Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond

Mundade, Rasika; Özer, Hatice Gülçin; Wang, Han; Prabhu, Lakshmi; Lü, Tao

doi:10.4161/15384101.2014.949201

Cited by 124 publications

(86 citation statements)

References 45 publications

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“…Second, we used chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) to conduct a genome-wide mapping of HDA101 binding sites in maize seed at an early developmental stage. Although genome-wide mapping has been employed to investigate HDAC function in yeast and mammals Wang et al, 2002;Robert et al, 2004;Wang et al, 2009;Mundade et al, 2014), it has not previously been used plants. Our results indicate that HDA101 is mainly targeted to genes with high and intermediate expression levels.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Mapping of Targets of Maize Histone Deacetylase HDA101 Reveals Its Function and Regulatory Mechanism during Seed Development

et al. 2016

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Histone deacetylases (HDACs) regulate histone acetylation levels by removing the acetyl group from lysine residues. The maize (Zea mays) HDAC HDA101 influences several aspects of development, including kernel size; however, the molecular mechanism by which HDA101 affects kernel development remains unknown. In this study, we find that HDA101 regulates the expression of transfer cell-specific genes, suggesting that their misregulation may be associated with the defects in differentiation of endosperm transfer cells and smaller kernels observed in hda101 mutants. To investigate HDA101 function during the early stages of seed development, we performed genome-wide mapping of HDA101 binding sites. We observed that, like mammalian HDACs, HDA101 mainly targets highly and intermediately expressed genes. Although loss of HDA101 can induce histone hyperacetylation of its direct targets, this often does not involve variation in transcript levels. A small subset of inactive genes that must be negatively regulated during kernel development is also targeted by HDA101 and its loss leads to hyperacetylation and increased expression of these inactive genes. Finally, we report that HDA101 interacts with members of different chromatin remodeling complexes, such as NFC103/MSI1 and SNL1/SIN3-like protein corepressors. Taken together, our results reveal a complex genetic network regulated by HDA101 during seed development and provide insight into the different mechanisms of HDA101-mediated regulation of transcriptionally active and inactive genes.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Mapping of Targets of Maize Histone Deacetylase HDA101 Reveals Its Function and Regulatory Mechanism during Seed Development

et al. 2016

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“…Apart from identifying interactions between specific proteins and DNA in living cells, the localization of proteins at a specific genomic region can also be determined. ChIP assays can further be combined with sequencing (ChIP-Seq) to allow for a genome-wide analysis of DNA-protein interactions and, thus, the identification of specific DNA-binding sites and direct target genes of individual transcription factors, 7,8 such as c-Jun. Recent studies have indicated that the AP-1 family member c-Jun is a main regulator of melanoma progression 6,9,10 and that it acts by up-regulating pro-oncogenic genes and down-regulating anti-oncogenic target genes, whose activation promotes the malignant phenotype.…”

Section: Introductionmentioning

confidence: 99%

Specific c-Jun target genes in malignant melanoma

Schummer

Kuphal

Vardimon

et al. 2016

Cancer Biology & Therapy

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“…This can be used for studying interactions between specific proteins and DNA in the cell and determining their localization on a specific genomic locus. In recent years, the combination of ChIP Thauera butanivorans 1-Butanol [90] with the second generation DNA-sequencing technology (ChIP-seq) allows precise genomic functional assay, especially in genome-wide mapping of transcription factor binding sites, the revelation of underlying molecular mechanisms of differential gene regulation governed by specific transcription factors, and the identification of epigenetic marks [17]. For the analysis of ChIP-seq data, a novel approach called ChIPModule has been developed to discover systematically transcription factors and their cofactors [18].…”

Section: Dna-level Bioswitchesmentioning

confidence: 99%

Engineering Biomolecular Switches for Dynamic Metabolic Control

Zhou

Zeng

2016

Synthetic Biology – Metabolic Engineering

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Living organisms have been exploited as production hosts for a large variety of compounds. To improve the efficiency of bioproduction, metabolic pathways in an organism are usually manipulated by various genetic modifications. However, bottlenecks during the conversion of substrate to a desired product may result from cellular regulations at different levels. Dynamic regulation of metabolic pathways according to the need of cultivation process is therefore essential for developing effective bioprocesses, but represents a major challenge in metabolic engineering and synthetic biology. To this end, switchable biomolecules which can sense the intracellular concentrations of metabolites with different response types and dynamic ranges are of great interest. This chapter summarizes recent progress in the development of biomolecular switches and their applications for improvement of bioproduction via dynamic control of metabolic fluxes. Further studies of bioswitches and their applications in industrial strain development are also discussed.

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Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond

Cited by 124 publications

References 45 publications

Genome-Wide Mapping of Targets of Maize Histone Deacetylase HDA101 Reveals Its Function and Regulatory Mechanism during Seed Development

Genome-Wide Mapping of Targets of Maize Histone Deacetylase HDA101 Reveals Its Function and Regulatory Mechanism during Seed Development

Specific c-Jun target genes in malignant melanoma

Engineering Biomolecular Switches for Dynamic Metabolic Control

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