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Zinc finger protein SALL4 functions through an AT-rich motif to regulate gene expression

ABSTRACT: Zinc finger protein SALL4 functions through an AT-rich motif to regulate gene expression

PROVIDER: PRJNA562266 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10022374_1.fastq.gz	Fastqsanger.gz
	SRR10022374_2.fastq.gz	Fastqsanger.gz
	SRR10022375_1.fastq.gz	Fastqsanger.gz
	SRR10022375_2.fastq.gz	Fastqsanger.gz
	SRR10022376_1.fastq.gz	Fastqsanger.gz

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Zinc finger protein SALL4 functions through an AT-rich motif to regulate gene expression

Project description:The zinc finger transcription factor SALL4 is highly expressed in embryonic stem cells, down-regulated in most adult tissues, but reactivated in many aggressive cancers. This unique expression pattern makes SALL4 an attractive target for designing therapeutic strategies. However, whether SALL4 binds DNA directly to regulate gene expression is unclear and many of its targets in cancer cells remain elusive. Here, through an unbiased screen of protein binding microarray (PBM) and Cleavage Under Targets and Release Using Nuclease (CUT&RUN) experiments, we identified and validated the DNA binding domain of SALL4 and its consensus binding sequence. Combined with RNA-seq analyses after SALL4 knockdown, we discovered hundreds of new SALL4 target genes that it directly regulates in aggressive liver cancer cells, including genes encoding a family of Histone 3 Lysine 9-specific Demethylases (KDMs). Taken together, these results elucidated the mechanism of SALL4 DNA binding and revealed novel pathways and molecules to target in SALL4-dependent tumors.

2021-01-13 | GSE136332 | GEO

HT-SELEX of recombinant C2H2 zinc finger domains of Sall4

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HT-SELEX of recombinant C2H2 zinc finger domains of Sall4

Project description: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. We re-sequenced the libraries from E-MTAB-9236 with very high coverage to estimate the minimum number of reads required per sample for accurate results.

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HT-SELEX of recombinant C2H2 zinc finger domains of Sall4

Project description:HT-SELEX of recombinant C2H2 zinc finger domains of Sall4

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HT-SELEX of recombinant C2H2 zinc finger domain of Sall4

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RNA-Seq of Sall4 mutants in mouse embryonic stem cells

Project description:Sall4 is a stem cell factor which is important for embryogenesis. We have genetically modified Sall4 in mouse embryonic stem cells to access the transcriptional changes. There are three different genetic modifications for the ES cells in the form of Sall4 Knockout (KO), Sall4 Zinc Finger Cluster 4 Mutation (ZFC4mut) and Sall4 Zinc Finger Cluster 1-2 Deletion (ZFC1-2Δ) respectively that we have considered for our study.

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ChIP-Seq of ES-E14 mouse embryonic stem cells investigating changes in Sall4

Project description:Sall4 is a stem cell factor which is important for embryogenesis. We have genetically modified Sall4 in mouse embryonic stem cells to access the preference of Sall4 binding site. There are three different genetic modifications for the ES cells in the form of Sall4 Knockout (KO), Sall4 Zinc Finger Cluster 4 Mutation (ZFC4mut) and Sall4 Zinc Finger Cluster 1-2 Deletion (ZFC1-2Δ) respectively that we have considered for our study.

2021-01-05 | E-MTAB-9197 | biostudies-arrayexpress

RNA-Seq of mouse embryonic stem cells in response to changes in Sall4

Project description:Sall4 is a stem cell factor which is important for embryogenesis. We have genetically modified Sall4 in mouse embryonic stem cells to access the transcriptional changes. There are three different genetic modifications for the ES cells in the form of Sall4 Knockout (KO), Sall4 Zinc Finger Cluster 4 Mutation (ZFC4mut) and Sall4 Zinc Finger Cluster 4 Deletion (ZFC4Δ) respectively that we have considered for our study.

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BCL11B_AP-MS - The N-terminal CCHC zinc finger motif mediates homodimerization of the transcription factor BCL11B

Project description:This study investigates whether the N-terminal CCHC zinc finger motif is necessary and sufficient for the formation of BCL11B dimers, using fluorescence microscopy and Förster resonance energy transfer-assisted fluorescence-activated cell sorting (FACSFRET). The role of the CCHC motif in homodimer assembly was further investigated using affinity purification followed by mass spectrometry (AP-MS). Functional studies investigated the role of dimerization in the induction of cell cycle arrest and protection against DNA damage-induced apoptosis.

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Zinc Finger Protein SALL4 Functions through an AT-Rich Motif to Regulate Gene Expression.

Project description:The zinc finger transcription factor SALL4 is highly expressed in embryonic stem cells, downregulated in most adult tissues, but reactivated in many aggressive cancers. This unique expression pattern makes SALL4 an attractive therapeutic target. However, whether SALL4 binds DNA directly to regulate gene expression is unclear, and many of its targets in cancer cells remain elusive. Here, through an unbiased screen of protein binding microarray (PBM) and cleavage under targets and release using nuclease (CUT&RUN) experiments, we identify and validate the DNA binding domain of SALL4 and its consensus binding sequence. Combined with RNA sequencing (RNA-seq) analyses after SALL4 knockdown, we discover hundreds of new SALL4 target genes that it directly regulates in aggressive liver cancer cells, including genes encoding a family of histone 3 lysine 9-specific demethylases (KDMs). Taken together, these results elucidate the mechanism of SALL4 DNA binding and reveal pathways and molecules to target in SALL4-dependent tumors.

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