CTCF mediates the cell-type specific spatial organization of the Kcnq5 locus and the local gene regulation.

PloS One
Licheng RenZhihu Zhao

Abstract

Chromatin loops play important roles in the dynamic spatial organization of genes in the nucleus. Growing evidence has revealed that the multivalent functional zinc finger protein CCCTC-binding factor (CTCF) is a master regulator of genome spatial organization, and mediates the ubiquitous chromatin loops within the genome. Using circular chromosome conformation capture (4C) methodology, we discovered that CTCF may be a master organizer in mediating the spatial organization of the kcnq5 gene locus. We characterized the cell-type specific spatial organization of the kcnq5 gene locus mediated by CTCF in detail using chromosome conformation capture (3C) and 3C-derived techniques. Cohesion also participated in mediating the organization of this locus. RNAi-mediated knockdown of CTCF sharply diminished the interaction frequencies between the chromatin loops of the kcnq5 gene locus and down-regulated local gene expression. Functional analysis showed that the interacting chromatin loops of the kcnq5 gene locus can repress the gene expression in a luciferase reporter assay. These interacting chromatin fragments were a series of repressing elements whose contacts were mediated by CTCF. Therefore, these findings suggested that the dynamic...Continue Reading

References

May 19, 2000·The Journal of Biological Chemistry·B C SchroederT J Jentsch
Feb 16, 2002·Science·Job DekkerNancy Kleckner
Feb 12, 2004·Methods in Enzymology·Erik SplinterWouter de Laat
Dec 21, 2004·Nature Genetics·Shin-ichi HorikeTerumi Kohwi-Shigematsu
Sep 2, 2005·Nature Reviews. Genetics·Keith D Robertson
Sep 28, 2006·PLoS Genetics·Gregory J HoganJason D Lieb
Feb 23, 2007·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Hua HuJohan F Storm
Feb 27, 2007·Cell·Tony Kouzarides
Feb 27, 2007·Cell·Bing LiJerry L Workman
Feb 27, 2007·The Journal of Biological Chemistry·Jenny EkbergDavid J Adams
May 25, 2007·Nature·Peter Fraser, Wendy Bickmore
Jul 21, 2007·Nature Protocols·Hélène HagègeThierry Forné
Oct 5, 2007·Current Opinion in Genetics & Development·Julie A Wallace, Gary Felsenfeld
Nov 1, 2007·Nature Methods·Marieke SimonisWouter de Laat
Feb 1, 2008·Nature·Kerstin S WendtJan-Michael Peters
Feb 2, 2008·Cell·Vania ParelhoMatthias Merkenschlager
Feb 16, 2008·Nature Protocols·Anita GöndörRolf Ohlsson
Mar 11, 2008·Cell·Dustin E SchonesKeji Zhao
Mar 19, 2008·The Journal of Experimental Medicine·Adam Williams, Richard A Flavell
Mar 25, 2008·Cell·R Ileng KumaranDavid L Spector
Feb 28, 2009·Journal of Cellular Biochemistry·Melissa J Fullwood, Yijun Ruan
Jul 1, 2009·Cell·Jennifer E Phillips, Victor G Corces
Sep 11, 2009·Nature·Anita Göndör, Rolf Ohlsson
Nov 6, 2009·Annual Review of Genetics·Kim Nasmyth, Christian H Haering
Dec 19, 2009·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Rolf OhlssonElena Klenova

❮ Previous
Next ❯

Citations

Nov 17, 2016·Nature Communications·Benjamin Joachim SchmiedelPandurangan Vijayanand
Apr 20, 2018·Nature Communications·Yu Amanda GuoAnders Jacobsen Skanderup
Aug 26, 2021·Genome Biology·Beisi XuChunliang Li

❮ Previous
Next ❯

Methods Mentioned

BETA
ChIP-chip
electrophoresis
PCR
immunoprecipitation
ChIP
reverse
Assay
FCS
transfection

Software Mentioned

UCSC Genome Browser
ENCODE
FAIRE
ENCONDE Genome Browser
Primers

Related Concepts

Related Feeds

CREs: Gene & Cell Therapy

Gene and cell therapy advances have shown promising outcomes for several diseases. The role of cis-regulatory elements (CREs) is crucial in the design of gene therapy vectors. Here is the latest research on CREs in gene and cell therapy.

Related Papers

BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology
Rolf OhlssonElena Klenova
The Journal of Experimental Medicine
Adam Williams, Richard A Flavell
Proceedings of the National Academy of Sciences of the United States of America
Chunhui HouAnn Dean
© 2022 Meta ULC. All rights reserved