BEND3 interacts with various chromatin modifiers, including the subunits of the NuRD complex
[8], suggesting its role in global gene regulation. The NuRD complex modulates the chromatin structure at the bivalent and poised rRNA genes
[17] and various other genes in the ESCs
[6][18]. It plays significant roles in processes like neural stem cell reprogramming into iPSC
[19], pericentric heterochromatin formation
[20], the maintenance of pluripotency
[17][21][22][23], transcription repression
[24][25], and S-phase progression
[8]. The NuRD complex comprises various subunits such as CHD3/4, HDAC1/2, MBD2/3, MTA1/2/3, and retinoblastoma-binding protein (RBBP4/7). Other subunits such as LSD1 and GATAD2A/B have also been reported to associate with this complex in certain types of cells. Several subunits of the NuRD complex have implications in cancer development and progression. Its components, including MTA1, HDACs, Sal4, and CHD4, are expressed in different cancer types and corroborate the tumor progression and poor prognosis
[11][26]. MTA1 is reported to be overexpressed in a wide range of cancer types and this overexpression correlates with tumor grade, poor prognosis, and invasion status of the tumor
[11]. MTA1 acts as a downstream effector molecule of the Myc oncogene
[27]. The NuRD complex is reported to interact with various oncogenic transcription factors and mediate the transcription repression of many target genes. In diffuse large B cell lymphoma (DLBCL), MTA3 associates with an oncogenic transcription repressor, BCL6
[28], which plays a significant role in the development of a significant proportion of DLBCL
[29]. BCl6 requires MTA3 to transcriptionally repress normal plasma cell differentiation
[28]. MTA proteins also interact with the transcriptional repressor BCL11B in leukemia and lymphoma cell lines. BCL11B has an indispensable role in early T cell development
[11]. In breast cancer cells, a transcription factor, TWIST, causes the recruitment of MTA2 containing the NuRD complex at the CDH1 (E-Cadherin) promoter so as to repress E-Cadherin and promote the epithelial to mesenchymal transition (EMT), which is a hallmark of cancer, while MTA3 of the NuRD complex has been reported to cause transcription repression of SNAIL, thus inhibiting EMT in breast cancer cells. Thus, the complex can act as either a promoter or inhibitor of EMT depending upon the context of cells
[11]. An oncogenic chimeric protein, PML-RARα, also recruits the NuRD complex, which in turn recruit other epigenetic regulators to cause transcriptional repression, leading to the impairment of cellular differentiation in human acute promyelocytic leukemias
[30]. It is speculated that transcription factors recruit this complex to the promoters of the genes implicated in cancer
[26]. Nine subunits of the NuRD complex are reported to be upregulated in hepatocellular carcinoma
[26]. LSD1, part of the complex, regulates metastasis in breast carcinoma and is found to be under-expressed in breast cancers
[31].
HDACs are important players in tumorigenesis and tumor progression and are overexpressed in several different kinds of malignancies including breast, colorectal, liver, pancreatic, ovarian, cervical, prostate, renal, bladder, melanoma, and certain blood cancers
[32]. The BEN domain might act as an adapter in the process of chromatin modification by HDACs
[15]. However, MTA1 and HDACs of the NuRD complex represent potential therapeutic targets for cancer chemoprevention. BEND3 also interacts with another NuRD complex transcription factor, Sal4, which is required to maintain the stemness and pluripotency of embryonic stem cells
[9]. Sal4 expression is mis-regulated in various hematological as well as solid malignancies
[33]. It plays a significant role in regulating various genes including apoptotic genes; cell-surface marker (EpCAM); EMT-related genes such as TWIST1, SNAI1, VIM, ZEB, E-Cadherin, etc.; and epigenetic modifiers such as DNMT1 and LSD1
[33]. Thus, it can be speculated that via its interaction with these subunits, BEND3 could aid in tumorigenesis mediated by the NuRD complex. Interestingly, BEND3 showed weak interaction with HDAC2 in our docking screen. The docking of BD4 was performed with HADDOCK 2.4 software and results are shown in
Figure 1.
Figure 1. Protein–protein interaction prediction through HADDOCK 2.4 Docking software
[34][35]. Interaction of BEN4 domain of BEND3 (Green) with HDAC2 (Cyan), Full protein structure along with interaction interface, the interaction area is zoomed in the insets. Protein structure with highlighted interacting amino acid. Interactions are shown by dotted lines. Amino acid labels color coded to match the contributing partner. Main chain shown only in cases it is involved in the proposed interaction.
BEND3 also interacts and stabilizes the nuclear remodeling complex (NoRC) by inhibiting the ubiquitination of TTF-1-interacting protein 5 (Tip5). BEND3 has two SUMOylation sites at K20 and K512 which are essential for NoRC stability. SUMOylated BEND3 interacts with the ubiquitin-specific protease 21 (USP21) deubiquitinase and prevents the ubiquitination of Tip5. Tip5 helps in the recruitment of this complex to the rDNA promoters via the TTF1 transcription factor. In the SUMOylation-deficient mutant of BEND3, USP21 was found to be destabilized, indicating the importance of BEND3 SUMOylation for its interaction with USP21. In the absence of BEND3, the interaction of Tip5 with the rDNA promoter along with the methylation of rDNA was severely decreased. Most of the rDNA repeats were kept epigenetically silent by the NoRC through the recruitment of DNMTs and histone-modifying enzymes
[7]. Being a highly repetitive, heavily methylated, and actively transcribed region, the rDNA locus is very prone to genomic instability, which could ultimately lead to cancer development
[36]. The rDNA locus is also known to exhibit notable contraction and expansion followed by the unequal exchange of sister chromatids
[36]. Repeated expansion of this locus has been detected in colon and lung cancers
[37], and may result in increased ribosome production in tumor cells
[38]. Myc oncogene also increases rRNA synthesis by increasing the expression of RNA polymerase I, along with other transcription factors
[36]. Several cancers show hypomethylation of the promoter region, while hypermethylation was observed in 28S and 5.8S rRNA coding regions and some spacer regions
[36]. The loss of BEND3 results in increased H3K4me3 and decreased DNA methylation at the rDNA gene promoters with an increase in the levels of pre-rRNA, whereas its overexpression results in decreased H3K4me3 and H4Ac (pan) and increased H4K20me3 and H3K27me3 at rDNA promoters
[7].