C11ORF31 Human

What is C11ORF31 and what are its alternative names?

C11ORF31 is a gene that encodes a selenoprotein which contains a selenocysteine (Sec) residue at its active site. This gene is also known by several synonyms including SELENOH, SELH, and C17ORF10, with the protein product being identified as SELH_HUMAN in protein databases . The gene has NCBI Gene ID 280636 and is part of the selenoprotein family, which are proteins containing the rare amino acid selenocysteine.

What is the structural and functional characterization of C11ORF31?

C11ORF31 contains a selenocysteine residue at its active site, which is encoded by the UGA codon (typically a stop codon). The proper translation of UGA as selenocysteine rather than termination is facilitated by a special stem-loop structure in the 3' UTR called the SECIS (selenocysteine insertion sequence) element . While the exact function of C11ORF31 is not fully characterized, as a selenoprotein, it likely contributes to cellular redox regulation and antioxidant defense mechanisms, which are common functions of selenoproteins.

The gene has 3,223 functional associations with biological entities spanning 8 categories extracted from 57 datasets, indicating its involvement in multiple biological processes and potential interactions with various molecular components .

How is selenocysteine incorporation achieved in C11ORF31 expression?

The incorporation of selenocysteine in C11ORF31 occurs through a specialized translation mechanism where the UGA codon, normally a stop signal, is recoded to specify selenocysteine insertion. This recoding requires:

• The presence of the SECIS element in the 3' UTR

• Specific translational machinery including selenocysteine-specific tRNA (tRNA^[Ser]Sec)

• SECIS-binding protein 2 (SBP2)

• Selenocysteine-specific elongation factor (eEFSec)

These components work together to ensure the UGA codon is interpreted as a signal for selenocysteine incorporation rather than translation termination . This mechanism is crucial for experimental designs involving recombinant expression of functional C11ORF31 protein.

What expression patterns does C11ORF31 show in human tissues?

Based on data from the Allen Brain Atlas, C11ORF31 shows expression in both adult and developing human brain tissues . The expression patterns vary across different brain regions, providing insights into potential neurological functions of this selenoprotein.

For researchers studying C11ORF31's potential role in neurodevelopment or neurological disorders, these expression datasets provide valuable baseline information for hypothesis generation and experimental design.

What methodologies can reveal C11ORF31's biological associations?

To investigate C11ORF31's biological associations, researchers can employ multiple approaches:

• Co-expression network analysis: Identify genes with correlated expression patterns across tissues or conditions

• Protein-protein interaction studies: Use techniques like co-immunoprecipitation or proximity labeling

• Functional enrichment analysis: Examine biological pathways enriched among associated genes

• RNA-binding studies: Investigate potential RNA targets if C11ORF31 functions in post-transcriptional regulation

The gene has been noted to have numerous functional associations across molecular profiles, functional terms, chemicals, diseases, and other biological entities , suggesting diverse roles that warrant further investigation.

What are effective methods for quantifying C11ORF31 expression?

Researchers can effectively measure C11ORF31 expression using several complementary techniques:

• Quantitative RT-PCR (qRT-PCR): Design specific primers targeting C11ORF31 mRNA. Normalization to appropriate housekeeping genes like RPLPO is essential for accurate quantification .

• RNA-Seq: For transcriptome-wide analysis, RNA-Seq provides comprehensive expression data. Processing with methods like GCRMA (Robust Multi-array Analysis that accounts for GC content) can normalize and summarize probe-level intensity measurements .

• Western blotting: Protein-level quantification using validated antibodies against C11ORF31/SELENOH.

How can researchers investigate C11ORF31's potential RNA-binding properties?

Recent proteomics studies have identified C11ORF31 in mRNA-bound proteome analyses, suggesting potential RNA-binding activities . To investigate these properties, researchers can employ:

• RNA immunoprecipitation (RIP): Pull down C11ORF31-associated RNAs for identification

• Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP): A method mentioned in the proteomics study that successfully validated RNA-binding proteins

• RNA electrophoretic mobility shift assays (EMSA): Confirm direct binding to specific RNA targets

• Structural studies: Identify potential RNA-binding domains within the protein

For reliable results, controls for specificity and validation across multiple methodologies are essential, as demonstrated in the mRNA-bound proteome studies that identified other novel RNA-binding proteins .

How does selenium availability affect C11ORF31 expression and function?

As a selenoprotein, C11ORF31 expression and function are likely influenced by selenium bioavailability. To study this relationship, researchers can:

• Culture cells in media with defined selenium concentrations

• Use selenium-deficient experimental models supplemented with various selenium levels

• Analyze hierarchical regulation among different selenoproteins under limited selenium conditions

• Investigate the efficiency of selenocysteine incorporation using reporter constructs

The insertion of selenocysteine via the SECIS element is selenium-dependent, making C11ORF31 expression potentially sensitive to selenium status . This relationship may have implications for understanding C11ORF31's role in conditions associated with selenium deficiency or supplementation.

What computational approaches can predict C11ORF31 interaction networks?

Computational prediction of C11ORF31 interaction networks can employ:

• Sequence-based prediction: Using conserved motifs to predict protein-protein or protein-RNA interactions

• Structural modeling: Predicting interaction interfaces based on 3D structure

• Co-expression analysis: Identifying genes with correlated expression patterns across tissues/conditions

• Text mining: Extracting relationships from scientific literature

• Network analysis: Integrating multiple data types to build comprehensive interaction networks

These approaches can generate testable hypotheses about C11ORF31's functional interactions, guiding experimental validation efforts.

What evidence connects C11ORF31 to cancer biology?

While direct evidence specifically linking C11ORF31 to cancer is limited in the provided search results, there is an association mentioned between genetic variation in several genes including C11ORF31 and rectal cancer . To further investigate potential cancer connections, researchers can:

• Analyze C11ORF31 expression across cancer types using cancer genomics databases

• Perform functional studies in cancer cell lines using gene editing technologies

• Investigate correlations between C11ORF31 expression/mutations and clinical outcomes

• Examine the role of selenium status in cancer contexts where C11ORF31 may be implicated

The potential connection to rectal cancer suggests this might be a priority area for investigating C11ORF31's role in cancer biology .

How might C11ORF31 be involved in inflammatory conditions?

The search results mention gene expression profiling in peripheral blood mononuclear cells in systemic Juvenile Idiopathic Arthritis (sJIA), suggesting potential involvement in inflammatory pathways . To explore this connection, researchers could:

• Compare C11ORF31 expression between healthy controls and inflammatory disease samples

• Analyze the effect of inflammatory cytokines on C11ORF31 expression

• Investigate whether C11ORF31 modulates inflammatory signaling pathways

• Examine potential interactions between C11ORF31 and known inflammatory mediators

Understanding these relationships could provide insights into C11ORF31's role in inflammatory conditions and potential therapeutic implications.

What are the main technical challenges in studying C11ORF31 and how can they be overcome?

Researchers face several technical challenges when studying C11ORF31:

For expression studies, researchers should consider the methods described for RNA extraction and microarray hybridization to Affymetrix arrays, with appropriate normalization using methods like GCRMA . For proteomics approaches, techniques successfully used to identify RNA-binding proteins in HEK293 cells could be adapted for C11ORF31 studies .

How can researchers validate C11ORF31 function in cellular models?

To validate C11ORF31 function in cellular models, researchers can employ:

• CRISPR-Cas9 gene editing: Generate knockout or knockin cell lines

• RNA interference: Use siRNA or shRNA for transient or stable knockdown

• Overexpression systems: Express wild-type or mutant versions of C11ORF31

• Rescue experiments: Restore function in knockout models with wild-type or mutant constructs

• Reporter assays: Monitor functional readouts related to predicted activities

When working with C11ORF31, it's important to monitor the purity and activation status of isolated cells, as demonstrated in neutrophil studies using flow cytometric analysis with surface markers like CD11b/Mac-1 and CD16 .

What emerging technologies could advance understanding of C11ORF31?

Several emerging technologies could significantly advance C11ORF31 research:

• Single-cell transcriptomics: Reveal cell-type specific expression patterns

• Spatial transcriptomics: Map expression across tissues with spatial resolution

• CRISPR screens: Identify genetic interactions on a genome-wide scale

• Cryo-EM structure determination: Resolve high-resolution protein structure

• Proteomics approaches: Similar to those used in mRNA-bound proteome studies

These technologies could help resolve current knowledge gaps regarding C11ORF31's tissue-specific functions, interaction partners, and structural properties, providing a more comprehensive understanding of this selenoprotein.

What are priority research questions for advancing C11ORF31 knowledge?

Based on current understanding, priority research questions include:

• What is the three-dimensional structure of C11ORF31 and how does the selenocysteine residue contribute to its function?

• What are the direct RNA and/or protein interaction partners of C11ORF31?

• How is C11ORF31 expression regulated across different tissues and developmental stages?

• What are the phenotypic consequences of C11ORF31 deficiency or mutation?

• How does C11ORF31 contribute to selenium's biological effects and health implications?

Addressing these questions would significantly advance understanding of C11ORF31's biological roles and potential therapeutic relevance.