Efficient and Orthogonal Transcription Regulation by Chemically Inducible Artificial Transcription Factors

Biochemistry ◽  
2018 ◽  
Vol 57 (45) ◽  
pp. 6452-6459 ◽  
Author(s):  
Wataru Nomura ◽  
Daisuke Matsumoto ◽  
Taisuke Sugii ◽  
Takuya Kobayakawa ◽  
Hirokazu Tamamura
Keyword(s):  
Transcription Factors ◽  
Transcription Regulation ◽  
Artificial Transcription Factors

scholarly journals Comprehensive network modeling from single cell RNA sequencing of human and mouse reveals well conserved transcription regulation of hematopoiesis

BMC Genomics ◽  
2020 ◽  
Vol 21 (S11) ◽  
Author(s):  
Shouguo Gao ◽  
Zhijie Wu ◽  
Xingmin Feng ◽  
Sachiko Kajigaya ◽  
Xujing Wang ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Transcription Factors ◽  
Single Cell ◽  
Rna Sequencing ◽  
Transcription Regulation ◽  
Regulatory Networks ◽  
Stem Cell Differentiation ◽  
Hematopoietic Stem ◽  
Single Cell Rna Sequencing ◽  
Human And Mouse

Abstract Background Presently, there is no comprehensive analysis of the transcription regulation network in hematopoiesis. Comparison of networks arising from gene co-expression across species can facilitate an understanding of the conservation of functional gene modules in hematopoiesis. Results We used single-cell RNA sequencing to profile bone marrow from human and mouse, and inferred transcription regulatory networks in each species in order to characterize transcriptional programs governing hematopoietic stem cell differentiation. We designed an algorithm for network reconstruction to conduct comparative transcriptomic analysis of hematopoietic gene co-expression and transcription regulation in human and mouse bone marrow cells. Co-expression network connectivity of hematopoiesis-related genes was found to be well conserved between mouse and human. The co-expression network showed “small-world” and “scale-free” architecture. The gene regulatory network formed a hierarchical structure, and hematopoiesis transcription factors localized to the hierarchy’s middle level. Conclusions Transcriptional regulatory networks are well conserved between human and mouse. The hierarchical organization of transcription factors may provide insights into hematopoietic cell lineage commitment, and to signal processing, cell survival and disease initiation.

scholarly journals Targeting Artificial Transcription Factors to the Utrophin A Promoter

2008 ◽  
Vol 283 (50) ◽  
pp. 34720-34727 ◽  
Author(s):  
Yifan Lu ◽  
Chai Tian ◽  
Gawiyou Danialou ◽  
Rénald Gilbert ◽  
Basil J. Petrof ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Artificial Transcription Factors

scholarly journals Poly(ADP-ribose) polymerase 1 in genome-wide expression control in Drosophila

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Guillaume Bordet ◽  
Niraj Lodhi ◽  
Danping Guo ◽  
Andrew Kossenkov ◽  
Alexei V. Tulin
Keyword(s):  
Cytochrome P450 ◽  
Transcription Factors ◽  
Transcription Regulation ◽  
Large Scale ◽  
Mobile Elements ◽  
Expression Control ◽  
Genome Wide ◽  
Cytochrome P450 Family ◽  
Parp 1

AbstractPoly(ADP-ribose) polymerase 1 (PARP-1) is a nuclear enzyme involved in DNA repair and transcription regulation, among other processes. Malignant transformations, tumor progression, the onset of some neuropathies and other disorders have been linked to misregulation of PARP-1 activity. Despite intensive studies during the last few decades, the role of PARP-1 in transcription regulation is still not well understood. In this study, a transcriptomic analysis in Drosophila melanogaster third instar larvae was carried out. A total of 602 genes were identified, showing large-scale changes in their expression levels in the absence of PARP-1 in vivo. Among these genes, several functional gene groups were present, including transcription factors and cytochrome family members. The transcription levels of genes from the same functional group were affected by the absence of PARP-1 in a similar manner. In the absence of PARP-1, all misregulated genes coding for transcription factors were downregulated, whereas all genes coding for members of the cytochrome P450 family were upregulated. The cytochrome P450 proteins contain heme as a cofactor and are involved in oxidoreduction. Significant changes were also observed in the expression of several mobile elements in the absence of PARP-1, suggesting that PARP-1 may be involved in regulating the expression of mobile elements.

Human zinc fingers as building blocks in the construction of artificial transcription factors

2003 ◽  
Vol 21 (3) ◽  
pp. 275-280 ◽  
Author(s):  
Kwang-Hee Bae ◽  
Young Do Kwon ◽  
Hyun-Chul Shin ◽  
Moon-Sun Hwang ◽  
Eun-Hyun Ryu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Zinc Fingers ◽  
Building Blocks ◽  
Artificial Transcription Factors

scholarly journals Reprogramming cell fate with artificial transcription factors

FEBS Letters ◽  
2018 ◽  
Vol 592 (6) ◽  
pp. 888-900 ◽  
Author(s):  
Evan A. Heiderscheit ◽  
Asuka Eguchi ◽  
Mackenzie C. Spurgat ◽  
Aseem Z. Ansari
Keyword(s):  
Transcription Factors ◽  
Cell Fate ◽  
Artificial Transcription Factors

scholarly journals GTRD: an integrated view of transcription regulation

2020 ◽  
Vol 49 (D1) ◽  
pp. D104-D111
Author(s):  
Semyon Kolmykov ◽  
Ivan Yevshin ◽  
Mikhail Kulyashov ◽  
Ruslan Sharipov ◽  
Yury Kondrakhin ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Data Integration ◽  
Transcription Regulation ◽  
Gene Transcription ◽  
Cell Types ◽  
Rna Seq ◽  
Web Interface ◽  
Gene Transcription Regulation ◽  
Cell Ontology ◽  
Ngs Data

Abstract The Gene Transcription Regulation Database (GTRD; http://gtrd.biouml.org/) contains uniformly annotated and processed NGS data related to gene transcription regulation: ChIP-seq, ChIP-exo, DNase-seq, MNase-seq, ATAC-seq and RNA-seq. With the latest release, the database has reached a new level of data integration. All cell types (cell lines and tissues) presented in the GTRD were arranged into a dictionary and linked with different ontologies (BRENDA, Cell Ontology, Uberon, Cellosaurus and Experimental Factor Ontology) and with related experiments in specialized databases on transcription regulation (FANTOM5, ENCODE and GTEx). The updated version of the GTRD provides an integrated view of transcription regulation through a dedicated web interface with advanced browsing and search capabilities, an integrated genome browser, and table reports by cell types, transcription factors, and genes of interest.

scholarly journals Modulation of endogenous VEGF-A expression by artificial transcription factors

2007 ◽  
Vol 51 (1) ◽  
pp. 345-346
Author(s):  
T. Mori ◽  
J. Sasaki ◽  
Y. Aoyama ◽  
T. Sera
Keyword(s):  
Transcription Factors ◽  
Artificial Transcription Factors
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