Table 3.
AUF-1 RIP-Seq-derived gene targets expressed as DEGS in COPD subjects vs smoker controls in both GSE 5058 and in RNAseq lung biopsies datasets (see Figure 8A ; full AUF-1 Rip Seq-derived gene target lists in Tables S4, S5 ).
| Gene Acronym | Gene Full name | Functions of encoded protein | Refs |
|---|---|---|---|
| BMPR2 | Bone morphogenetic protein receptor type 2 | Gene mutations are the main genetic cause of pulmonary arterial hypertension. BMPR2 signaling is anti-inflammatory in vascular endothelium. Genetic factor involved in the development of COPD. Expression is decreased by exposure to cigarette smoke in lung tissue samples. |
(122–126) |
| BPTF | Bromodomain PHD Finger Transcription Factor | Facilitates access to DNA during DNA-templated processes such as DNA replication, transcription, and repair. | (127, 128) |
| CEBPZ | CCAAT Enhancer Binding Protein Zeta | DNA-binding as transcriptional activator, regulates the heat-shock protein 70 (HSP70) promoter. RNA binding. |
(129, 130) |
| CHD1 | Chromodomain Helicase DNA Binding Protein 1 | ATP-dependent helicase Involved in transcription-related chromatin-remodeling. Associated with histone deacetylase (HDAC) activity. Targeted disruption of the CHD1 gene in human cells leads to a defect in early double-strand break (DSB) repair via homologous recombination (HR). Modulates the efficiency of pre-mRNA splicing in part through physical bridging of spliceosomal components to H3K4me3. |
(131–134) |
| DDHD1 | DDHD Domain Containing 1 | Phospholipase required for the organization of the endoplasmic reticulum exit sites (ERES), also known as transitional endoplasmic reticulum (tER). | (135) |
| DHX36 | DEAH-Box Helicase 36 | ATP-dependent DNA/RNA helicase that unwinds G-quadruplex (G4) structures. Plays a role in genomic integrity. Plays a role in transcriptional regulation. Plays a role in post-transcriptional regulation. Binds also to ARE sequences present in several mRNAs mediating exosome-mediated 3’-5’ mRNA degradation. DHX36 regulates transcription, genomic stability, telomere maintenance, translation and RNA metabolism. |
(136–143) |
| DOCK1 | Dedicator Of Cytokinesis 1 | Involved in cytoskeletal rearrangements required for phagocytosis of apoptotic cells and cell motility. | (144) |
| FBXO11 | F-Box Protein 11 | Substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. | (145) |
| KIAA1109 | as BLTP1, Bridge-Like Lipid Transfer Protein Family Member 1 | Plays a role in endosomal trafficking and endosome recycling. Involved in the actin cytoskeleton and cilia structural dynamics. Acts as regulator of phagocytosis. | (146, 147) |
| KPNB1 | Karyopherin Subunit Beta 1 | Functions in nuclear protein import. Gene Ontology (GO) annotations related to this gene include RNA binding and enzyme binding. | (148) |
| LPP | LIM Domain Containing Preferred Translocation Partner In Lipoma | Localizes to the cell periphery in focal adhesions and may be involved in cell-cell adhesion and cell motility. Shuttles through the nucleus and may function as a transcriptional co-activator. | (149) |
| MACF1 | Microtubule Actin Crosslinking Factor 1 | F-actin-binding protein which plays a role in cross-linking actin to other cytoskeletal proteins and binds to microtubules. Plays a key role in wound healing and epidermal cell migration (By similarity). |
(150, 151) |
| MYO6 | Myosin VI | A reverse-direction motor protein that moves towards the minus-end of actin filaments. Functions in multiple intracellular processes such as vesicular membrane trafficking and cell migration. Required for the structural integrity of the Golgi apparatus via the p53-dependent pro-survival pathway. |
(152, 153) |
| NEU3 | Neuraminidase 3 | Exo-alpha-sialidase. Plays a role in the regulation of transmembrane signaling through the modulation of ganglioside content of the lipid bilayer and by direct interaction with signaling receptors, such as EGFR. Desialylates EGFR and activates downstream signaling in proliferating cells. | (154, 155) |
| PBRM1 | Polybromo 1 | Component of ATP-dependent chromatin remodeling complex involved in transcriptional regulation of select genes by alteration of DNA-nucleosome topology). Acts as a negative regulator of cell proliferation. |
(156, 157) |
| PSMD12 | Proteasome 26S Subunit, Non-ATPase 12 | Component of the 26S proteasome, multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. | (158) |
| RANBP2 | RAN Binding Protein 2 | A component of the nuclear pore complex, plays a role in facilitation of protein import and export, sumoylation of protein cargoes, intracellular trafficking, and energy maintenance. | (159) |
| SETX | Senataxin | Probable RNA/DNA helicase involved in diverse aspects of RNA metabolism and genomic integrity. Involved in DNA double-strand breaks damage response generated by oxidative stress. In association with RRP45, targets the RNA exosome complex to sites of transcription-induced DNA damage. May be involved in telomeric stability through the regulation of telomere repeat-containing RNA (TERRA) transcription. Contributes to the mRNA splicing efficiency and splice site selection. |
(160–163) |
| SF3A2 | Splicing Factor 3a Subunit 2 | Involved in pre-mRNA splicing as a component of pre-catalytic spliceosome ‘B’ complexes. | (164–166) |
| SMC3 | Structural Maintenance Of Chromosomes 3 | Central component of cohesin, a complex required for chromosome cohesion during the cell cycle. Cohesion is coupled to DNA replication and is involved in DNA repair. |
(167, 168) |
| SON | SON DNA And RNA Binding Protein | DNA/RNA-binding protein that acts as mRNA splicing cofactor. Specifically promotes splicing of many cell-cycle and DNA-repair transcripts. |
(169, 170) |