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GenomicsOff-Target Analysis of Zinc Finger Nucleases
Zinc Finger Nucleases (ZFNs) facilitate precise editing of DNA enabling targeted genomic modifications in vivo. ZFNs have been employed to obtain genetically modified plants and animals, and cell-based therapies utilizing ZFNs are undergoing clinical trials. However, many ZFNs display dose-dependent...
ORGANISM(S): Danio rerio 
2010-08-25 | E-GEOD-23762 | biostudies-arrayexpress
GenomicsGenomic targets of the KRAB and scan domain-containing zinc finger protein 263 (ZNF263).
Half of all human transcription factors use C2H2 zinc finger domains to specify site-specific DNA binding and yet very little is known about their role in gene regulation. Based on in vitro studies, a zinc finger code has been developed that predicts a binding motif for a particular zinc finger fact...
ORGANISM(S): Homo sapiens 
2009-12-03 | E-GEOD-19235 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of Arabidopsis transgenic seedlings overexpressing MINI ZINC FINGER 1 (MIF1)
Phytohormones play crucial roles in regulating many aspects of plant development. Although much has been learned about the effects of individual hormones, cross-talk between and integration of different hormonal signals are still not well understood. We present a study of MINI ZINC FINGER 1 (MIF1), ...
ORGANISM(S): Arabidopsis thaliana 
2008-11-13 | E-GEOD-12729 | biostudies-arrayexpress
GenomicsSelective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros (ChIP-seq: Thymocytes)
The C2H2 zinc finger is the most prevalent DNA-binding motif in the mammalian proteome, with DNA-binding domains usually containing more tandem fingers than are needed for stable sequence-specific DNA recognition. To examine the reason for the frequent presence of multiple zinc fingers, we generated...
ORGANISM(S): Mus musculus 
2013-09-08 | E-GEOD-33679 | biostudies-arrayexpress
TranscriptomicsSelective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros (RNA-seq: sorted DP thymocytes)
The C2H2 zinc finger is the most prevalent DNA-binding motif in the mammalian proteome, with DNA-binding domains usually containing more tandem fingers than are needed for stable sequence-specific DNA recognition. To examine the reason for the frequent presence of multiple zinc fingers, we generated...
ORGANISM(S): Mus musculus 
2013-09-08 | E-GEOD-47496 | biostudies-arrayexpress
TranscriptomicsGlobal analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants.
Cys2-His2 zinc finger proteins (ZFPs) are the largest group of transcription factors in higher metazoans. A complete characterization of these ZFPs and their associated target sequences is pivotal to fully annotate transcriptional regulatory networks in metazoan genomes. As a first step in this proc...
ORGANISM(S): synthetic construct 
2012-12-06 | E-GEOD-42709 | biostudies-arrayexpress
TranscriptomicsSelective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros (RNA-seq: Thymocytes)
The C2H2 zinc finger is the most prevalent DNA-binding motif in the mammalian proteome, with DNA-binding domains usually containing more tandem fingers than are needed for stable sequence-specific DNA recognition. To examine the reason for the frequent presence of multiple zinc fingers, we generated...
ORGANISM(S): Mus musculus 
2013-09-08 | E-GEOD-32190 | biostudies-arrayexpress
GenomicsGenome-wide binding profiles of an artificial zinc finger protein with or without a KLF3 functional domain
Transcription factors are often regarded as having two distinct components: a DNA binding domain (DBD) to allow binding to the regulatory region of a target gene and a trans-acting functional domain (FD) to modulate gene expression. Recently, it is becoming clear that the DBDs of transcription facto...
ORGANISM(S): Homo sapiens 
2016-01-05 | E-GEOD-69739 | biostudies-arrayexpress
TranscriptomicsHT-SELEX of recombinant C2H2 zinc finger domains of Sall4
To define the sequence preference of SALL4 C2H2 zinc finger domains, we performed SELEX coupled with high-throughput sequencing (HT-SELEX) using the purified SALL4 ZFC1, ZFC2 and ZFC4 domains combined with no protein control experiment.
ORGANISM(S): artificial sequences 
2021-01-05 | E-MTAB-9236 | biostudies-arrayexpress
TranscriptomicsSelective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros (RNA-seq: sorted proB cell Hardy Fractions B and C+C')
The C2H2 zinc finger is the most prevalent DNA-binding motif in the mammalian proteome, with DNA-binding domains usually containing more tandem fingers than are needed for stable sequence-specific DNA recognition. To examine the reason for the frequent presence of multiple zinc fingers, we generated...
ORGANISM(S): Mus musculus 
2013-09-08 | E-GEOD-38842 | biostudies-arrayexpress
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