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Binding of Protein Factor CTCF within Chicken Genome Alpha-Globin Locus.

Kotova ES, Akopov SB, Didych DA, Petrova NV, Iarovaia OV, Razin SV, Nikolaev LG - Acta Naturae (2016 Jan-Mar)

Bottom Line: So, binding of CTCF to the DNA fragment in vitro in most cases does not mean that this fragment will be occupied by CTCF in the cell nucleus.Yet, CTCF binding in vivo, as a rule, is accompanied by the binding of the protein to this DNA region in vitro.During the erythroid differentiation, no significant changes in CTCF binding to the DNA fragments studied were detected.

View Article: PubMed Central - PubMed

Affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow 117997, Russia.

ABSTRACT
A systematic search for DNA fragments containing potential CTCF transcription factor binding sites in the chicken alpha-globin domain and its flanking regions was performed by means of the two-dimension electrophoretic mobility shift assay. For the alpha-globin domain fragments selected, the occupancy by the CTCF in erythroid and lymphoid chicken cells was tested by chromatin immunoprecipitation. Only one of 13 DNA fragments capable of CTCF binding in vitro was efficiently bound to this protein in vivo in erythroid cells, and somewhat less efficiently - in lymphoid cells. So, binding of CTCF to the DNA fragment in vitro in most cases does not mean that this fragment will be occupied by CTCF in the cell nucleus. Yet, CTCF binding in vivo, as a rule, is accompanied by the binding of the protein to this DNA region in vitro. During the erythroid differentiation, no significant changes in CTCF binding to the DNA fragments studied were detected.

No MeSH data available.


Distribution of CTCF binding sites and some regulatory elements in the regionoverlapping the chicken genome alpha-globin domain. Upper map shows thepositions of all selected DNA fragments. The arrows indicate DNA regions withhigh affinity to CTCF. Lower part shows the enlarged map of the immediatesurroundings of the globin genes. In the “CTCF sites” panel theidentified previously CTCF binding sites M9, C10-C14 [7], CDS [8] and 5d1-5d3,10d1-10d3 [9] are shown, the“Regulatory elements” panel demonstrates the positions of the MRE[2] and the enhancer and silencer[25]. In the ChIP region the positions ofDNA fragments amplified in the chromatin immunoprecipitation experiment are shown(see text)
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Figure 3: Distribution of CTCF binding sites and some regulatory elements in the regionoverlapping the chicken genome alpha-globin domain. Upper map shows thepositions of all selected DNA fragments. The arrows indicate DNA regions withhigh affinity to CTCF. Lower part shows the enlarged map of the immediatesurroundings of the globin genes. In the “CTCF sites” panel theidentified previously CTCF binding sites M9, C10-C14 [7], CDS [8] and 5d1-5d3,10d1-10d3 [9] are shown, the“Regulatory elements” panel demonstrates the positions of the MRE[2] and the enhancer and silencer[25]. In the ChIP region the positions ofDNA fragments amplified in the chromatin immunoprecipitation experiment are shown(see text)

Mentions: All 208 sequenced fragments were mapped to the Gallus gallus genome (galGal4,2011). A table with the coordinates of all mapped DNA fragments in BED formatis available upon request. A full map of the fragments distribution ispresented in the upper partof Fig. 3. Ascan be seen, the locus had a number of sites with higher selection efficiency(indicated by vertical arrows); i.e., with higher affinity for CTCF in EMSAconditions. The bottom partof Fig. 3 showsan enlarged map of the immediatesurroundings of the globin genes with indicated genes positions (RefSeq), aswell as some previously identified regulatory elements, in particular theenhancer/silencer [25] and MRE (MajorRegulatory Element, [2]). It also showsDNA fragments that had been previously identified in various cell types andtissues as capable of binding CTCF: M9, C10-C14 [7],and a fragment of the CTCF-dependent silencer [8].CTCF-binding fragments 5d1–5d3 and10d1–10d3 have been previously identified by ChIP-seq in five- andten-day chick embryos, respectively [9].


Binding of Protein Factor CTCF within Chicken Genome Alpha-Globin Locus.

Kotova ES, Akopov SB, Didych DA, Petrova NV, Iarovaia OV, Razin SV, Nikolaev LG - Acta Naturae (2016 Jan-Mar)

Distribution of CTCF binding sites and some regulatory elements in the regionoverlapping the chicken genome alpha-globin domain. Upper map shows thepositions of all selected DNA fragments. The arrows indicate DNA regions withhigh affinity to CTCF. Lower part shows the enlarged map of the immediatesurroundings of the globin genes. In the “CTCF sites” panel theidentified previously CTCF binding sites M9, C10-C14 [7], CDS [8] and 5d1-5d3,10d1-10d3 [9] are shown, the“Regulatory elements” panel demonstrates the positions of the MRE[2] and the enhancer and silencer[25]. In the ChIP region the positions ofDNA fragments amplified in the chromatin immunoprecipitation experiment are shown(see text)
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4837575&req=5

Figure 3: Distribution of CTCF binding sites and some regulatory elements in the regionoverlapping the chicken genome alpha-globin domain. Upper map shows thepositions of all selected DNA fragments. The arrows indicate DNA regions withhigh affinity to CTCF. Lower part shows the enlarged map of the immediatesurroundings of the globin genes. In the “CTCF sites” panel theidentified previously CTCF binding sites M9, C10-C14 [7], CDS [8] and 5d1-5d3,10d1-10d3 [9] are shown, the“Regulatory elements” panel demonstrates the positions of the MRE[2] and the enhancer and silencer[25]. In the ChIP region the positions ofDNA fragments amplified in the chromatin immunoprecipitation experiment are shown(see text)
Mentions: All 208 sequenced fragments were mapped to the Gallus gallus genome (galGal4,2011). A table with the coordinates of all mapped DNA fragments in BED formatis available upon request. A full map of the fragments distribution ispresented in the upper partof Fig. 3. Ascan be seen, the locus had a number of sites with higher selection efficiency(indicated by vertical arrows); i.e., with higher affinity for CTCF in EMSAconditions. The bottom partof Fig. 3 showsan enlarged map of the immediatesurroundings of the globin genes with indicated genes positions (RefSeq), aswell as some previously identified regulatory elements, in particular theenhancer/silencer [25] and MRE (MajorRegulatory Element, [2]). It also showsDNA fragments that had been previously identified in various cell types andtissues as capable of binding CTCF: M9, C10-C14 [7],and a fragment of the CTCF-dependent silencer [8].CTCF-binding fragments 5d1–5d3 and10d1–10d3 have been previously identified by ChIP-seq in five- andten-day chick embryos, respectively [9].

Bottom Line: So, binding of CTCF to the DNA fragment in vitro in most cases does not mean that this fragment will be occupied by CTCF in the cell nucleus.Yet, CTCF binding in vivo, as a rule, is accompanied by the binding of the protein to this DNA region in vitro.During the erythroid differentiation, no significant changes in CTCF binding to the DNA fragments studied were detected.

View Article: PubMed Central - PubMed

Affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow 117997, Russia.

ABSTRACT
A systematic search for DNA fragments containing potential CTCF transcription factor binding sites in the chicken alpha-globin domain and its flanking regions was performed by means of the two-dimension electrophoretic mobility shift assay. For the alpha-globin domain fragments selected, the occupancy by the CTCF in erythroid and lymphoid chicken cells was tested by chromatin immunoprecipitation. Only one of 13 DNA fragments capable of CTCF binding in vitro was efficiently bound to this protein in vivo in erythroid cells, and somewhat less efficiently - in lymphoid cells. So, binding of CTCF to the DNA fragment in vitro in most cases does not mean that this fragment will be occupied by CTCF in the cell nucleus. Yet, CTCF binding in vivo, as a rule, is accompanied by the binding of the protein to this DNA region in vitro. During the erythroid differentiation, no significant changes in CTCF binding to the DNA fragments studied were detected.

No MeSH data available.