Roles of the NFI/CTF gene family in transcription and development.

doi:10.1016/S0378-1119(00)00140-2

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Roles of the NFI/CTF gene family in transcription and development.

Journal Article•DOI•

Roles of the NFI/CTF gene family in transcription and development.

Richard M. Gronostajski¹•Institutions (1)

Case Western Reserve University¹

16 May 2000-Gene (Gene)-Vol. 249, Iss: 1, pp 31-45

TL;DR: The Nuclear Factor I (NFI) family of site-specific DNA-binding proteins (also known as CTF or CAAT box transcription factor) functions both in viral DNA replication and in the regulation of gene expression.

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About: This article is published in Gene.The article was published on 2000-05-16. It has received 509 citations till now. The article focuses on the topics: NFI Transcription Factors & Gene family.

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Journal Article•DOI•

A Minicircuitry Comprised of MicroRNA-223 and Transcription Factors NFI-A and C/EBPα Regulates Human Granulopoiesis

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Francesco Fazi¹, Alessandro Rosa¹, Alessandro Fatica¹, Vania Gelmetti¹, Maria Laura De Marchis¹, Clara Nervi¹, Irene Bozzoni¹ - Show less +3 more•Institutions (1)

Sapienza University of Rome¹

02 Dec 2005-Cell

TL;DR: The data indicate that miR-223 plays a crucial role during granulopoiesis and point to the NFI-A repression as an important molecular pathway mediating gene reprogramming in this cell lineage.

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1,007 citations

Cites background from "Roles of the NFI/CTF gene family in..."

...X) and a large number of splice Cell 123, 819–831, December 2, 2005 ª2005 Elsevier Inc. 827 variants that form homodimers and heterodimers, thus creating an extensive network of possible functional dimers (Gronostajski, 2000)....
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...NFI-A Competes with C/EBPa for Promoter Binding Among the hundreds of predicted regulatory targets of miR223 (Lewis et al., 2005; Krek et al., 2005), we noticed transcription factor NFI-A, a protein known to bind sequences related to the ones of C/EBPa (Gronostajski, 2000)....
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...variants that form homodimers and heterodimers, thus creating an extensive network of possible functional dimers (Gronostajski, 2000)....
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...One of the two C/EBPa binding elements in the miR-223 promoter overlaps with a NFI-A binding site (Meisterernst et al., 1988; Bachurski et al., 1997; Gronostajski, 2000)....
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...On the other hand, NFI-A has been implicated in replication as well as in controlling changes in cell growth (Gronostajski, 2000)....
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Journal Article•DOI•

HMGB1 in Health and Disease

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Rui Kang¹, Ruochan Chen¹, Qiuhong Zhang¹, Wen Hou¹, Sha Wu¹, Lizhi Cao², Jin Huang², Yan Yu², Xue Gong Fan², Zhengwen Yan¹, Zhengwen Yan³, Xiaofang Sun⁴, Haichao Wang⁵, Qingde Wang¹, Allan Tsung¹, Timothy R. Billiar¹, Herbert J. Zeh¹, Michael T. Lotze¹, Daolin Tang¹ - Show less +15 more•Institutions (5)

University of Pittsburgh¹, Central South University², Sun Yat-sen University³, Guangzhou Medical University⁴, The Feinstein Institute for Medical Research⁵

01 Dec 2014-Molecular Aspects of Medicine

TL;DR: High-mobility group box 1 (HMGB1), the most abundant and well-studied HMG protein, senses and coordinates the cellular stress response and plays a critical role not only inside of the cell as a DNA chaperone, chromosome guardian, autophagy sustainer, and protector from apoptotic cell death, but also outside thecell as the prototypic damage associated molecular pattern molecule (DAMP).

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717 citations

Journal Article•DOI•

Timing Is Everything: Making Neurons versus Glia in the Developing Cortex

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Freda D. Miller¹, Andrée S. Gauthier¹•Institutions (1)

University of Toronto¹

03 May 2007-Neuron

TL;DR: Work addressing the mechanisms underlying this timed cell genesis, with a particular focus on the developing cortex, is reviewed, finding an intriguing interplay between intrinsic epigenetic status, transcription factors, and environmental cues.

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527 citations

Journal Article•DOI•

miR-21 Gene Expression Triggered by AP-1 Is Sustained through a Double-Negative Feedback Mechanism

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Shuji Fujita¹, Taiji Ito¹, Taketoshi Mizutani¹, Shigeru Minoguchi¹, Nobutake Yamamichi¹, Kouhei Sakurai¹, Hideo Iba¹ - Show less +3 more•Institutions (1)

University of Tokyo¹

02 May 2008-Journal of Molecular Biology

TL;DR: It is shown that activation protein 1 (AP-1) activates the miR-21 transcription in conjugation with the SWI/SNF complex, after PMA stimulation, through the conserved AP-1 and PU.1 binding sites in the promoter identified here.

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462 citations

Journal Article•DOI•

The Transcription Factor NFIA Controls the Onset of Gliogenesis in the Developing Spinal Cord

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Benjamin Deneen¹, Ritchie Ho¹, Agnès Lukaszewicz¹, Christian Hochstim¹, Richard M. Gronostajski², David J. Anderson¹ - Show less +2 more•Institutions (2)

California Institute of Technology¹, University at Buffalo²

21 Dec 2006-Neuron

TL;DR: NFI genes are identified, which are induced throughout the spinal cord ventricular zone (VZ) concomitantly with the induction of GLAST, an early marker of gliogenesis, and NFIA links the abrogation of neurogenesis to a generic program of gl iogenesis, in both astrocyte and oligodendrocytes VZ progenitors.

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450 citations

Cites background from "Roles of the NFI/CTF gene family in..."

...Here we show that NFIA and NFIB, members of a family of CCAAT box element-binding transcription factors (Gronostajski, 2000), are both necessary and sufficient to promote glial-fate specification in embryonic spinal cord progenitors, in vivo....
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...These proteins are members of a family of CAATT box-binding transcription factors, whose DNA-binding domains are distinct from those of other CCAAT box element-binding proteins (C/EBPs) (Meisterernst et al., 1988; Bandyopadhyay and Gronostajski, 1994; Gronostajski, 2000)....
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References

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Journal Article•DOI•

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

[...]

Stephen F. Altschul¹, Thomas L. Madden, Alejandro A. Schäffer¹, Jinghui Zhang, Zheng Zhang², Webb Miller², David J. Lipman - Show less +3 more•Institutions (2)

National Institutes of Health¹, Pennsylvania State University²

01 Sep 1997-Nucleic Acids Research

TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.

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Abstract: The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

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70,111 citations

Patent•DOI•

Expression monitoring by hybridization to high density oligonucleotide arrays

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David J. Lockhart¹, Eugene L. Brown¹, Gordon G. Wong¹, Mark S. Chee¹, Thomas R. Gingeras¹ - Show less +1 more•Institutions (1)

Affymetrix¹

13 Sep 1996-Nature Biotechnology

TL;DR: In this article, the authors proposed a method for monitoring the expression levels of a multiplicity of genes by hybridizing a nucleic acid sample to a high density array of oligonucleotide probes and quantifying the hybridized nucleic acids in the array.

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Abstract: This invention provides methods of monitoring the expression levels of a multiplicity of genes. The methods involve hybridizing a nucleic acid sample to a high density array of oligonucleotide probes where the high density array contains oligonucleotide probes complementary to subsequences of target nucleic acids in the nucleic acid sample. In one embodiment, the method involves providing a pool of target nucleic acids comprising RNA transcripts of one or more target genes, or nucleic acids derived from the RNA transcripts, hybridizing said pool of nucleic acids to an array of oligonucleotide probes immobilized on surface, where the array comprising more than 100 different oligonucleotides and each different oligonucleotide is localized in a predetermined region of the surface, the density of the different oligonucleotides is greater than about 60 different oligonucleotides per 1 cm2, and the oligonucleotide probes are complementary to the RNA transcripts or nucleic acids derived from the RNA transcripts; and quantifying the hybridized nucleic acids in the array.

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4,382 citations

Journal Article•DOI•

Redox regulation of fos and jun DNA-binding activity in vitro

[...]

Cory Abate¹, L Patel¹, Frank J. Rauscher¹, Tom Curran¹•Institutions (1)

Roche Institute of Molecular Biology¹

07 Sep 1990-Science

TL;DR: DNA binding of the Fos-Jun heterodimer was modulated by reduction-oxidation of a single conserved cysteine residue in the DNA-binding domains of the two proteins, suggesting that transcriptional activity mediated by AP-1 binding factors may be regulated by a redox mechanism.

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Abstract: The proto-oncogenes c-fos and c-jun function cooperatively as inducible transcription factors in signal transduction processes. Their protein products, Fos and Jun, form a heterodimeric complex that interacts with the DNA regulatory element known as the activator protein-1 (AP-1) binding site. Dimerization occurs via interaction between leucine zipper domains and serves to bring into proper juxtaposition a region in each protein that is rich in basic amino acids and that forms a DNA-binding domain. DNA binding of the Fos-Jun heterodimer was modulated by reduction-oxidation (redox) of a single conserved cysteine residue in the DNA-binding domains of the two proteins. Furthermore, a nuclear protein was identified that reduced Fos and Jun and stimulated DNA-binding activity in vitro. These results suggest that transcriptional activity mediated by AP-1 binding factors may be regulated by a redox mechanism.

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1,581 citations

Journal Article•DOI•

What's Up and Down with Histone Deacetylation and Transcription?

[...]

Michael J. Pazin¹, James T. Kadonaga¹•Institutions (1)

University of California, San Diego¹

02 May 1997-Cell

TL;DR: It will be important to analyze the expression of endogenous or stably integrated genes rather than transiently transfected templates that are not efficiently packaged into chromatin to address some of the questions of protein acetylation.

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864 citations

"Roles of the NFI/CTF gene family in..." refers background in this paper

...…of NFI proteins can be affected by the growth and differentiation state of cells (Goyal et al., 1990; Kulkarniand Hansen, 1996; Manley et al., 1996; Pazin and Kadonaga, 1997 for reviews). and Gronostajski, 1996), it is difficult to determine whether the effects of some hormones/growth factorsWhile…...
[...]

Journal Article•DOI•

Microarrays: biotechnology's discovery platform for functional genomics

[...]

Mark Schena¹, Renu A. Heller², Thomas P. Theriault³, Ken Konrad³, Eric Lachenmeier³, Ronald W. Davis¹ - Show less +2 more•Institutions (3)

Stanford University¹, Hoffmann-La Roche², Incyte³

01 Jul 1998-Trends in Biotechnology

TL;DR: Advances in microarray technology enable massive parallel mining of biological data, with biological chips providing hybridization-based expression monitoring, polymorphism detection and genotyping on a genomic scale.

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863 citations