scholarly journals CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the β-globin locus

2012 ◽  
Vol 40 (16) ◽  
pp. 7718-7727 ◽  
Author(s):  
Ivan Junier ◽  
Ryan K. Dale ◽  
Chunhui Hou ◽  
François Képès ◽  
Ann Dean
Keyword(s):  
Transcriptional Regulation ◽  
Chromosome Organization ◽  
Cell Type ◽  
Specific Chromosome ◽  
Cell Type Specific

Cell type-specific transcriptional regulation of the drosophila FMRFamide neuropeptide gene

Neuron ◽  
1993 ◽  
Vol 10 (2) ◽  
pp. 279-291 ◽  
Author(s):  
Lynne E. Schneider ◽  
Marie S. Roberts ◽  
Paul H. Taghert
Keyword(s):  
Transcriptional Regulation ◽  
Cell Type ◽  
Cell Type Specific

scholarly journals Cell type-specific transcriptional regulation of the human adenosine deaminase gene

1989 ◽  
Vol 17 (3) ◽  
pp. 1061-1076 ◽  
Author(s):  
David L. Lattier ◽  
J.Christopher States ◽  
John J. Hutton ◽  
Dan A. Wiginton
Keyword(s):  
Transcriptional Regulation ◽  
Adenosine Deaminase ◽  
Cell Type ◽  
Cell Type Specific

scholarly journals Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization

2017 ◽  
Author(s):  
Aleksandar Kojic ◽  
Ana Cuadrado ◽  
Magali De Koninck ◽  
Miriam Rodríguez-Corsino ◽  
Gonzalo Gómez-López ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Sister Chromatid ◽  
Cell Types ◽  
Dna Looping ◽  
Chromosome Organization ◽  
Genome Architecture ◽  
Cell Type ◽  
Chromatid Cohesion ◽  
Cell Type Specific ◽  
Specific Contribution

AbstractIn addition to mediating sister chromatid cohesion, cohesin plays a central role in DNA looping and segmentation of the genome into contact domains (TADs). Two variant cohesin complexes that contain either STAG/SA1 or SA2 are present in all cell types. Here we addressed their specific contribution to genome architecture in non-transformed human cells. We found that cohesin-SA1 drives stacking of cohesin rings at CTCF-bound sites and thereby contributes to the stabilization and preservation of TAD boundaries. In contrast, a more dynamic cohesin-SA2 promotes cell type-specific contacts between enhancers and promoters within TADs independently of CTCF. SA2 loss, a condition frequently observed in cancer cells, results in increased intra-TAD interactions, likely altering the expression of key cell identity genes.

scholarly journals Nr2e3-directed transcriptional regulation of genes involved in photoreceptor development and cell-type specific phototransduction

2009 ◽  
Vol 89 (3) ◽  
pp. 365-372 ◽  
Author(s):  
Neena B. Haider ◽  
Nissa Mollema ◽  
Meghan Gaule ◽  
Yang Yuan ◽  
Andrew J. Sachs ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Cell Type ◽  
Cell Type Specific ◽  
Photoreceptor Development

scholarly journals Dynamic CTCF binding directly mediates interactions among cis-regulatory elements essential for hematopoiesis

Blood ◽  
2020 ◽  
Author(s):  
Qian Qi ◽  
Li Cheng ◽  
Xing Tang ◽  
Yanghua He ◽  
Yichao Li ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Blood Cell ◽  
Binding Sites ◽  
Specific Binding ◽  
Regulatory Elements ◽  
Cell Development ◽  
Ctcf Binding ◽  
Cell Type ◽  
Dynamic Cell ◽  
Cell Type Specific

While constitutive CTCF-binding sites are needed to maintain relatively invariant chromatin structures, such as topologically associating domains, the precise roles of CTCF to control cell type-specific transcriptional regulation remain poorly explored. We examined CTCF occupancy in different types of primary blood cells derived from the same donor to elucidate a new role for CTCF in gene regulation during blood cell development. We identified dynamic, cell type-specific binding sites for CTCF that colocalize with lineage-specific transcription factors. These dynamic sites are enriched for single nucleotide polymorphisms that are associated with blood cell traits in different linages, and they coincide with the key regulatory elements governing hematopoiesis. CRISPR/Cas9-based perturbation experiments demonstrated that these dynamic CTCF-binding sites play a critical role in red blood cell development. Furthermore, precise deletion of CTCF-binding motifs in dynamic sites abolished interactions of erythroid genes, such as RBM38, with their associated enhancers and led to abnormal erythropoiesis. These results suggest a novel, cell type-specific function for CTCF in which it may serve to facilitate interaction of distal regulatory emblements with target promoters. Our study of the dynamic, cell type-specific binding and function of CTCF provides new insights into transcriptional regulation during hematopoiesis.

scholarly journals Developmentally Programmed 3′ CpG Island Methylation Confers Tissue- and Cell-Type-Specific Transcriptional Activation

2013 ◽  
Vol 33 (9) ◽  
pp. 1845-1858 ◽  
Author(s):  
Da-Hai Yu ◽  
Carol Ware ◽  
Robert A. Waterland ◽  
Jiexin Zhang ◽  
Miao-Hsueh Chen ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Transcriptional Activation ◽  
Functional Role ◽  
Cpg Island ◽  
Embryonic Stem ◽  
Luciferase Reporter ◽  
Specific Gene ◽  
Cell Type ◽  
Cell Type Specific

During development, a small but significant number of CpG islands (CGIs) become methylated. The timing of developmentally programmed CGI methylation and associated mechanisms of transcriptional regulation during cellular differentiation, however, remain poorly characterized. Here, we used genome-wide DNA methylation microarrays to identify epigenetic changes during human embryonic stem cell (hESC) differentiation. We discovered a group of CGIs associated with developmental genes that gain methylation after hESCs differentiate. Conversely, erasure of methylation was observed at the identified CGIs during subsequent reprogramming to induced pluripotent stem cells (iPSCs), further supporting a functional role for the CGI methylation. Both global gene expression profiling and quantitative reverse transcription-PCR (RT-PCR) validation indicated opposing effects of CGI methylation in transcriptional regulation during differentiation, with promoter CGI methylation repressing and 3′ CGI methylation activating transcription. By studying diverse human tissues and mouse models, we further confirmed that developmentally programmed 3′ CGI methylation confers tissue- and cell-type-specific gene activationin vivo. Importantly, luciferase reporter assays provided evidence that 3′ CGI methylation regulates transcriptional activation via a CTCF-dependent enhancer-blocking mechanism. These findings expand the classic view of mammalian CGI methylation as a mechanism for transcriptional silencing and indicate a functional role for 3′ CGI methylation in developmental gene regulation.

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