Table 1.
A summarized ChIP-seq research findings highlighting the kind of research and type of antibody used.
| Application | Findings | Antibody Type | Refernce |
|---|---|---|---|
| Abiotic factor | Abscisic acid stress (ASR5) a TF binds Sensitive To Aluminum Rhizotoxicity 1 (STAR1) promoter in other to positively response against Aluminum stress in rice. | Anti-ASR5 | Arenhart et al. (2014) [145] |
| Developmental + immunity | ROS and defense responsive genes were repressed by HBI1 indicating defense function of HBI1 and also indirectly plays a role in repressing growth through activation of growth-inhibiting HLH genes. HBI1 was also learned to bind to positive activators brassinosteroids function. | Anti-YFP | Fan et al. (2014) [112] |
| Genetics | In genetic imprinting, some subsets of genes are expressed according to their parental origin. Paternally expressed genes (PEGs) were associated to maternal-specific H3K27me3. | Anti-H3K27me3 | Zhang et al. (2014) [146] |
| Abiotic + developmental | Abscisic, Stress, Ripening (ASR1) from tomato is upregulated in drought stress which acts primarily in the cell wall. | Anti-ASR1 | Ricardi et al. (2014) [134] |
| Developmental | SQUAMOSA Promoter Binding Protein-Like3 (SPL3) bind GTAC motif of phosphate starvation responsive gene promoters like PLDZ2, miR399f, and Pht1;5. | Anti-HA | Lei et al. (2016) [147] |
| Developmental | Combinatorial action affect MADS-box transcription factors FLC and SVP in flowering shows gibberellins’ processing genes. | Anti-GFP | Mateos et al. (2015) [137] |
| Genetics | In circadian clock of Maize hybrids, expression of morning-phased genes from binding with ZmCCA1 encourages growth vigor and photosynthesis. | Anti-CCA1 | Ko et al. (2016) [110] |
| Photosynthesis | Discovers E-box variant binding motif for Phytochrome interacting factor 4/5 (PIF4 and PIF5) in Cryptochromes (CRYs) during exposure to low blue light and CRY2 association with PIF4/5. | Anti-HA | Pedmale et al. (2016) [148] |
| Cellular | Shows chromatin domain organization at the nuclei periphery of Arabidopsis. The domain is a clear translation of a repressed environment that contains jumping genes, heterochromatic marks and silenced coding genes. | Anti-GFP | Bi et al. (2017) [149] |
| Immunity | Using both ChIP-seq and RNA-seq, 655 MYC2 binding were identified in response to Jasmonic acid genes. Also found MYC2 TFs that function in late defense stage. | Anti-GFP | Du et al. (2017) [40] |
| Immunity | After flagellin (flg22) treatment, HD2B targets chromatin were hyperacetylated responsible in plant immune defense and phosphorylation while hypoacetylated marks function in metabolic regulation, plastid organization, and chloroplast. | Anti-GFP | Latrasse et al. (2017) [133] |
| Biochemical | A zinc finger TF of rice ZFP36 inhibits ROS production by binding to ascorbate peroxidase known to have specificity to hydrogen peroxide. | Anti-ZFP36 | Huang et al. (2018) [150] |
| Developmental | Maize GIF in leaves and stems promotes meristematic determinacy and shoot architecture. ChIP-seq has found several GIF1 targets including mostly some transcriptional regulators like UB3, ZMPLATZ5, ZMARR7, bHLH and MYB family members. | Anti-GFP | Zhang et al. (2018) [114] |
| Developmental | FRUITFULL (FUL), a TF that directly repressed APETALA2 expression promotes meristem arrest and maintains the sequential expression of meristem maintenance factor WUSCHEL. | Anti-GFP | Balanzà et al. (2018) [151] |
| Abiotic factor | bZIP10 found to be active in Zinc regulation in Brachypodium which relate to oxidative stress and a motif homologous to Arabidopsis was found TGDCGACA. | Anti-GFP | Martin et al. (2018) [152] |
| Abiotic factor | Growth-Regulating Factor 4 (GRF4) TF co-interacts with growth inhibition regulator DELLA to regulate carbon, nitrogen metabolism and growth. | Anti-FLAG | Li et al. (2018) [153] |
| Abiotic factor | Rice OsTF1L mapped drought related stress and lignin biosynthesis genes. | Anti-MYC and anti-RNA Pol II | Bang et al. (2019) [154] |
| Epigenetics | Genome-wide ADCP1 is linked with chromosome enrichment site (pericentrome) and co-localization with H3K9me2. | Anti-GFP | Zhao et al. (2019) [155] |
| General | GmBZL3 is a brassinesteroids signaling molecule cross talking with many pathways like disease-related, immunity response pathways and hormone signaling. | GmBZL3 antibody | Song et al. (2019) [156] |
| Developmental | A Leucine zipper domain TF FD plays a crucial role in floral transition. | Anti-GFP | Collani et al. (2019) [157] |
| General | Found new Oryza VIP1 response element (OVRE) cis-element in abiotic and biotic responses. | Anti-FLAG | Liu et al. (2019) [39] |