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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.


CTCF binding to selected DNA fragments 10 and 13. Anti-CTCF (A) andanti-polyHistidine (B) antibodies were used for the supershift assay. AB– antibodies, NE – nuclear extract
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Figure 2: CTCF binding to selected DNA fragments 10 and 13. Anti-CTCF (A) andanti-polyHistidine (B) antibodies were used for the supershift assay. AB– antibodies, NE – nuclear extract

Mentions: Ten selected DNA fragments (1–4, 6–10, 13) were used as probes to testtheir ability to bind CTCF by electrophoretic mobility shift and supershiftassays (EMSA, supershift). Two fragments (10 and 13) are shownin Fig. 2.All 10 fragments were able to bind CTCF, which indicates the high efficiency of the selection.


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)

CTCF binding to selected DNA fragments 10 and 13. Anti-CTCF (A) andanti-polyHistidine (B) antibodies were used for the supershift assay. AB– antibodies, NE – nuclear extract
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: CTCF binding to selected DNA fragments 10 and 13. Anti-CTCF (A) andanti-polyHistidine (B) antibodies were used for the supershift assay. AB– antibodies, NE – nuclear extract
Mentions: Ten selected DNA fragments (1–4, 6–10, 13) were used as probes to testtheir ability to bind CTCF by electrophoretic mobility shift and supershiftassays (EMSA, supershift). Two fragments (10 and 13) are shownin Fig. 2.All 10 fragments were able to bind CTCF, which indicates the high efficiency of the selection.

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.