). The genome forms extensive and dynamic physical interactions in the form of chromatin loops and bridges, which bring distal elements of the chromosome into close physical proximity, with potential consequences for gene expression and/or propagation of the genome. With advances in detection technology, it is now possible to examine these interactions at molecular level. The physical interactions of chromatin fibers can be measured by using chromosome conformation capture (3C) (Dekker et al., 2002) and related techniques including circular chromosome conformation capture (4C) (Simonis et al., 2006; Zhao et al., 2006), chromosome conformation capture carbon copy (5C) (Dostie et al., 2006), and Hi-C (Lieberman-Aiden et al., 2009) (Fig. 1). The common steps in all 3C-related techniques are that chromosomes should be crosslinked with formaldehyde and fragmented by restriction digestion (de Laat and Dekker, 2012). Classical 3C can detect chromosome interaction between two interested loci by checking the ligation products with PCR using locus-specific primers (one to one). 4C can capture genome-wide interaction profiles for a single locus with an inverse PCR. It is genome-wild but only focus on a single locus (one to many). 5C approach combines 3C and hybrid capture, so it can identify many chromosome interactions between two large loci (many to many). Hi-C is the first method that can get unbiased genome-wide chromosome interaction conformation (all to all). In Hi-C experiment, the restriction ends are filled in with biotin-labeled nucleotides before intramolecular ligation, and the ligated fragments are selected for further analysis with biotin pull-down. These genome-wide advances greatly contribute to our understanding on the mechanism of the genome organization, as well as its adaptive plasticity in response to environmental changes during development and disease. For example, analyses of β-globin gene loci and the regulatory regions of the H19 using 4C and 5C have revealed large domains of interacting chromatin fibers (Dostie et al., 2006; Zhao et al., 2006). Collaborated with Dr. MG Rosenfeld and Dr. XD Fu (UCSD), we also developed three-dimensional DNA selection and ligation (3D-DSL) method (Fig. 1) and successfully detected the long-range enhancer interactional network in human chromosome 9p21 region (Harismendy et al., 2011). 3D-DSL is similar to 5C to identify chromosome interactions at pre-selected genomic locus (many to many). However, it includes further purification steps which can greatly reduce background and increase signal/noise ratio. A recent study by Fanucchi et al. indicated that co-regulated genes can form long range chromosomal contacts and that these long-range interactions may regulate these co-regulated genes’ transcription. After knocking down the factors which participate in the formation of the chromosomal contacts, the contacts will lose and these co-regulated genes transcription will not happen (Fanucchi et al., 2013).Figure 1

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