# RPAP2

## Overview
RPAP2, or RNA polymerase II associated protein 2, is a gene that encodes the protein RNA polymerase II associated protein 2, which is integral to the transcription machinery of eukaryotic cells. The RPAP2 protein plays a critical role in the transcription and processing of small nuclear RNA (snRNA) genes by interacting with the phosphorylated C-terminal domain (CTD) of RNA polymerase II. This interaction is crucial for the recruitment of the Integrator complex, essential for the 3' end maturation of snRNAs. Additionally, RPAP2 exhibits phosphatase activity and is involved in the transcription regulation of various protein-coding genes, highlighting its multifaceted role in gene expression regulation and transcription machinery stability (Egloff2012Ser7; Wani2014Human).

## Structure
The molecular structure of RPAP2 (RNA polymerase II associated protein 2) has been characterized through cryo-electron microscopy (cryo-EM) studies. The RPAP2 protein includes a highly conserved N-terminal domain that plays a crucial role in binding between the jaw domains of the RNA Polymerase II subunits RPB1 and RPB5. This domain is composed of residues 48-155, which are confidently modeled, including side chains. The structure of this domain features α-helices and insertion β-strands, with the insertion (residues 116-128) forming two β-strands, a feature conserved from Drosophila to humans but absent in yeast, indicating a metazoan-specific adaptation (Fianu2021Cryo-EM).

The interaction of RPAP2 with RPB5 involves helices α₁ and α₃ of RPAP2 and helices α₅ and α₆ of RPB5, facilitated by hydrophobic, ionic, and hydrogen bonding interactions. Specific residues such as L59, L66, I96, E63, D92, D89, and E93 in RPAP2 interact with corresponding residues in RPB5 through van der Waals contacts, salt bridges, and hydrogen bonds (Fianu2021Cryo-EM).

The C-terminal region of RPAP2, although not involved in the observed structural interactions detailed in the cryo-EM study, might interact with Pol II under certain conditions and possibly engage with hyperphosphorylated Pol II via proteins RPRD1A and RPRD1B, influencing the dephosphorylation of the Pol II CTD (Fianu2021Cryo-EM). However, no detailed structural information is available for the C-terminal region or for any post-translational modifications, prominent folds, or splice variant isoforms of RPAP2.

## Function
RPAP2 (RNA polymerase II associated protein 2) plays a crucial role in the transcription and processing of small nuclear RNA (snRNA) genes by interacting with the phosphorylated C-terminal domain (CTD) of RNA polymerase II (Pol II). Specifically, RPAP2 recognizes the phosphorylated Ser7 on the CTD, which is essential for the recruitment of the Integrator complex, crucial for the 3' end maturation of snRNAs (Egloff2012Ser7). RPAP2 also exhibits phosphatase activity, targeting the Ser5 phosphorylation on the CTD, thereby influencing the transcription cycle and the expression of snRNA genes (Egloff2012Ser7).

Beyond snRNA genes, RPAP2 is involved in the transcription regulation of protein-coding genes such as MYC and GAPDH. It is recruited to the coding and 3' regions of these genes, playing a role in the 3'-end formation of pre-mRNAs, which is vital for proper mRNA processing (Wani2014Human).

Additionally, RPAP2 is implicated in the nuclear import of Pol II, essential for the transcription of protein-coding genes. Its interaction with the Pol II subunit Rpb6 is significant for the assembly of Pol II, highlighting its role in maintaining the functionality of the transcription machinery within the cell (Wani2014Human). This multifaceted involvement of RPAP2 underscores its importance in both the regulation of gene expression and the stability of the transcription machinery in human cells.

## Clinical Significance
RPAP2, through its derivative circular RNA circRPAP2, plays a significant role in the pathogenesis of breast cancer (BC). Research indicates that circRPAP2 is notably downregulated in BC tissues and cell lines compared to normal counterparts. This downregulation correlates with more aggressive clinical features, including axillary lymph node metastasis and higher TNM stages, suggesting its potential as a biomarker for BC prognosis (Yu2022CircRPAP2).

The tumor-suppressive function of circRPAP2 in BC is mediated by its interaction with the oncoprotein SRSF1. This interaction disrupts the normal splicing activity of SRSF1 on the PTK2 pre-mRNA, a gene implicated in oncogenic pathways through its roles in cell proliferation and migration. By binding to SRSF1, circRPAP2 competitively inhibits the formation of PTK2 mRNA and protein, thereby hindering BC cell proliferation and migration. This mechanism highlights the therapeutic potential of targeting circRPAP2-SRSF1 interactions in BC treatment strategies (Yu2022CircRPAP2).

Overall, the alterations in the expression and function of circRPAP2 derived from RPAP2 significantly contribute to the progression and severity of breast cancer, underscoring the clinical importance of this gene and its products in oncology.

## Interactions
RPAP2 interacts with various components of the transcription machinery, notably with RNA Polymerase II (Pol II) and the Integrator complex. RPAP2 has been shown to strongly interact with Rpb1, the largest subunit of Pol II, indicating its role in transcriptionally active complexes. It also interacts with several subunits of the Integrator complex, including Int1, Int4, Int5, Int6, and Int7, which are involved in snRNA 3' end formation. However, RPAP2 does not stably interact with the catalytic subunit of the Integrator complex, Int11, suggesting selective interactions within this complex (Egloff2012Ser7).

Further studies have demonstrated that RPAP2 exists in at least two distinct complexes: a large complex containing Pol II subunits and a smaller complex devoid of Rpb1 but containing Integrator subunits and other proteins such as members of the chaperonin-containing TCP1 complex, XAB1, and GPN3. The DUF408 domain of RPAP2, particularly its cysteine-rich motif, is essential for binding to both Pol II and the Integrator complex (Egloff2012Ser7).

Additionally, RPAP2 directly interacts with the RNA polymerase II subunit Rpb6 and has a significant role in the assembly of the Pol II complex and its nuclear import. This interaction is facilitated by the C-terminus of RPAP2, which is crucial for binding to Rpb6 (Wani2014Human). RPAP2 also exhibits phosphatase activity specific to the phosphorylated Ser5 in the C-terminal domain (CTD) of Pol II, crucial for the regulation of Pol II activity during transcription (Wani2014Human).


## References


[1. (Fianu2021Cryo-EM) Isaac Fianu, Christian Dienemann, Shintaro Aibara, Sandra Schilbach, and Patrick Cramer. Cryo-em structure of mammalian rna polymerase ii in complex with human rpap2. Communications Biology, May 2021. URL: http://dx.doi.org/10.1038/s42003-021-02088-z, doi:10.1038/s42003-021-02088-z. (15 citations) 10.1038/s42003-021-02088-z](https://doi.org/10.1038/s42003-021-02088-z)

[2. (Egloff2012Ser7) Sylvain Egloff, Justyna Zaborowska, Clélia Laitem, Tamás Kiss, and Shona Murphy. Ser7 phosphorylation of the ctd recruits the rpap2 ser5 phosphatase to snrna genes. Molecular Cell, 45(1):111–122, January 2012. URL: http://dx.doi.org/10.1016/j.molcel.2011.11.006, doi:10.1016/j.molcel.2011.11.006. (162 citations) 10.1016/j.molcel.2011.11.006](https://doi.org/10.1016/j.molcel.2011.11.006)

[3. (Yu2022CircRPAP2) Yunhe Yu and Lin Fang. Circrpap2 regulates the alternative splicing of ptk2 by binding to srsf1 in breast cancer. Cell Death Discovery, April 2022. URL: http://dx.doi.org/10.1038/s41420-022-00965-y, doi:10.1038/s41420-022-00965-y. (17 citations) 10.1038/s41420-022-00965-y](https://doi.org/10.1038/s41420-022-00965-y)

[4. (Wani2014Human) Shotaro Wani, Yutaka Hirose, and Yoshiaki Ohkuma. Human rna polymerase ii-associated protein 2 (rpap2) interacts directly with the rna polymerase ii subunit rpb6 and participates in pre-mrna 3'-end formation. Drug Discoveries & Therapeutics, 8(6):255–261, 2014. URL: http://dx.doi.org/10.5582/ddt.2014.01044, doi:10.5582/ddt.2014.01044. (12 citations) 10.5582/ddt.2014.01044](https://doi.org/10.5582/ddt.2014.01044)