DNAAF8

DNAAF8
Identifiers
AliasesDNAAF8, chromosome 16 open reading frame 71, C16orf71, dynein axonemal assembly factor 8
External IDsGeneCards: DNAAF8
Orthologs
DatabasesNCBI: entry; OMA: entry
SpeciesHumanMouse
Entrez

146562

n/a

Ensembl

ENSG00000166246

n/a

UniProt

Q8IYS4

n/a

RefSeq (mRNA)

NM_139170

n/a

RefSeq (protein)

NP_631909

n/a

Location (UCSC)Chr 16: 4.73 – 4.75 Mbn/a
PubMed search[2]n/a
Wikidata
View/Edit Human

Dynein axonemal assembly factor 8 is a protein which in humans is encoded by the gene DNAAF8 (formerly C16orf71).[3] This gene is involved in the assembly of the outer arms of dyneins, a type of motor protein.[3] The gene is expressed in epithelial tissue of the respiratory system, adipose tissue, and the testes.[4] 1357 bp of the gene are antisense to spliced genes ZNF500 and ANKS3.[5]

Gene

Locus

The gene is located on the short arm of chromosome 16 at 16p13.1.[6] Its genomic sequence begins on the plus strand at 4,734,242 bp and ends at 4,749,396 bp.[3]

A diagram of C16orf71 and nearby genes on human chromosome 16.[7]

mRNA

Alternative splicing

Three different protein encoding transcript variants, or isoforms, have been identified for C16orf71.[8] One non-protein coding transcript variant was identified for the gene.[9]

Name Length (bp) Protein (aa) Mass (kDa) Biotype
Uncharacterized protein C16orf71 (primary assembly)[8] 2716 520 55.7 Protein coding
Uncharacterized protein C16orf71 isoform X2[10] 2324 136 14.6 Protein coding
Uncharacterized protein C16orf71 isoform X3[11] 2435 156 16.8 Protein coding
Uncharacterized protein C16orf71 isoform X1[12] 2562 537 57.5 Protein coding
Uncharacterized protein C16orf71 Transcript-003[9] 3705 No protein – Retained intron

Protein

A map indicating the predicted interacting proteins of C16orf71.[13]
Evidence of localization at nuclear speckles of the nucleus, indicated by the green spots where in situ hybridization occurred with the antibody.[14]

General properties

The primary encoded protein consists of 520 amino acid residues, 11 total exons, and is 15.14 kb long, with a molecular weight of approximately 55.68 kDa.[3] The predicted isoelectric point was reported to be 4.81, indicating it is relatively unstable.[15] The gene was reported to be well expressed, at 1.1 times the average gene level.[5]

Composition

Alanine was the most abundant amino acid, contributing to 11.54% of the molecular weight of the protein.[15] Serine was the second most abundant, contributing 10.19% to the overall molecular weight.[15] The average Alanine frequency in vertebrate proteins is approximately 7.4% and the average Serine frequency is approximately 8.1%.[16]

Domains

C16orf71 has one identified domain of unknown function, DUF4701, that is conserved in all mammals and some species of reptiles and birds.[3] DUF4701 spans from amino acid residue 21 to 520 in the protein.[3]

Post-translational modifications

C16orf71 is predicted to undergo multiple post-translational modifications such as phosphorylation, N-glycosylation, and amidation.

Protein interactions

Experimentally proven interactions

Experimentation with C16orf71 has revealed interactions with four other proteins, ARHGAP1, ZNFX1, PLVAP, and MBTPS1.[17] ARHGAP1, ZNFX1, and MBTPS1 are associated with regulation in signaling and metabolism while PLVAP is associated with the formation of small lipid rafts in the plasma membrane of vertebrate endothelial and adipose cells.[13]

Subcellular localization

C16orf71 was observed in nuclear speckles of the nucleus through experimental protocols involving fluorescent in situ hybridization with antibodies.[4] Nuclear speckles, also known as interchromatin granule clusters, are enriched in pre-mRNA splicing factors.[18] These highly dynamic structures are located in interchromatin regions of the nucleoplasm in mammalian cells and have been observed to cycle throughout various nuclear regions and active transcription sites.[18]

Expression

Expression levels of C16orf71 from microarray analysis in obese omental adipose tissue.[19]

Tissue expression pattern

Human expression for the gene has been observed primarily in respiratory epithelial tissue, specifically the trachea, larynx, nasopharynx, and bronchus.[4] C16orf71 is also moderately expressed in adipose tissue and testes.[4]

DNA microarray experimental data

DNA microarray analysis from various experiments provided information on the expression levels of C16orf71 in unique, varying conditions.

The gene appears to have higher levels of expression in the omental adipose tissue of obese subjects compared to non-obese subjects.[19]

Expression levels of C16orf71 in the occurrence of HIF-1 alpha/HIF-2 alpha depletion.[20]
Expression levels of C16orf71 in sperm with teratozoospermia.[21]

C16orf71 was also observed to have decreased expression when there was a depletion of HIF-1 alpha, HIF-2 beta, or both. HIF, or hypoxia-inducible factors, are responsible for the mediation of hypoxia effects within the body.[20] In addition, HIFs promote clotting and restoration of various epithelial tissues and are vital in the development of mammalian embryos, sperm, and ova.[22]

Data from an experiment also indicated noticeably lower expression of the gene in sperm affected with teratozoospermia, a condition where sperm have abnormal morphology affecting the fertility in males, compared to normal sperm.[21]

C16orf71 was observed to be present in all stages of development, with similar levels of expression throughout.[23]

Toxicogenomics experimental data

Three chemicals, bisphenol A, butyraldehyde, and polychlorinated biphenyls, have been experimentally tested with C16orf71 for evidence of interaction.[24]

Bisphenol A is suspected to cause impairment in male reproduction.[25] An experiment utilizing seminiferous tubule culture was conducted to observe the effects on meiosis and potential germ-line abnormalities.[25] Gene expression analysis revealed decrease expression for C16orf71 when exposed to the chemical.[25]

Butyraldehyde has been observed to affect inflammatory responses in bronchial airway tissue on a genetic level.[26] Microarray analysis was used to determine levels of expression in human alveolar epithelial cells after exposure to the compound.[26] Results indicated decreased expression for C16orf71 when exposed to the chemical.[26]

Polychlorinated biphenyl was used in an experiment to determine its effects on external male genital development.[27] Human fetal corpora cavernosa cells were used as the model tissue.[27] Toxicogenomic analysis indicated the chemical affected all genes involved with genitourinary development and revealed lowered expression levels for C16orf71.[27]

Regulation of expression

1357 bp of the gene are antisense to spliced genes ZNF500 and ANKS3.[5]

Predicted transcription factors

Transcription factor[28] Associated functions[28]
Ascl1 (Mammaliam achaete scute homolog 1) B-cell differentiation, maturation, and development

Negative regulation of transcription and apoptosis

Positive regulation of cell cycle and cellular differentiation

Response to hypoxia and epidermal growth factor

Regulation of epithelial cell differentiation

ZNF500 (Zinc finger with KRAB and SCAN domains 3) Cartilage development

Negative regulation of gene expression and cellular senescence

T-cell and stem cell differentiation

Positive regulation of transcription

SMAD4 transcription factor involved in TGF-beta signaling Regulation of apoptosis, T-cell and endothelial cell activation

Endoderm formation and development

Negative regulation of cell growth and death

Response to hypoxia

Thyroid gland development

Tissue morphogenesis

Cysteine-serine-rich nuclear protein 1 TGF-beta induced apoptosis

Regulation of early development and differentiation

Extracellular matrix formation

Homology

Orthologs

Orthologs have been identified in most mammals for which complete genome data is available.[29] C16orf71 and its domain of unknown function, DUF4701, was present in mammals.[29] The most distant orthologs identified were reptilian.[29][30]

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000166246 – Ensembl, May 2017
  2. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  3. ^ a b c d e f "DNAAF8 Gene". www.genecards.org. Retrieved 2016-07-31.
  4. ^ a b c d "Tissue expression of C16orf71 - Summary - The Human Protein Atlas". www.proteinatlas.org. Retrieved 2017-04-23.
  5. ^ a b c Thierry-Mieg D, Thierry-Mieg J. "AceView: Gene:C16orf71, a comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView". www.ncbi.nlm.nih.gov. Retrieved 2017-05-06.
  6. ^ "C16orf71 Symbol Report | HUGO Gene Nomenclature Committee". www.genenames.org. Archived from the original on 2017-04-24. Retrieved 2017-02-19.
  7. ^ "C16orf71 chromosome 16 open reading frame 71 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2017-04-27.
  8. ^ a b "C16orf71 chromosome 16 open reading frame 71 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2017-04-23.
  9. ^ a b "Transcript: C16orf71-003 (ENST00000586256.1) - Summary - Homo sapiens - Ensembl genome browser 88". www.ensembl.org. Retrieved 2017-05-02.
  10. ^ "PREDICTED: Homo sapiens chromosome 16 open reading frame 71 (C16orf71) - Nucleotide - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2017-04-27.
  11. ^ "PREDICTED: Homo sapiens chromosome 16 open reading frame 71 (C16orf71) - Nucleotide - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2017-04-27.
  12. ^ "PREDICTED: Homo sapiens chromosome 16 open reading frame 71 (C16orf71) - Nucleotide - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2017-04-27.
  13. ^ a b "C16orf71 protein (Homo sapiens) - STRING network view". string-db.org. Retrieved 2017-05-05.
  14. ^ "Cell atlas - C16orf71 - The Human Protein Atlas". www.proteinatlas.org. Retrieved 2017-04-27.
  15. ^ a b c "SDSC Biology Workbench". seqtool.sdsc.edu. Archived from the original on 2003-08-11. Retrieved 2017-04-23.
  16. ^ "Amino ACID Frequency". www.tiem.utk.edu. Archived from the original on 2017-04-29. Retrieved 2017-04-30.
  17. ^ Aungier SP, Roche JF, Duffy P, Scully S, Crowe MA (March 2015). "The relationship between activity clusters detected by an automatic activity monitor and endocrine changes during the periestrous period in lactating dairy cows". Journal of Dairy Science. 98 (3): 1666–1684. doi:10.3168/jds.2013-7405. PMID 25529424.
  18. ^ a b Spector DL, Lamond AI (February 2011). "Nuclear speckles". Cold Spring Harbor Perspectives in Biology. 3 (2) a000646. doi:10.1101/cshperspect.a000646. PMC 3039535. PMID 20926517.
  19. ^ a b "GDS3688 / 222089_s_at". www.ncbi.nlm.nih.gov. Retrieved 2017-05-06.
  20. ^ a b "GDS2761 / GI_21040258-S". www.ncbi.nlm.nih.gov. Retrieved 2017-05-06.
  21. ^ a b "GDS2696 / GI_21040258-S". www.ncbi.nlm.nih.gov. Retrieved 2017-05-06.
  22. ^ Semenza GL (February 2012). "Hypoxia-inducible factors in physiology and medicine". Cell. 148 (3): 399–408. doi:10.1016/j.cell.2012.01.021. PMC 3437543. PMID 22304911.
  23. ^ "Home - EST - NCBI". www.ncbi.nlm.nih.gov. Archived from the original on 12 June 2013. Retrieved 2017-04-23.
  24. ^ "C16ORF71 - Chemical Interactions | CTD". ctd.mdibl.org. Retrieved 2017-05-06.
  25. ^ a b c Ali S, Steinmetz G, Montillet G, Perrard MH, Loundou A, Durand P, et al. (2014). "Exposure to low-dose bisphenol A impairs meiosis in the rat seminiferous tubule culture model: a physiotoxicogenomic approach". PLOS ONE. 9 (9) e106245. Bibcode:2014PLoSO...9j6245A. doi:10.1371/journal.pone.0106245. PMC 4152015. PMID 25181051.
  26. ^ a b c Song MK, Lee HS, Ryu JC (August 2015). "Integrated analysis of microRNA and mRNA expression profiles highlights aldehyde-induced inflammatory responses in cells relevant for lung toxicity". Toxicology. 334: 111–121. doi:10.1016/j.tox.2015.06.007. PMID 26079696.
  27. ^ a b c Tait S, La Rocca C, Mantovani A (July 2011). "Exposure of human fetal penile cells to different PCB mixtures: transcriptome analysis points to diverse modes of interference on external genitalia programming". Reproductive Toxicology. 32 (1). Elmsford, N.Y.: 1–14. doi:10.1016/j.reprotox.2011.02.001. PMID 21334430.
  28. ^ a b "Genomatix - NGS Data Analysis & Personalized Medicine". www.genomatix.de. Archived from the original on 2021-12-02. Retrieved 2017-04-23.
  29. ^ a b c "BLAST: Basic Local Alignment Search Tool". blast.ncbi.nlm.nih.gov. Retrieved 2017-04-23.
  30. ^ "Human BLAT Search". genome.ucsc.edu. Retrieved 2017-04-23.

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